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From: Carlos H. F. <car...@so...> - 2021-09-30 13:20:12
|
Dear Grigory,
Thanks for all support. Cryolo training worked very well; however, I'm facing some problems with cryolo picking.
I obtain this error:
Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5 -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc 4 --otf' returned non-zero exit status 1
When I execute in bash conda activate cryolo-1.7.6 && which cryolo_predict.py , I obtain a normal response
/home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py
I'm sorry, I thought that the problems were solved...
I attached the run.stderr and run.stdout files
Thanks again for the support.
From: "Grigory Sharov" <sha...@gm...>
To: "scipion-users" <sci...@li...>
Sent: Thursday, September 30, 2021 2:08:45 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Oh, that's great that it worked!
You are welcome!
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
Dear Grigory,
Thanks so so much!
Cryolo is running now in Scipion.
Best regards,
Carlos.
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Thursday, September 30, 2021 12:18:43 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hi Carlos,
ok, can you run pip uninstall cryolo and then execute in that order:
1) which cryolo_train.py
2) conda activate cryolo-1.7.6 && which cryolo_train.py
The first one should fail but the second one should show /home/impmc/eman2-sphire- sparx/envs/cryolo-1.7.6/bin/...
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
When I run conda activate cryolo-1.7.6 && which cryolo_train.py and which cryolo_train.py in bash I receive as response:
/home/impmc/.local/bin/cryolo_train.py
And when I go to this address, I can run all cryolo python files normally.
Best regards,
Carlos.
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Thursday, September 30, 2021 11:58:30 AM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Can you run conda activate cryolo-1.7.6 && which cryolo_train.py ?
Can you also run which cryolo_train.py ? (in case you installed cryolo into conda base env)
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dears Grigory and Pablo,
Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them.
And, thanks again for the messages and for the support.
About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2:
/home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2
It is possible to change to libcudnn.so.8 inside these folders?
About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman.
Best regards,
Carlos.
From: "Pablo Conesa" < [ mailto:pc...@cn... | pc...@cn... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Thursday, September 30, 2021 10:29:11 AM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
I agree with Grigory, using eman2 conda is not a good practice.
Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one.
If you want to undo this you will need to install miniconda, and have it available instead of eman2 one.
"which conda" will tell you the available one.
On 29/9/21 18:54, Grigory Sharov wrote:
BQ_BEGIN
Thanks! In run.stderr you can see the reason it has failed:
2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib
For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that
a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env"
b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be
In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0)
1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
The files that you requested are attached.
Thanks so much again
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 6:18:12 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hi,
The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44
(0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this).
However, I tried to run the cryolo training and I obtained the same previous error:
eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune
00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1.
00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982
Bellow, it is my current scipion.conf file
[PYWORKFLOW]
SCIPION_DOMAIN = pwem
SCIPION_FONT_NAME = Helvetica
SCIPION_GUI_REFRESH_IN_THREAD = False
SCIPION_LOG = ~/ScipionUserData/logs/scipion.log
SCIPION_LOGO = scipion_logo.gif
SCIPION_LOGS = ~/ScipionUserData/logs
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = True
SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ]
SCIPION_SOFTWARE = ${SCIPION_HOME}/software
SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ]
SCIPION_TESTS = ${SCIPION_HOME}/data/tests
SCIPION_TESTS_CMD = scipion3 tests
SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests
SCIPION_TMP = ~/ScipionUserData/tmp
SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ]
SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ]
SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ]
SCIPION_USER_DATA = ~/ScipionUserData
WIZARD_MASK_COLOR = [0.125, 0.909, 0.972]
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"
[PLUGINS]
CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056
CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5
CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6
CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5
CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5
CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5
CRYOSPARC_HOME = /home/impmc/
CRYO_PROJECTS_DIR = scipion_projects
CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14
EMAN2SCRATCHDIR = /tmp
EMAN2_HOME = %(EM_ROOT)s/eman-2.91
EM_ROOT = software/em
JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5
MAXIT_HOME = %(EM_ROOT)s/maxit-10.1
MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101
MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64
MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0
PHENIX_HOME = %(EM_ROOT)s/phenix-
RELION_CUDA_LIB = /usr/local/cuda/lib64
RELION_HOME = %(EM_ROOT)s/relion-3.1.2
XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src
XMIPP_HOME = %(EM_ROOT)s/xmipp
Thanks again.
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:51:06 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hello Carlos,
to start, you are missing a space between eval and the rest in:
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)"
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thanks for the message. The all output is bellow:
Scipion v3.0.9 - Eugenius
Building scipion-em-sphire ...
/home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7
Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ]
Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7)
Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13)
Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76)
Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8)
Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17)
Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4)
Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3)
Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0)
Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0)
Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0)
Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1)
Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2)
Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3)
Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1)
Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2)
Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0)
Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4)
Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0)
Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10)
Done (0.84 seconds)
Building cryolo-1.7.6 ...
Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ]
mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz
All targets exist.
Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6
All targets exist.
Skipping command: tar -xf void.tgz -C cryolo-1.7.6
All targets exist.
cd /home/impmc/scipion/software/em/cryolo-1.7.6
eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed
/bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python'
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
__add_sys_prefix_to_path() {
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
SYSP=$(\dirname "${CONDA_EXE}")
else
SYSP=$(\dirname "${CONDA_EXE}")
SYSP=$(\dirname "${SYSP}")
fi
if [ -n "${WINDIR+x}" ]; then
PATH="${SYSP}/bin:${PATH}"
PATH="${SYSP}/Scripts:${PATH}"
PATH="${SYSP}/Library/bin:${PATH}"
PATH="${SYSP}/Library/usr/bin:${PATH}"
PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
PATH="${SYSP}:${PATH}"
else
PATH="${SYSP}/bin:${PATH}"
fi
\export PATH
}
__conda_exe() (
__add_sys_prefix_to_path
"$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
)
__conda_hashr() {
if [ -n "${ZSH_VERSION:+x}" ]; then
\rehash
elif [ -n "${POSH_VERSION:+x}" ]; then
: # pass
else
\hash -r
fi
}
__conda_activate() {
if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
# Handle transition from shell activated with conda <= 4.3 to a subsequent activation
# after conda updated to >= 4.4. See issue #6173.
PS1="$CONDA_PS1_BACKUP"
\unset CONDA_PS1_BACKUP
fi
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
\eval "$ask_conda"
__conda_hashr
}
__conda_reactivate() {
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
\eval "$ask_conda"
__conda_hashr
}
conda() {
\local cmd="${1-__missing__}"
case "$cmd" in
activate|deactivate)
__conda_activate "$@"
;;
install|update|upgrade|remove|uninstall)
__conda_exe "$@" || \return
__conda_reactivate
;;
*)
__conda_exe "$@"
;;
esac
}
if [ -z "${CONDA_SHLVL+x}" ]; then
\export CONDA_SHLVL=0
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
else
PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
fi
\export PATH
# We're not allowing PS1 to be unbound. It must at least be set.
# However, we're not exporting it, which can cause problems when starting a second shell
# via a first shell (i.e. starting zsh from bash).
if [ -z "${PS1+x}" ]; then
PS1=
fi
fi
conda activate base: not found
Traceback (most recent call last):
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module>
main()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main
installPluginMethods()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
command.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:33:09 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Dear Carlos,
given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear all,
I'm facing some problems using cryolo training at Scipion.
I found the following error:
Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127.
I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it.
In my scipion.conf file, I inserted
CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh
or even
CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)"
(I saw these pathways in my bash.rc)
Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears:
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
I am not sure if these errors are related and hinder performing cryolo in Scipion.
I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command).
Anyone know what I'm doing wrong?
Thanks in advance,
Carlos.
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--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
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|
From: Grigory S. <sha...@gm...> - 2021-09-30 12:09:10
|
Oh, that's great that it worked! You are welcome! Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > Thanks so so much! > Cryolo is running now in Scipion. > Best regards, > Carlos. > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 12:18:43 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Hi Carlos, > ok, can you run *pip uninstall cryolo* and then execute in that order: > 1) *which cryolo_train.py * > 2) *conda activate* *cryolo-1.7.6 && which cryolo_train.py* > > The first one should fail but the second one should show > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> When I run *conda activate* *cryolo-1.7.6 && which cryolo_train.py* and *which >> cryolo_train.py *in bash I receive as response: >> */home/impmc/.local/bin/cryolo_train.py* >> >> And when I go to this address, I can run all cryolo python files normally. >> Best regards, >> Carlos. >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Thursday, September 30, 2021 11:58:30 AM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? >> Can you also run *which cryolo_train.py *? (in case you installed cryolo >> into conda base env) >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dears Grigory and Pablo, >>> >>> Sorry for the problems with conda; these things are very recent to me; >>> I'm still learning how to deal with them. >>> And, thanks again for the messages and for the support. >>> >>> About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in >>> cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: >>> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 >>> /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 >>> >>> /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 >>> It is possible to change to libcudnn.so.8 inside these folders? >>> >>> About conda; Yes, cryolo 1.8 are using conda from eman... I installed >>> miniconda and anaconda3; however when I type 'which conda', I have as only >>> response the conda from eman. >>> Best regards, >>> Carlos. >>> >>> ------------------------------ >>> *From: *"Pablo Conesa" <pc...@cn...> >>> *To: *"scipion-users" <sci...@li...> >>> *Sent: *Thursday, September 30, 2021 10:29:11 AM >>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >>> Cryolo >>> >>> I agree with Grigory, using eman2 conda is not a good practice. >>> >>> Probably he did not decided that but Scipion installer used the >>> available one, and probably that one was eman2 one. >>> >>> If you want to undo this you will need to install miniconda, and have it >>> available instead of eman2 one. >>> >>> "which conda" will tell you the available one. >>> >>> >>> On 29/9/21 18:54, Grigory Sharov wrote: >>> >>> Thanks! In run.stderr you can see the reason it has failed: >>> >>> 2021-09-30 02:14:42.492074: W >>> tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not >>> load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open >>> shared object file: No such file or directory; LD_LIBRARY_PATH: >>> /usr/local/cuda/lib64::/home/impmc/scipion/software/lib >>> >>> For some reason it's looking for libcudnn.so.8 but the cryolo package >>> should have installed libcudnn.so.7.1.2 for you. Can you check that >>> a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I >>> dont know where is your env is installed. You can activate conda and "check >>> conda list env" >>> b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct >>> path for cryolo env. The previous command should tell you where it should be >>> >>> In general, my advice would be to not use eman2 conda for anything >>> except eman. You'd be better off using a separate miniconda3 installation. >>> Which conda did you use for cryolo 1.8? From eman? >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < >>> car...@so...> wrote: >>> >>>> Dear Grigory, >>>> >>>> The files that you requested are attached. >>>> Thanks so much again >>>> >>>> ------------------------------ >>>> *From: *"Grigory Sharov" <sha...@gm...> >>>> *To: *"scipion-users" <sci...@li...> >>>> *Sent: *Wednesday, September 29, 2021 6:18:12 PM >>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>> using Cryolo >>>> >>>> Hi, >>>> The config files look ok. Could you attach run.stderr and run.stdout >>>> for the failed protocol? >>>> >>>> Best regards, >>>> Grigory >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> >>>> >>>> On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < >>>> car...@so...> wrote: >>>> >>>>> Dear Grigory, >>>>> >>>>> Thank you so much, fixing this space solved the problem with >>>>> cryolo_1.7.6_installing (shame on me for this). >>>>> However, I tried to run the cryolo training and I obtained the same >>>>> previous error: >>>>> >>>>> eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune >>>>> 00022: Protocol failed: Command ' eval >>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. >>>>> 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 >>>>> 02:14:42.822982 >>>>> >>>>> Bellow, it is my current scipion.conf file >>>>> [PYWORKFLOW] >>>>> SCIPION_DOMAIN = pwem >>>>> SCIPION_FONT_NAME = Helvetica >>>>> SCIPION_GUI_REFRESH_IN_THREAD = False >>>>> SCIPION_LOG = ~/ScipionUserData/logs/scipion.log >>>>> SCIPION_LOGO = scipion_logo.gif >>>>> SCIPION_LOGS = ~/ScipionUserData/logs >>>>> SCIPION_NOTES_FILE = notes.txt >>>>> SCIPION_NOTIFY = True >>>>> SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ >>>>> SCIPION_SOFTWARE = ${SCIPION_HOME}/software >>>>> SCIPION_SUPPORT_EMAIL = sc...@cn... >>>>> SCIPION_TESTS = ${SCIPION_HOME}/data/tests >>>>> SCIPION_TESTS_CMD = scipion3 tests >>>>> SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests >>>>> SCIPION_TMP = ~/ScipionUserData/tmp >>>>> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion >>>>> SCIPION_URL_SOFTWARE = >>>>> http://scipion.cnb.csic.es/downloads/scipion/software >>>>> SCIPION_URL_TESTDATA = >>>>> http://scipion.cnb.csic.es/downloads/scipion/data/tests >>>>> SCIPION_USER_DATA = ~/ScipionUserData >>>>> WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] >>>>> CONDA_ACTIVATION_CMD = eval >>>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" >>>>> >>>>> [PLUGINS] >>>>> CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 >>>>> CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 >>>>> CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta >>>>> CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 >>>>> CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 >>>>> CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 >>>>> CRYOLO_GENERIC_DENOISED_MODEL = >>>>> %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 >>>>> CRYOLO_GENERIC_MODEL = >>>>> %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 >>>>> CRYOLO_NS_GENERIC_MODEL = >>>>> %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 >>>>> CRYOSPARC_HOME = /home/impmc/ >>>>> CRYO_PROJECTS_DIR = scipion_projects >>>>> CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 >>>>> EMAN2SCRATCHDIR = /tmp >>>>> EMAN2_HOME = %(EM_ROOT)s/eman-2.91 >>>>> EM_ROOT = software/em >>>>> JANNI_GENERIC_MODEL = >>>>> %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 >>>>> MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 >>>>> MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 >>>>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 >>>>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 >>>>> PHENIX_HOME = %(EM_ROOT)s/phenix- >>>>> RELION_CUDA_LIB = /usr/local/cuda/lib64 >>>>> RELION_HOME = %(EM_ROOT)s/relion-3.1.2 >>>>> XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src >>>>> XMIPP_HOME = %(EM_ROOT)s/xmipp >>>>> >>>>> >>>>> Thanks again. >>>>> >>>>> ------------------------------ >>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>> *To: *"scipion-users" <sci...@li...> >>>>> *Sent: *Wednesday, September 29, 2021 5:51:06 PM >>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>> using Cryolo >>>>> >>>>> Hello Carlos, >>>>> >>>>> to start, you are missing a space between eval and the rest in: >>>>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>> shell.bash hook)" >>>>> >>>>> Best regards, >>>>> Grigory >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> Grigory Sharov, Ph.D. >>>>> >>>>> MRC Laboratory of Molecular Biology, >>>>> Francis Crick Avenue, >>>>> Cambridge Biomedical Campus, >>>>> Cambridge CB2 0QH, UK. >>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>> e-mail: gs...@mr... >>>>> >>>>> >>>>> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < >>>>> car...@so...> wrote: >>>>> >>>>>> Dear Grigory, >>>>>> >>>>>> Thanks for the message. The all output is bellow: >>>>>> >>>>>> Scipion v3.0.9 - Eugenius >>>>>> Building scipion-em-sphire ... >>>>>> /home/impmc/scipion/.scipion3/bin/python -m pip install >>>>>> scipion-em-sphire==3.0.7 >>>>>> Looking in indexes: https://pypi.org/simple, >>>>>> https://pypi.ngc.nvidia.com >>>>>> Requirement already satisfied: scipion-em-sphire==3.0.7 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >>>>>> Requirement already satisfied: scipion-em in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-em-sphire==3.0.7) (3.0.13) >>>>>> Requirement already satisfied: biopython==1.76 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-em->scipion-em-sphire==3.0.7) (1.76) >>>>>> Requirement already satisfied: tifffile in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >>>>>> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >>>>>> Requirement already satisfied: numpy in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >>>>>> Requirement already satisfied: mpi4py<=3.0.3 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >>>>>> Requirement already satisfied: configparser<=5.0.2 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >>>>>> Requirement already satisfied: psutil<=5.8.0 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >>>>>> Requirement already satisfied: pillow<=8.2.0 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >>>>>> Requirement already satisfied: bibtexparser<=1.2.0 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >>>>>> Requirement already satisfied: requests<=2.25.1 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >>>>>> Requirement already satisfied: matplotlib==3.2.2 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >>>>>> Requirement already satisfied: tkcolorpicker<=2.1.3 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >>>>>> Requirement already satisfied: cycler>=0.10 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (0.10.0) >>>>>> Requirement already satisfied: python-dateutil>=2.1 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (2.8.1) >>>>>> Requirement already satisfied: >>>>>> pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (2.4.7) >>>>>> Requirement already satisfied: kiwisolver>=1.0.1 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (1.3.1) >>>>>> Requirement already satisfied: future>=0.16.0 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (0.18.2) >>>>>> Requirement already satisfied: six in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (1.16.0) >>>>>> Requirement already satisfied: certifi>=2017.4.17 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (2020.12.5) >>>>>> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (1.26.4) >>>>>> Requirement already satisfied: chardet<5,>=3.0.2 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (4.0.0) >>>>>> Requirement already satisfied: idna<3,>=2.5 in >>>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>>> (2.10) >>>>>> Done (0.84 seconds) >>>>>> Building cryolo-1.7.6 ... >>>>>> Skipping command: wget -nv -c -O >>>>>> /home/impmc/scipion/software/em/void.tgz.part >>>>>> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >>>>>> mv -v /home/impmc/scipion/software/em/void.tgz.part >>>>>> /home/impmc/scipion/software/em/void.tgz >>>>>> All targets exist. >>>>>> Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>> All targets exist. >>>>>> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >>>>>> All targets exist. >>>>>> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>>> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >>>>>> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >>>>>> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >>>>>> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >>>>>> /bin/sh: 1: evalexport >>>>>> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >>>>>> export _CE_M='' >>>>>> export _CE_CONDA='' >>>>>> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >>>>>> >>>>>> # Copyright (C) 2012 Anaconda, Inc >>>>>> # SPDX-License-Identifier: BSD-3-Clause >>>>>> >>>>>> __add_sys_prefix_to_path() { >>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>> # it is in a different relative location to condabin. >>>>>> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>> else >>>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>>> SYSP=$(\dirname "${SYSP}") >>>>>> fi >>>>>> >>>>>> if [ -n "${WINDIR+x}" ]; then >>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>> PATH="${SYSP}/Scripts:${PATH}" >>>>>> PATH="${SYSP}/Library/bin:${PATH}" >>>>>> PATH="${SYSP}/Library/usr/bin:${PATH}" >>>>>> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >>>>>> PATH="${SYSP}:${PATH}" >>>>>> else >>>>>> PATH="${SYSP}/bin:${PATH}" >>>>>> fi >>>>>> \export PATH >>>>>> } >>>>>> >>>>>> __conda_exe() ( >>>>>> __add_sys_prefix_to_path >>>>>> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >>>>>> ) >>>>>> >>>>>> __conda_hashr() { >>>>>> if [ -n "${ZSH_VERSION:+x}" ]; then >>>>>> \rehash >>>>>> elif [ -n "${POSH_VERSION:+x}" ]; then >>>>>> : # pass >>>>>> else >>>>>> \hash -r >>>>>> fi >>>>>> } >>>>>> >>>>>> __conda_activate() { >>>>>> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >>>>>> # Handle transition from shell activated with conda <= 4.3 to >>>>>> a subsequent activation >>>>>> # after conda updated to >= 4.4. See issue #6173. >>>>>> PS1="$CONDA_PS1_BACKUP" >>>>>> \unset CONDA_PS1_BACKUP >>>>>> fi >>>>>> \local ask_conda >>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || >>>>>> \return >>>>>> \eval "$ask_conda" >>>>>> __conda_hashr >>>>>> } >>>>>> >>>>>> __conda_reactivate() { >>>>>> \local ask_conda >>>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" >>>>>> || \return >>>>>> \eval "$ask_conda" >>>>>> __conda_hashr >>>>>> } >>>>>> >>>>>> conda() { >>>>>> \local cmd="${1-__missing__}" >>>>>> case "$cmd" in >>>>>> activate|deactivate) >>>>>> __conda_activate "$@" >>>>>> ;; >>>>>> install|update|upgrade|remove|uninstall) >>>>>> __conda_exe "$@" || \return >>>>>> __conda_reactivate >>>>>> ;; >>>>>> *) >>>>>> __conda_exe "$@" >>>>>> ;; >>>>>> esac >>>>>> } >>>>>> >>>>>> if [ -z "${CONDA_SHLVL+x}" ]; then >>>>>> \export CONDA_SHLVL=0 >>>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>>> # it is in a different relative location to condabin. >>>>>> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >>>>>> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >>>>>> else >>>>>> PATH="$(\dirname "$(\dirname >>>>>> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >>>>>> fi >>>>>> \export PATH >>>>>> >>>>>> # We're not allowing PS1 to be unbound. It must at least be set. >>>>>> # However, we're not exporting it, which can cause problems when >>>>>> starting a second shell >>>>>> # via a first shell (i.e. starting zsh from bash). >>>>>> if [ -z "${PS1+x}" ]; then >>>>>> PS1= >>>>>> fi >>>>>> fi >>>>>> >>>>>> conda activate base: not found >>>>>> Traceback (most recent call last): >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>> line 470, in <module> >>>>>> main() >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>>> line 293, in main >>>>>> installPluginMethods() >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>>>>> line 232, in installPluginMethods >>>>>> plugin.installBin({'args': ['-j', numberProcessor]}) >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>>>>> line 166, in installBin >>>>>> environment.execute() >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>> line 748, in execute >>>>>> self._executeTargets(targetList) >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>> line 690, in _executeTargets >>>>>> tgt.execute() >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>> line 221, in execute >>>>>> command.execute() >>>>>> File >>>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>>> line 161, in execute >>>>>> assert glob(t), ("target '%s' not built (after " >>>>>> AssertionError: target >>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>> Error at main: target >>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>>> >>>>>> ------------------------------ >>>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>>> *To: *"scipion-users" <sci...@li...> >>>>>> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >>>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>>> using Cryolo >>>>>> >>>>>> Dear Carlos, >>>>>> given the fact that the installation has failed, could you attach all >>>>>> output after "scipion3 installp -p scipion-em-sphire" command? >>>>>> >>>>>> Best regards, >>>>>> Grigory >>>>>> >>>>>> >>>>>> -------------------------------------------------------------------------------- >>>>>> Grigory Sharov, Ph.D. >>>>>> >>>>>> MRC Laboratory of Molecular Biology, >>>>>> Francis Crick Avenue, >>>>>> Cambridge Biomedical Campus, >>>>>> Cambridge CB2 0QH, UK. >>>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>>> e-mail: gs...@mr... >>>>>> >>>>>> >>>>>> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >>>>>> car...@so...> wrote: >>>>>> >>>>>>> Dear all, >>>>>>> >>>>>>> I'm facing some problems using cryolo training at Scipion. >>>>>>> I found the following error: >>>>>>> >>>>>>> *Protocol failed: Command ' source >>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>>>>>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>>>>>> --fine_tune' returned non-zero exit status 127. * >>>>>>> >>>>>>> I saw some discussion about that at Scipion lists, but I'm still >>>>>>> little lost in how to fix it. >>>>>>> In my scipion.conf file, I inserted >>>>>>> *CONDA_ACTIVATION_CMD = source >>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>>>>>> or even >>>>>>> CONDA_ACTIVATION_CMD = >>>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" >>>>>>> (I saw these pathways in my bash.rc) >>>>>>> >>>>>>> Moreover, when I try to install cryolo using command line (scipion3 >>>>>>> installp -p scipion-em-sphire), the following error apears: >>>>>>> *AssertionError: target >>>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>>> built (after running 'source >>>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>>>>>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>>>>>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>>>>>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>>>>>> cryolo_1.7.6_installed')* >>>>>>> >>>>>>> I am not sure if these errors are related and hinder performing >>>>>>> cryolo in Scipion. >>>>>>> I have conda installed in the computer and I'm able to use cryolo >>>>>>> 1.8 outside from Scipion in the same computer (using *source >>>>>>> activate cryolo *command). >>>>>>> >>>>>>> Anyone know what I'm doing wrong? >>>>>>> Thanks in advance, >>>>>>> Carlos. >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> scipion-users mailing list >>>>>>> sci...@li... >>>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >>> -- >>> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Carlos H. F. <car...@so...> - 2021-09-30 12:04:23
|
Dear Grigory,
Thanks so so much!
Cryolo is running now in Scipion.
Best regards,
Carlos.
From: "Grigory Sharov" <sha...@gm...>
To: "scipion-users" <sci...@li...>
Sent: Thursday, September 30, 2021 12:18:43 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hi Carlos,
ok, can you run pip uninstall cryolo and then execute in that order:
1) which cryolo_train.py
2) conda activate cryolo-1.7.6 && which cryolo_train.py
The first one should fail but the second one should show /home/impmc/eman2-sphire- sparx/envs/cryolo-1.7.6/bin/...
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
Dear Grigory,
When I run conda activate cryolo-1.7.6 && which cryolo_train.py and which cryolo_train.py in bash I receive as response:
/home/impmc/.local/bin/cryolo_train.py
And when I go to this address, I can run all cryolo python files normally.
Best regards,
Carlos.
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Thursday, September 30, 2021 11:58:30 AM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Can you run conda activate cryolo-1.7.6 && which cryolo_train.py ?
Can you also run which cryolo_train.py ? (in case you installed cryolo into conda base env)
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dears Grigory and Pablo,
Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them.
And, thanks again for the messages and for the support.
About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2:
/home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2
It is possible to change to libcudnn.so.8 inside these folders?
About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman.
Best regards,
Carlos.
From: "Pablo Conesa" < [ mailto:pc...@cn... | pc...@cn... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Thursday, September 30, 2021 10:29:11 AM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
I agree with Grigory, using eman2 conda is not a good practice.
Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one.
If you want to undo this you will need to install miniconda, and have it available instead of eman2 one.
"which conda" will tell you the available one.
On 29/9/21 18:54, Grigory Sharov wrote:
BQ_BEGIN
Thanks! In run.stderr you can see the reason it has failed:
2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib
For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that
a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env"
b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be
In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0)
1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
The files that you requested are attached.
Thanks so much again
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 6:18:12 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hi,
The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44
(0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this).
However, I tried to run the cryolo training and I obtained the same previous error:
eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune
00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1.
00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982
Bellow, it is my current scipion.conf file
[PYWORKFLOW]
SCIPION_DOMAIN = pwem
SCIPION_FONT_NAME = Helvetica
SCIPION_GUI_REFRESH_IN_THREAD = False
SCIPION_LOG = ~/ScipionUserData/logs/scipion.log
SCIPION_LOGO = scipion_logo.gif
SCIPION_LOGS = ~/ScipionUserData/logs
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = True
SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ]
SCIPION_SOFTWARE = ${SCIPION_HOME}/software
SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ]
SCIPION_TESTS = ${SCIPION_HOME}/data/tests
SCIPION_TESTS_CMD = scipion3 tests
SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests
SCIPION_TMP = ~/ScipionUserData/tmp
SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ]
SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ]
SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ]
SCIPION_USER_DATA = ~/ScipionUserData
WIZARD_MASK_COLOR = [0.125, 0.909, 0.972]
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"
[PLUGINS]
CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056
CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5
CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6
CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5
CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5
CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5
CRYOSPARC_HOME = /home/impmc/
CRYO_PROJECTS_DIR = scipion_projects
CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14
EMAN2SCRATCHDIR = /tmp
EMAN2_HOME = %(EM_ROOT)s/eman-2.91
EM_ROOT = software/em
JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5
MAXIT_HOME = %(EM_ROOT)s/maxit-10.1
MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101
MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64
MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0
PHENIX_HOME = %(EM_ROOT)s/phenix-
RELION_CUDA_LIB = /usr/local/cuda/lib64
RELION_HOME = %(EM_ROOT)s/relion-3.1.2
XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src
XMIPP_HOME = %(EM_ROOT)s/xmipp
Thanks again.
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:51:06 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hello Carlos,
to start, you are missing a space between eval and the rest in:
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)"
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thanks for the message. The all output is bellow:
Scipion v3.0.9 - Eugenius
Building scipion-em-sphire ...
/home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7
Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ]
Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7)
Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13)
Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76)
Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8)
Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17)
Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4)
Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3)
Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0)
Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0)
Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0)
Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1)
Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2)
Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3)
Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1)
Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2)
Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0)
Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4)
Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0)
Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10)
Done (0.84 seconds)
Building cryolo-1.7.6 ...
Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ]
mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz
All targets exist.
Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6
All targets exist.
Skipping command: tar -xf void.tgz -C cryolo-1.7.6
All targets exist.
cd /home/impmc/scipion/software/em/cryolo-1.7.6
eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed
/bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python'
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
__add_sys_prefix_to_path() {
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
SYSP=$(\dirname "${CONDA_EXE}")
else
SYSP=$(\dirname "${CONDA_EXE}")
SYSP=$(\dirname "${SYSP}")
fi
if [ -n "${WINDIR+x}" ]; then
PATH="${SYSP}/bin:${PATH}"
PATH="${SYSP}/Scripts:${PATH}"
PATH="${SYSP}/Library/bin:${PATH}"
PATH="${SYSP}/Library/usr/bin:${PATH}"
PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
PATH="${SYSP}:${PATH}"
else
PATH="${SYSP}/bin:${PATH}"
fi
\export PATH
}
__conda_exe() (
__add_sys_prefix_to_path
"$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
)
__conda_hashr() {
if [ -n "${ZSH_VERSION:+x}" ]; then
\rehash
elif [ -n "${POSH_VERSION:+x}" ]; then
: # pass
else
\hash -r
fi
}
__conda_activate() {
if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
# Handle transition from shell activated with conda <= 4.3 to a subsequent activation
# after conda updated to >= 4.4. See issue #6173.
PS1="$CONDA_PS1_BACKUP"
\unset CONDA_PS1_BACKUP
fi
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
\eval "$ask_conda"
__conda_hashr
}
__conda_reactivate() {
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
\eval "$ask_conda"
__conda_hashr
}
conda() {
\local cmd="${1-__missing__}"
case "$cmd" in
activate|deactivate)
__conda_activate "$@"
;;
install|update|upgrade|remove|uninstall)
__conda_exe "$@" || \return
__conda_reactivate
;;
*)
__conda_exe "$@"
;;
esac
}
if [ -z "${CONDA_SHLVL+x}" ]; then
\export CONDA_SHLVL=0
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
else
PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
fi
\export PATH
# We're not allowing PS1 to be unbound. It must at least be set.
# However, we're not exporting it, which can cause problems when starting a second shell
# via a first shell (i.e. starting zsh from bash).
if [ -z "${PS1+x}" ]; then
PS1=
fi
fi
conda activate base: not found
Traceback (most recent call last):
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module>
main()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main
installPluginMethods()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
command.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:33:09 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Dear Carlos,
given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear all,
I'm facing some problems using cryolo training at Scipion.
I found the following error:
Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127.
I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it.
In my scipion.conf file, I inserted
CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh
or even
CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)"
(I saw these pathways in my bash.rc)
Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears:
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
I am not sure if these errors are related and hinder performing cryolo in Scipion.
I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command).
Anyone know what I'm doing wrong?
Thanks in advance,
Carlos.
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--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
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From: Grigory S. <sha...@gm...> - 2021-09-30 10:19:04
|
Hi Carlos, ok, can you run *pip uninstall cryolo* and then execute in that order: 1) *which cryolo_train.py * 2) *conda activate* *cryolo-1.7.6 && which cryolo_train.py* The first one should fail but the second one should show /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/... Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > When I run *conda activate* *cryolo-1.7.6 && which cryolo_train.py* and *which > cryolo_train.py *in bash I receive as response: > */home/impmc/.local/bin/cryolo_train.py* > > And when I go to this address, I can run all cryolo python files normally. > Best regards, > Carlos. > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 11:58:30 AM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? > Can you also run *which cryolo_train.py *? (in case you installed cryolo > into conda base env) > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dears Grigory and Pablo, >> >> Sorry for the problems with conda; these things are very recent to me; >> I'm still learning how to deal with them. >> And, thanks again for the messages and for the support. >> >> About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in >> cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: >> /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 >> /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 >> >> /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 >> It is possible to change to libcudnn.so.8 inside these folders? >> >> About conda; Yes, cryolo 1.8 are using conda from eman... I installed >> miniconda and anaconda3; however when I type 'which conda', I have as only >> response the conda from eman. >> Best regards, >> Carlos. >> >> ------------------------------ >> *From: *"Pablo Conesa" <pc...@cn...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Thursday, September 30, 2021 10:29:11 AM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> I agree with Grigory, using eman2 conda is not a good practice. >> >> Probably he did not decided that but Scipion installer used the available >> one, and probably that one was eman2 one. >> >> If you want to undo this you will need to install miniconda, and have it >> available instead of eman2 one. >> >> "which conda" will tell you the available one. >> >> >> On 29/9/21 18:54, Grigory Sharov wrote: >> >> Thanks! In run.stderr you can see the reason it has failed: >> >> 2021-09-30 02:14:42.492074: W >> tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not >> load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open >> shared object file: No such file or directory; LD_LIBRARY_PATH: >> /usr/local/cuda/lib64::/home/impmc/scipion/software/lib >> >> For some reason it's looking for libcudnn.so.8 but the cryolo package >> should have installed libcudnn.so.7.1.2 for you. Can you check that >> a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I >> dont know where is your env is installed. You can activate conda and "check >> conda list env" >> b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct >> path for cryolo env. The previous command should tell you where it should be >> >> In general, my advice would be to not use eman2 conda for anything except >> eman. You'd be better off using a separate miniconda3 installation. Which >> conda did you use for cryolo 1.8? From eman? >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear Grigory, >>> >>> The files that you requested are attached. >>> Thanks so much again >>> >>> ------------------------------ >>> *From: *"Grigory Sharov" <sha...@gm...> >>> *To: *"scipion-users" <sci...@li...> >>> *Sent: *Wednesday, September 29, 2021 6:18:12 PM >>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >>> Cryolo >>> >>> Hi, >>> The config files look ok. Could you attach run.stderr and run.stdout for >>> the failed protocol? >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < >>> car...@so...> wrote: >>> >>>> Dear Grigory, >>>> >>>> Thank you so much, fixing this space solved the problem with >>>> cryolo_1.7.6_installing (shame on me for this). >>>> However, I tried to run the cryolo training and I obtained the same >>>> previous error: >>>> >>>> eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune >>>> 00022: Protocol failed: Command ' eval >>>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. >>>> 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 >>>> 02:14:42.822982 >>>> >>>> Bellow, it is my current scipion.conf file >>>> [PYWORKFLOW] >>>> SCIPION_DOMAIN = pwem >>>> SCIPION_FONT_NAME = Helvetica >>>> SCIPION_GUI_REFRESH_IN_THREAD = False >>>> SCIPION_LOG = ~/ScipionUserData/logs/scipion.log >>>> SCIPION_LOGO = scipion_logo.gif >>>> SCIPION_LOGS = ~/ScipionUserData/logs >>>> SCIPION_NOTES_FILE = notes.txt >>>> SCIPION_NOTIFY = True >>>> SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ >>>> SCIPION_SOFTWARE = ${SCIPION_HOME}/software >>>> SCIPION_SUPPORT_EMAIL = sc...@cn... >>>> SCIPION_TESTS = ${SCIPION_HOME}/data/tests >>>> SCIPION_TESTS_CMD = scipion3 tests >>>> SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests >>>> SCIPION_TMP = ~/ScipionUserData/tmp >>>> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion >>>> SCIPION_URL_SOFTWARE = >>>> http://scipion.cnb.csic.es/downloads/scipion/software >>>> SCIPION_URL_TESTDATA = >>>> http://scipion.cnb.csic.es/downloads/scipion/data/tests >>>> SCIPION_USER_DATA = ~/ScipionUserData >>>> WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] >>>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>>> shell.bash hook 2> /dev/null)" >>>> >>>> [PLUGINS] >>>> CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 >>>> CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 >>>> CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta >>>> CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 >>>> CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 >>>> CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 >>>> CRYOLO_GENERIC_DENOISED_MODEL = >>>> %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 >>>> CRYOLO_GENERIC_MODEL = >>>> %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 >>>> CRYOLO_NS_GENERIC_MODEL = >>>> %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 >>>> CRYOSPARC_HOME = /home/impmc/ >>>> CRYO_PROJECTS_DIR = scipion_projects >>>> CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 >>>> EMAN2SCRATCHDIR = /tmp >>>> EMAN2_HOME = %(EM_ROOT)s/eman-2.91 >>>> EM_ROOT = software/em >>>> JANNI_GENERIC_MODEL = >>>> %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 >>>> MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 >>>> MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 >>>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 >>>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 >>>> PHENIX_HOME = %(EM_ROOT)s/phenix- >>>> RELION_CUDA_LIB = /usr/local/cuda/lib64 >>>> RELION_HOME = %(EM_ROOT)s/relion-3.1.2 >>>> XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src >>>> XMIPP_HOME = %(EM_ROOT)s/xmipp >>>> >>>> >>>> Thanks again. >>>> >>>> ------------------------------ >>>> *From: *"Grigory Sharov" <sha...@gm...> >>>> *To: *"scipion-users" <sci...@li...> >>>> *Sent: *Wednesday, September 29, 2021 5:51:06 PM >>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>> using Cryolo >>>> >>>> Hello Carlos, >>>> >>>> to start, you are missing a space between eval and the rest in: >>>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>>> shell.bash hook)" >>>> >>>> Best regards, >>>> Grigory >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> >>>> >>>> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < >>>> car...@so...> wrote: >>>> >>>>> Dear Grigory, >>>>> >>>>> Thanks for the message. The all output is bellow: >>>>> >>>>> Scipion v3.0.9 - Eugenius >>>>> Building scipion-em-sphire ... >>>>> /home/impmc/scipion/.scipion3/bin/python -m pip install >>>>> scipion-em-sphire==3.0.7 >>>>> Looking in indexes: https://pypi.org/simple, >>>>> https://pypi.ngc.nvidia.com >>>>> Requirement already satisfied: scipion-em-sphire==3.0.7 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >>>>> Requirement already satisfied: scipion-em in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-em-sphire==3.0.7) (3.0.13) >>>>> Requirement already satisfied: biopython==1.76 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-em->scipion-em-sphire==3.0.7) (1.76) >>>>> Requirement already satisfied: tifffile in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >>>>> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >>>>> Requirement already satisfied: numpy in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >>>>> Requirement already satisfied: mpi4py<=3.0.3 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >>>>> Requirement already satisfied: configparser<=5.0.2 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >>>>> Requirement already satisfied: psutil<=5.8.0 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >>>>> Requirement already satisfied: pillow<=8.2.0 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >>>>> Requirement already satisfied: bibtexparser<=1.2.0 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >>>>> Requirement already satisfied: requests<=2.25.1 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >>>>> Requirement already satisfied: matplotlib==3.2.2 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >>>>> Requirement already satisfied: tkcolorpicker<=2.1.3 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >>>>> Requirement already satisfied: cycler>=0.10 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (0.10.0) >>>>> Requirement already satisfied: python-dateutil>=2.1 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (2.8.1) >>>>> Requirement already satisfied: >>>>> pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (2.4.7) >>>>> Requirement already satisfied: kiwisolver>=1.0.1 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (1.3.1) >>>>> Requirement already satisfied: future>=0.16.0 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (0.18.2) >>>>> Requirement already satisfied: six in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (1.16.0) >>>>> Requirement already satisfied: certifi>=2017.4.17 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (2020.12.5) >>>>> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (1.26.4) >>>>> Requirement already satisfied: chardet<5,>=3.0.2 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (4.0.0) >>>>> Requirement already satisfied: idna<3,>=2.5 in >>>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>>> (2.10) >>>>> Done (0.84 seconds) >>>>> Building cryolo-1.7.6 ... >>>>> Skipping command: wget -nv -c -O >>>>> /home/impmc/scipion/software/em/void.tgz.part >>>>> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >>>>> mv -v /home/impmc/scipion/software/em/void.tgz.part >>>>> /home/impmc/scipion/software/em/void.tgz >>>>> All targets exist. >>>>> Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>> All targets exist. >>>>> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >>>>> All targets exist. >>>>> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>>> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >>>>> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >>>>> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >>>>> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >>>>> /bin/sh: 1: evalexport >>>>> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >>>>> export _CE_M='' >>>>> export _CE_CONDA='' >>>>> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >>>>> >>>>> # Copyright (C) 2012 Anaconda, Inc >>>>> # SPDX-License-Identifier: BSD-3-Clause >>>>> >>>>> __add_sys_prefix_to_path() { >>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>> # it is in a different relative location to condabin. >>>>> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>> else >>>>> SYSP=$(\dirname "${CONDA_EXE}") >>>>> SYSP=$(\dirname "${SYSP}") >>>>> fi >>>>> >>>>> if [ -n "${WINDIR+x}" ]; then >>>>> PATH="${SYSP}/bin:${PATH}" >>>>> PATH="${SYSP}/Scripts:${PATH}" >>>>> PATH="${SYSP}/Library/bin:${PATH}" >>>>> PATH="${SYSP}/Library/usr/bin:${PATH}" >>>>> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >>>>> PATH="${SYSP}:${PATH}" >>>>> else >>>>> PATH="${SYSP}/bin:${PATH}" >>>>> fi >>>>> \export PATH >>>>> } >>>>> >>>>> __conda_exe() ( >>>>> __add_sys_prefix_to_path >>>>> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >>>>> ) >>>>> >>>>> __conda_hashr() { >>>>> if [ -n "${ZSH_VERSION:+x}" ]; then >>>>> \rehash >>>>> elif [ -n "${POSH_VERSION:+x}" ]; then >>>>> : # pass >>>>> else >>>>> \hash -r >>>>> fi >>>>> } >>>>> >>>>> __conda_activate() { >>>>> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >>>>> # Handle transition from shell activated with conda <= 4.3 to >>>>> a subsequent activation >>>>> # after conda updated to >= 4.4. See issue #6173. >>>>> PS1="$CONDA_PS1_BACKUP" >>>>> \unset CONDA_PS1_BACKUP >>>>> fi >>>>> \local ask_conda >>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || >>>>> \return >>>>> \eval "$ask_conda" >>>>> __conda_hashr >>>>> } >>>>> >>>>> __conda_reactivate() { >>>>> \local ask_conda >>>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" >>>>> || \return >>>>> \eval "$ask_conda" >>>>> __conda_hashr >>>>> } >>>>> >>>>> conda() { >>>>> \local cmd="${1-__missing__}" >>>>> case "$cmd" in >>>>> activate|deactivate) >>>>> __conda_activate "$@" >>>>> ;; >>>>> install|update|upgrade|remove|uninstall) >>>>> __conda_exe "$@" || \return >>>>> __conda_reactivate >>>>> ;; >>>>> *) >>>>> __conda_exe "$@" >>>>> ;; >>>>> esac >>>>> } >>>>> >>>>> if [ -z "${CONDA_SHLVL+x}" ]; then >>>>> \export CONDA_SHLVL=0 >>>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>>> # it is in a different relative location to condabin. >>>>> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >>>>> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >>>>> else >>>>> PATH="$(\dirname "$(\dirname >>>>> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >>>>> fi >>>>> \export PATH >>>>> >>>>> # We're not allowing PS1 to be unbound. It must at least be set. >>>>> # However, we're not exporting it, which can cause problems when >>>>> starting a second shell >>>>> # via a first shell (i.e. starting zsh from bash). >>>>> if [ -z "${PS1+x}" ]; then >>>>> PS1= >>>>> fi >>>>> fi >>>>> >>>>> conda activate base: not found >>>>> Traceback (most recent call last): >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>> line 470, in <module> >>>>> main() >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>>> line 293, in main >>>>> installPluginMethods() >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>>>> line 232, in installPluginMethods >>>>> plugin.installBin({'args': ['-j', numberProcessor]}) >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>>>> line 166, in installBin >>>>> environment.execute() >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>> line 748, in execute >>>>> self._executeTargets(targetList) >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>> line 690, in _executeTargets >>>>> tgt.execute() >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>> line 221, in execute >>>>> command.execute() >>>>> File >>>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>>> line 161, in execute >>>>> assert glob(t), ("target '%s' not built (after " >>>>> AssertionError: target >>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>> Error at main: target >>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>>> >>>>> ------------------------------ >>>>> *From: *"Grigory Sharov" <sha...@gm...> >>>>> *To: *"scipion-users" <sci...@li...> >>>>> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >>>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>>> using Cryolo >>>>> >>>>> Dear Carlos, >>>>> given the fact that the installation has failed, could you attach all >>>>> output after "scipion3 installp -p scipion-em-sphire" command? >>>>> >>>>> Best regards, >>>>> Grigory >>>>> >>>>> >>>>> -------------------------------------------------------------------------------- >>>>> Grigory Sharov, Ph.D. >>>>> >>>>> MRC Laboratory of Molecular Biology, >>>>> Francis Crick Avenue, >>>>> Cambridge Biomedical Campus, >>>>> Cambridge CB2 0QH, UK. >>>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>>> e-mail: gs...@mr... >>>>> >>>>> >>>>> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >>>>> car...@so...> wrote: >>>>> >>>>>> Dear all, >>>>>> >>>>>> I'm facing some problems using cryolo training at Scipion. >>>>>> I found the following error: >>>>>> >>>>>> *Protocol failed: Command ' source >>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>>>>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>>>>> --fine_tune' returned non-zero exit status 127. * >>>>>> >>>>>> I saw some discussion about that at Scipion lists, but I'm still >>>>>> little lost in how to fix it. >>>>>> In my scipion.conf file, I inserted >>>>>> *CONDA_ACTIVATION_CMD = source >>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>>>>> or even >>>>>> CONDA_ACTIVATION_CMD = >>>>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" >>>>>> (I saw these pathways in my bash.rc) >>>>>> >>>>>> Moreover, when I try to install cryolo using command line (scipion3 >>>>>> installp -p scipion-em-sphire), the following error apears: >>>>>> *AssertionError: target >>>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>>> built (after running 'source >>>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>>>>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>>>>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>>>>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>>>>> cryolo_1.7.6_installed')* >>>>>> >>>>>> I am not sure if these errors are related and hinder performing >>>>>> cryolo in Scipion. >>>>>> I have conda installed in the computer and I'm able to use cryolo 1.8 >>>>>> outside from Scipion in the same computer (using *source activate >>>>>> cryolo *command). >>>>>> >>>>>> Anyone know what I'm doing wrong? >>>>>> Thanks in advance, >>>>>> Carlos. >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> scipion-users mailing list >>>>>> sci...@li... >>>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users >> >> -- >> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Carlos H. F. <car...@so...> - 2021-09-30 10:11:36
|
Dear Grigory,
When I run conda activate cryolo-1.7.6 && which cryolo_train.py and which cryolo_train.py in bash I receive as response:
/home/impmc/.local/bin/cryolo_train.py
And when I go to this address, I can run all cryolo python files normally.
Best regards,
Carlos.
From: "Grigory Sharov" <sha...@gm...>
To: "scipion-users" <sci...@li...>
Sent: Thursday, September 30, 2021 11:58:30 AM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Can you run conda activate cryolo-1.7.6 && which cryolo_train.py ?
Can you also run which cryolo_train.py ? (in case you installed cryolo into conda base env)
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
Dears Grigory and Pablo,
Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them.
And, thanks again for the messages and for the support.
About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2:
/home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2
It is possible to change to libcudnn.so.8 inside these folders?
About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman.
Best regards,
Carlos.
From: "Pablo Conesa" < [ mailto:pc...@cn... | pc...@cn... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Thursday, September 30, 2021 10:29:11 AM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
I agree with Grigory, using eman2 conda is not a good practice.
Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one.
If you want to undo this you will need to install miniconda, and have it available instead of eman2 one.
"which conda" will tell you the available one.
On 29/9/21 18:54, Grigory Sharov wrote:
BQ_BEGIN
Thanks! In run.stderr you can see the reason it has failed:
2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib
For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that
a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env"
b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be
In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0)
1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
The files that you requested are attached.
Thanks so much again
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 6:18:12 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hi,
The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44
(0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this).
However, I tried to run the cryolo training and I obtained the same previous error:
eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune
00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1.
00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982
Bellow, it is my current scipion.conf file
[PYWORKFLOW]
SCIPION_DOMAIN = pwem
SCIPION_FONT_NAME = Helvetica
SCIPION_GUI_REFRESH_IN_THREAD = False
SCIPION_LOG = ~/ScipionUserData/logs/scipion.log
SCIPION_LOGO = scipion_logo.gif
SCIPION_LOGS = ~/ScipionUserData/logs
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = True
SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ]
SCIPION_SOFTWARE = ${SCIPION_HOME}/software
SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ]
SCIPION_TESTS = ${SCIPION_HOME}/data/tests
SCIPION_TESTS_CMD = scipion3 tests
SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests
SCIPION_TMP = ~/ScipionUserData/tmp
SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ]
SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ]
SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ]
SCIPION_USER_DATA = ~/ScipionUserData
WIZARD_MASK_COLOR = [0.125, 0.909, 0.972]
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"
[PLUGINS]
CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056
CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5
CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6
CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5
CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5
CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5
CRYOSPARC_HOME = /home/impmc/
CRYO_PROJECTS_DIR = scipion_projects
CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14
EMAN2SCRATCHDIR = /tmp
EMAN2_HOME = %(EM_ROOT)s/eman-2.91
EM_ROOT = software/em
JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5
MAXIT_HOME = %(EM_ROOT)s/maxit-10.1
MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101
MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64
MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0
PHENIX_HOME = %(EM_ROOT)s/phenix-
RELION_CUDA_LIB = /usr/local/cuda/lib64
RELION_HOME = %(EM_ROOT)s/relion-3.1.2
XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src
XMIPP_HOME = %(EM_ROOT)s/xmipp
Thanks again.
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:51:06 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hello Carlos,
to start, you are missing a space between eval and the rest in:
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)"
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thanks for the message. The all output is bellow:
Scipion v3.0.9 - Eugenius
Building scipion-em-sphire ...
/home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7
Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ]
Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7)
Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13)
Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76)
Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8)
Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17)
Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4)
Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3)
Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0)
Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0)
Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0)
Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1)
Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2)
Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3)
Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7)
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Done (0.84 seconds)
Building cryolo-1.7.6 ...
Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ]
mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz
All targets exist.
Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6
All targets exist.
Skipping command: tar -xf void.tgz -C cryolo-1.7.6
All targets exist.
cd /home/impmc/scipion/software/em/cryolo-1.7.6
eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed
/bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python'
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
__add_sys_prefix_to_path() {
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
SYSP=$(\dirname "${CONDA_EXE}")
else
SYSP=$(\dirname "${CONDA_EXE}")
SYSP=$(\dirname "${SYSP}")
fi
if [ -n "${WINDIR+x}" ]; then
PATH="${SYSP}/bin:${PATH}"
PATH="${SYSP}/Scripts:${PATH}"
PATH="${SYSP}/Library/bin:${PATH}"
PATH="${SYSP}/Library/usr/bin:${PATH}"
PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
PATH="${SYSP}:${PATH}"
else
PATH="${SYSP}/bin:${PATH}"
fi
\export PATH
}
__conda_exe() (
__add_sys_prefix_to_path
"$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
)
__conda_hashr() {
if [ -n "${ZSH_VERSION:+x}" ]; then
\rehash
elif [ -n "${POSH_VERSION:+x}" ]; then
: # pass
else
\hash -r
fi
}
__conda_activate() {
if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
# Handle transition from shell activated with conda <= 4.3 to a subsequent activation
# after conda updated to >= 4.4. See issue #6173.
PS1="$CONDA_PS1_BACKUP"
\unset CONDA_PS1_BACKUP
fi
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
\eval "$ask_conda"
__conda_hashr
}
__conda_reactivate() {
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
\eval "$ask_conda"
__conda_hashr
}
conda() {
\local cmd="${1-__missing__}"
case "$cmd" in
activate|deactivate)
__conda_activate "$@"
;;
install|update|upgrade|remove|uninstall)
__conda_exe "$@" || \return
__conda_reactivate
;;
*)
__conda_exe "$@"
;;
esac
}
if [ -z "${CONDA_SHLVL+x}" ]; then
\export CONDA_SHLVL=0
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
else
PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
fi
\export PATH
# We're not allowing PS1 to be unbound. It must at least be set.
# However, we're not exporting it, which can cause problems when starting a second shell
# via a first shell (i.e. starting zsh from bash).
if [ -z "${PS1+x}" ]; then
PS1=
fi
fi
conda activate base: not found
Traceback (most recent call last):
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module>
main()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main
installPluginMethods()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
command.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:33:09 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Dear Carlos,
given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear all,
I'm facing some problems using cryolo training at Scipion.
I found the following error:
Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127.
I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it.
In my scipion.conf file, I inserted
CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh
or even
CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)"
(I saw these pathways in my bash.rc)
Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears:
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
I am not sure if these errors are related and hinder performing cryolo in Scipion.
I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command).
Anyone know what I'm doing wrong?
Thanks in advance,
Carlos.
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BQ_END
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BQ_END
--
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team
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|
|
From: Grigory S. <sha...@gm...> - 2021-09-30 09:58:51
|
Can you run *conda activate cryolo-1.7.6 && which cryolo_train.py* ? Can you also run *which cryolo_train.py *? (in case you installed cryolo into conda base env) Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dears Grigory and Pablo, > > Sorry for the problems with conda; these things are very recent to me; I'm > still learning how to deal with them. > And, thanks again for the messages and for the support. > > About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in > cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2: > /home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2 > /home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2 > > /home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2 > It is possible to change to libcudnn.so.8 inside these folders? > > About conda; Yes, cryolo 1.8 are using conda from eman... I installed > miniconda and anaconda3; however when I type 'which conda', I have as only > response the conda from eman. > Best regards, > Carlos. > > ------------------------------ > *From: *"Pablo Conesa" <pc...@cn...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Thursday, September 30, 2021 10:29:11 AM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > I agree with Grigory, using eman2 conda is not a good practice. > > Probably he did not decided that but Scipion installer used the available > one, and probably that one was eman2 one. > > If you want to undo this you will need to install miniconda, and have it > available instead of eman2 one. > > "which conda" will tell you the available one. > > > On 29/9/21 18:54, Grigory Sharov wrote: > > Thanks! In run.stderr you can see the reason it has failed: > > 2021-09-30 02:14:42.492074: W > tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not > load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open > shared object file: No such file or directory; LD_LIBRARY_PATH: > /usr/local/cuda/lib64::/home/impmc/scipion/software/lib > > For some reason it's looking for libcudnn.so.8 but the cryolo package > should have installed libcudnn.so.7.1.2 for you. Can you check that > a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I > dont know where is your env is installed. You can activate conda and "check > conda list env" > b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct > path for cryolo env. The previous command should tell you where it should be > > In general, my advice would be to not use eman2 conda for anything except > eman. You'd be better off using a separate miniconda3 installation. Which > conda did you use for cryolo 1.8? From eman? > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> The files that you requested are attached. >> Thanks so much again >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Wednesday, September 29, 2021 6:18:12 PM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Hi, >> The config files look ok. Could you attach run.stderr and run.stdout for >> the failed protocol? >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear Grigory, >>> >>> Thank you so much, fixing this space solved the problem with >>> cryolo_1.7.6_installing (shame on me for this). >>> However, I tried to run the cryolo training and I obtained the same >>> previous error: >>> >>> eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune >>> 00022: Protocol failed: Command ' eval >>> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >>> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. >>> 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 >>> 02:14:42.822982 >>> >>> Bellow, it is my current scipion.conf file >>> [PYWORKFLOW] >>> SCIPION_DOMAIN = pwem >>> SCIPION_FONT_NAME = Helvetica >>> SCIPION_GUI_REFRESH_IN_THREAD = False >>> SCIPION_LOG = ~/ScipionUserData/logs/scipion.log >>> SCIPION_LOGO = scipion_logo.gif >>> SCIPION_LOGS = ~/ScipionUserData/logs >>> SCIPION_NOTES_FILE = notes.txt >>> SCIPION_NOTIFY = True >>> SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ >>> SCIPION_SOFTWARE = ${SCIPION_HOME}/software >>> SCIPION_SUPPORT_EMAIL = sc...@cn... >>> SCIPION_TESTS = ${SCIPION_HOME}/data/tests >>> SCIPION_TESTS_CMD = scipion3 tests >>> SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests >>> SCIPION_TMP = ~/ScipionUserData/tmp >>> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion >>> SCIPION_URL_SOFTWARE = >>> http://scipion.cnb.csic.es/downloads/scipion/software >>> SCIPION_URL_TESTDATA = >>> http://scipion.cnb.csic.es/downloads/scipion/data/tests >>> SCIPION_USER_DATA = ~/ScipionUserData >>> WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] >>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>> shell.bash hook 2> /dev/null)" >>> >>> [PLUGINS] >>> CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 >>> CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 >>> CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta >>> CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 >>> CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 >>> CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 >>> CRYOLO_GENERIC_DENOISED_MODEL = >>> %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 >>> CRYOLO_GENERIC_MODEL = >>> %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 >>> CRYOLO_NS_GENERIC_MODEL = >>> %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 >>> CRYOSPARC_HOME = /home/impmc/ >>> CRYO_PROJECTS_DIR = scipion_projects >>> CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 >>> EMAN2SCRATCHDIR = /tmp >>> EMAN2_HOME = %(EM_ROOT)s/eman-2.91 >>> EM_ROOT = software/em >>> JANNI_GENERIC_MODEL = >>> %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 >>> MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 >>> MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 >>> MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 >>> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 >>> PHENIX_HOME = %(EM_ROOT)s/phenix- >>> RELION_CUDA_LIB = /usr/local/cuda/lib64 >>> RELION_HOME = %(EM_ROOT)s/relion-3.1.2 >>> XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src >>> XMIPP_HOME = %(EM_ROOT)s/xmipp >>> >>> >>> Thanks again. >>> >>> ------------------------------ >>> *From: *"Grigory Sharov" <sha...@gm...> >>> *To: *"scipion-users" <sci...@li...> >>> *Sent: *Wednesday, September 29, 2021 5:51:06 PM >>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >>> Cryolo >>> >>> Hello Carlos, >>> >>> to start, you are missing a space between eval and the rest in: >>> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >>> shell.bash hook)" >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < >>> car...@so...> wrote: >>> >>>> Dear Grigory, >>>> >>>> Thanks for the message. The all output is bellow: >>>> >>>> Scipion v3.0.9 - Eugenius >>>> Building scipion-em-sphire ... >>>> /home/impmc/scipion/.scipion3/bin/python -m pip install >>>> scipion-em-sphire==3.0.7 >>>> Looking in indexes: https://pypi.org/simple, >>>> https://pypi.ngc.nvidia.com >>>> Requirement already satisfied: scipion-em-sphire==3.0.7 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >>>> Requirement already satisfied: scipion-em in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-em-sphire==3.0.7) (3.0.13) >>>> Requirement already satisfied: biopython==1.76 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-em->scipion-em-sphire==3.0.7) (1.76) >>>> Requirement already satisfied: tifffile in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >>>> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >>>> Requirement already satisfied: numpy in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >>>> Requirement already satisfied: mpi4py<=3.0.3 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >>>> Requirement already satisfied: configparser<=5.0.2 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >>>> Requirement already satisfied: psutil<=5.8.0 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >>>> Requirement already satisfied: pillow<=8.2.0 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >>>> Requirement already satisfied: bibtexparser<=1.2.0 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >>>> Requirement already satisfied: requests<=2.25.1 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >>>> Requirement already satisfied: matplotlib==3.2.2 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >>>> Requirement already satisfied: tkcolorpicker<=2.1.3 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >>>> Requirement already satisfied: cycler>=0.10 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (0.10.0) >>>> Requirement already satisfied: python-dateutil>=2.1 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (2.8.1) >>>> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 >>>> in ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (2.4.7) >>>> Requirement already satisfied: kiwisolver>=1.0.1 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (1.3.1) >>>> Requirement already satisfied: future>=0.16.0 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (0.18.2) >>>> Requirement already satisfied: six in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (1.16.0) >>>> Requirement already satisfied: certifi>=2017.4.17 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (2020.12.5) >>>> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (1.26.4) >>>> Requirement already satisfied: chardet<5,>=3.0.2 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (4.0.0) >>>> Requirement already satisfied: idna<3,>=2.5 in >>>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>>> (2.10) >>>> Done (0.84 seconds) >>>> Building cryolo-1.7.6 ... >>>> Skipping command: wget -nv -c -O >>>> /home/impmc/scipion/software/em/void.tgz.part >>>> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >>>> mv -v /home/impmc/scipion/software/em/void.tgz.part >>>> /home/impmc/scipion/software/em/void.tgz >>>> All targets exist. >>>> Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 >>>> All targets exist. >>>> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >>>> All targets exist. >>>> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >>>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>>> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >>>> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >>>> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >>>> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >>>> /bin/sh: 1: evalexport >>>> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >>>> export _CE_M='' >>>> export _CE_CONDA='' >>>> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >>>> >>>> # Copyright (C) 2012 Anaconda, Inc >>>> # SPDX-License-Identifier: BSD-3-Clause >>>> >>>> __add_sys_prefix_to_path() { >>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>> # it is in a different relative location to condabin. >>>> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >>>> SYSP=$(\dirname "${CONDA_EXE}") >>>> else >>>> SYSP=$(\dirname "${CONDA_EXE}") >>>> SYSP=$(\dirname "${SYSP}") >>>> fi >>>> >>>> if [ -n "${WINDIR+x}" ]; then >>>> PATH="${SYSP}/bin:${PATH}" >>>> PATH="${SYSP}/Scripts:${PATH}" >>>> PATH="${SYSP}/Library/bin:${PATH}" >>>> PATH="${SYSP}/Library/usr/bin:${PATH}" >>>> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >>>> PATH="${SYSP}:${PATH}" >>>> else >>>> PATH="${SYSP}/bin:${PATH}" >>>> fi >>>> \export PATH >>>> } >>>> >>>> __conda_exe() ( >>>> __add_sys_prefix_to_path >>>> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >>>> ) >>>> >>>> __conda_hashr() { >>>> if [ -n "${ZSH_VERSION:+x}" ]; then >>>> \rehash >>>> elif [ -n "${POSH_VERSION:+x}" ]; then >>>> : # pass >>>> else >>>> \hash -r >>>> fi >>>> } >>>> >>>> __conda_activate() { >>>> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >>>> # Handle transition from shell activated with conda <= 4.3 to a >>>> subsequent activation >>>> # after conda updated to >= 4.4. See issue #6173. >>>> PS1="$CONDA_PS1_BACKUP" >>>> \unset CONDA_PS1_BACKUP >>>> fi >>>> \local ask_conda >>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || >>>> \return >>>> \eval "$ask_conda" >>>> __conda_hashr >>>> } >>>> >>>> __conda_reactivate() { >>>> \local ask_conda >>>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || >>>> \return >>>> \eval "$ask_conda" >>>> __conda_hashr >>>> } >>>> >>>> conda() { >>>> \local cmd="${1-__missing__}" >>>> case "$cmd" in >>>> activate|deactivate) >>>> __conda_activate "$@" >>>> ;; >>>> install|update|upgrade|remove|uninstall) >>>> __conda_exe "$@" || \return >>>> __conda_reactivate >>>> ;; >>>> *) >>>> __conda_exe "$@" >>>> ;; >>>> esac >>>> } >>>> >>>> if [ -z "${CONDA_SHLVL+x}" ]; then >>>> \export CONDA_SHLVL=0 >>>> # In dev-mode CONDA_EXE is python.exe and on Windows >>>> # it is in a different relative location to condabin. >>>> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >>>> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >>>> else >>>> PATH="$(\dirname "$(\dirname >>>> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >>>> fi >>>> \export PATH >>>> >>>> # We're not allowing PS1 to be unbound. It must at least be set. >>>> # However, we're not exporting it, which can cause problems when >>>> starting a second shell >>>> # via a first shell (i.e. starting zsh from bash). >>>> if [ -z "${PS1+x}" ]; then >>>> PS1= >>>> fi >>>> fi >>>> >>>> conda activate base: not found >>>> Traceback (most recent call last): >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>> line 470, in <module> >>>> main() >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>>> line 293, in main >>>> installPluginMethods() >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>>> line 232, in installPluginMethods >>>> plugin.installBin({'args': ['-j', numberProcessor]}) >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>>> line 166, in installBin >>>> environment.execute() >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 748, in execute >>>> self._executeTargets(targetList) >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 690, in _executeTargets >>>> tgt.execute() >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 221, in execute >>>> command.execute() >>>> File >>>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>>> line 161, in execute >>>> assert glob(t), ("target '%s' not built (after " >>>> AssertionError: target >>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>> Error at main: target >>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>>> >>>> ------------------------------ >>>> *From: *"Grigory Sharov" <sha...@gm...> >>>> *To: *"scipion-users" <sci...@li...> >>>> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >>>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD >>>> using Cryolo >>>> >>>> Dear Carlos, >>>> given the fact that the installation has failed, could you attach all >>>> output after "scipion3 installp -p scipion-em-sphire" command? >>>> >>>> Best regards, >>>> Grigory >>>> >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>>> e-mail: gs...@mr... >>>> >>>> >>>> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >>>> car...@so...> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I'm facing some problems using cryolo training at Scipion. >>>>> I found the following error: >>>>> >>>>> *Protocol failed: Command ' source >>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>>>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>>>> --fine_tune' returned non-zero exit status 127. * >>>>> >>>>> I saw some discussion about that at Scipion lists, but I'm still >>>>> little lost in how to fix it. >>>>> In my scipion.conf file, I inserted >>>>> *CONDA_ACTIVATION_CMD = source >>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>>>> or even >>>>> CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>>> shell.bash hook)" >>>>> (I saw these pathways in my bash.rc) >>>>> >>>>> Moreover, when I try to install cryolo using command line (scipion3 >>>>> installp -p scipion-em-sphire), the following error apears: >>>>> *AssertionError: target >>>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>>> built (after running 'source >>>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>>>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>>>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>>>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>>>> cryolo_1.7.6_installed')* >>>>> >>>>> I am not sure if these errors are related and hinder performing cryolo >>>>> in Scipion. >>>>> I have conda installed in the computer and I'm able to use cryolo 1.8 >>>>> outside from Scipion in the same computer (using *source activate >>>>> cryolo *command). >>>>> >>>>> Anyone know what I'm doing wrong? >>>>> Thanks in advance, >>>>> Carlos. >>>>> >>>>> >>>>> _______________________________________________ >>>>> scipion-users mailing list >>>>> sci...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>>> >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos H. F. <car...@so...> - 2021-09-30 09:47:09
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Dears Grigory and Pablo,
Sorry for the problems with conda; these things are very recent to me; I'm still learning how to deal with them.
And, thanks again for the messages and for the support.
About libcudnn.so.8; indeed there is no libcudnn.so.8 installed in cryolo-1.7.6 environment lib folder. There is only libcudnn.so.7.1.2:
/home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/envs/cryoloCPU-1.7.6/lib/libcudnn.so.7.1.2
/home/impmc/eman2-sphire-sparx/pkgs/cudnn-7.1.2-cuda9.0_0/lib/libcudnn.so.7.1.2
It is possible to change to libcudnn.so.8 inside these folders?
About conda; Yes, cryolo 1.8 are using conda from eman... I installed miniconda and anaconda3; however when I type 'which conda', I have as only response the conda from eman.
Best regards,
Carlos.
From: "Pablo Conesa" <pc...@cn...>
To: "scipion-users" <sci...@li...>
Sent: Thursday, September 30, 2021 10:29:11 AM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
I agree with Grigory, using eman2 conda is not a good practice.
Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one.
If you want to undo this you will need to install miniconda, and have it available instead of eman2 one.
"which conda" will tell you the available one.
On 29/9/21 18:54, Grigory Sharov wrote:
Thanks! In run.stderr you can see the reason it has failed:
2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib
For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that
a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env"
b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be
In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0)
1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
The files that you requested are attached.
Thanks so much again
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 6:18:12 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hi,
The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44
(0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this).
However, I tried to run the cryolo training and I obtained the same previous error:
eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune
00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1.
00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982
Bellow, it is my current scipion.conf file
[PYWORKFLOW]
SCIPION_DOMAIN = pwem
SCIPION_FONT_NAME = Helvetica
SCIPION_GUI_REFRESH_IN_THREAD = False
SCIPION_LOG = ~/ScipionUserData/logs/scipion.log
SCIPION_LOGO = scipion_logo.gif
SCIPION_LOGS = ~/ScipionUserData/logs
SCIPION_NOTES_FILE = notes.txt
SCIPION_NOTIFY = True
SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ]
SCIPION_SOFTWARE = ${SCIPION_HOME}/software
SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ]
SCIPION_TESTS = ${SCIPION_HOME}/data/tests
SCIPION_TESTS_CMD = scipion3 tests
SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests
SCIPION_TMP = ~/ScipionUserData/tmp
SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ]
SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ]
SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ]
SCIPION_USER_DATA = ~/ScipionUserData
WIZARD_MASK_COLOR = [0.125, 0.909, 0.972]
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"
[PLUGINS]
CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056
CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5
CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta
CRYOLO_CUDA_LIB = /usr/local/cuda/lib64
CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6
CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6
CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5
CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5
CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5
CRYOSPARC_HOME = /home/impmc/
CRYO_PROJECTS_DIR = scipion_projects
CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14
EMAN2SCRATCHDIR = /tmp
EMAN2_HOME = %(EM_ROOT)s/eman-2.91
EM_ROOT = software/em
JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5
MAXIT_HOME = %(EM_ROOT)s/maxit-10.1
MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101
MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64
MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0
PHENIX_HOME = %(EM_ROOT)s/phenix-
RELION_CUDA_LIB = /usr/local/cuda/lib64
RELION_HOME = %(EM_ROOT)s/relion-3.1.2
XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src
XMIPP_HOME = %(EM_ROOT)s/xmipp
Thanks again.
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:51:06 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Hello Carlos,
to start, you are missing a space between eval and the rest in:
CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)"
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear Grigory,
Thanks for the message. The all output is bellow:
Scipion v3.0.9 - Eugenius
Building scipion-em-sphire ...
/home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7
Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ]
Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7)
Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13)
Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76)
Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8)
Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17)
Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4)
Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3)
Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0)
Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0)
Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2)
Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0)
Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1)
Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2)
Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3)
Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0)
Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1)
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7)
Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1)
Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2)
Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0)
Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5)
Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4)
Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0)
Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10)
Done (0.84 seconds)
Building cryolo-1.7.6 ...
Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ]
mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz
All targets exist.
Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6
All targets exist.
Skipping command: tar -xf void.tgz -C cryolo-1.7.6
All targets exist.
cd /home/impmc/scipion/software/em/cryolo-1.7.6
eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed
/bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda'
export _CE_M=''
export _CE_CONDA=''
export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python'
# Copyright (C) 2012 Anaconda, Inc
# SPDX-License-Identifier: BSD-3-Clause
__add_sys_prefix_to_path() {
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then
SYSP=$(\dirname "${CONDA_EXE}")
else
SYSP=$(\dirname "${CONDA_EXE}")
SYSP=$(\dirname "${SYSP}")
fi
if [ -n "${WINDIR+x}" ]; then
PATH="${SYSP}/bin:${PATH}"
PATH="${SYSP}/Scripts:${PATH}"
PATH="${SYSP}/Library/bin:${PATH}"
PATH="${SYSP}/Library/usr/bin:${PATH}"
PATH="${SYSP}/Library/mingw-w64/bin:${PATH}"
PATH="${SYSP}:${PATH}"
else
PATH="${SYSP}/bin:${PATH}"
fi
\export PATH
}
__conda_exe() (
__add_sys_prefix_to_path
"$CONDA_EXE" $_CE_M $_CE_CONDA "$@"
)
__conda_hashr() {
if [ -n "${ZSH_VERSION:+x}" ]; then
\rehash
elif [ -n "${POSH_VERSION:+x}" ]; then
: # pass
else
\hash -r
fi
}
__conda_activate() {
if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then
# Handle transition from shell activated with conda <= 4.3 to a subsequent activation
# after conda updated to >= 4.4. See issue #6173.
PS1="$CONDA_PS1_BACKUP"
\unset CONDA_PS1_BACKUP
fi
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return
\eval "$ask_conda"
__conda_hashr
}
__conda_reactivate() {
\local ask_conda
ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return
\eval "$ask_conda"
__conda_hashr
}
conda() {
\local cmd="${1-__missing__}"
case "$cmd" in
activate|deactivate)
__conda_activate "$@"
;;
install|update|upgrade|remove|uninstall)
__conda_exe "$@" || \return
__conda_reactivate
;;
*)
__conda_exe "$@"
;;
esac
}
if [ -z "${CONDA_SHLVL+x}" ]; then
\export CONDA_SHLVL=0
# In dev-mode CONDA_EXE is python.exe and on Windows
# it is in a different relative location to condabin.
if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then
PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}"
else
PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}"
fi
\export PATH
# We're not allowing PS1 to be unbound. It must at least be set.
# However, we're not exporting it, which can cause problems when starting a second shell
# via a first shell (i.e. starting zsh from bash).
if [ -z "${PS1+x}" ]; then
PS1=
fi
fi
conda activate base: not found
Traceback (most recent call last):
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module>
main()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main
installPluginMethods()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods
plugin.installBin({'args': ['-j', numberProcessor]})
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin
environment.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute
self._executeTargets(targetList)
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets
tgt.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute
command.execute()
File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute
assert glob(t), ("target '%s' not built (after "
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] >
To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] >
Sent: Wednesday, September 29, 2021 5:33:09 PM
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo
Dear Carlos,
given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command?
Best regards,
Grigory
--------------------------------------------------------------------------------
Grigory Sharov, Ph.D.
MRC Laboratory of Molecular Biology,
Francis Crick Avenue,
Cambridge Biomedical Campus,
Cambridge CB2 0QH, UK.
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ]
e-mail: [ mailto:gs...@mr... | gs...@mr... ]
On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote:
BQ_BEGIN
Dear all,
I'm facing some problems using cryolo training at Scipion.
I found the following error:
Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127.
I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it.
In my scipion.conf file, I inserted
CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh
or even
CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)"
(I saw these pathways in my bash.rc)
Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears:
AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed')
I am not sure if these errors are related and hinder performing cryolo in Scipion.
I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command).
Anyone know what I'm doing wrong?
Thanks in advance,
Carlos.
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From: Dmitry S. <Sem...@gm...> - 2021-09-30 09:31:28
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Dear colleagues,
Issue while using xmipp - validate overfilling protocol
_ERROR 1: Errors on command line parameters
Unrecognized parameter: --thr
[1;31mFile: core/argsparser.cpp line: 1005[0m
For more info use --help
[1;31mXMIPP_ERROR 1: Errors on command line parameters[0m
[1;31m[1;31mUnrecognized parameter: --thr
[0m[0m
[1;31mFile: core/argsparser.cpp line: 1005[0m
For more info use --help
Traceback (most recent call last):
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 201, in run
self._run()
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 252, in _run
resultFiles = self._runFunc()
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 248, in _runFunc
return self._func(*self._args)
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/xmipp3/protocols/protocol_validate_overfitting.py", line 362, in reconstructionStep
self.runJob('xmipp_reconstruct_fourier_accel', params)
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 1388, in runJob
self._stepsExecutor.runJob(self._log, program, arguments, **kwargs)
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/protocol/executor.py", line 65, in runJob
process.runJob(log, programName, params,
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 52, in runJob
return runCommand(command, env, cwd)
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/site-packages/pyworkflow/utils/process.py", line 67, in runCommand
check_call(command, shell=True, stdout=sys.stdout, stderr=sys.stderr,
File "/home/user/Data/Software/miniconda/envs/scipion3/lib/python3.8/subprocess.py", line 364, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command ' mpirun -np 8 `which xmipp_mpi_reconstruct_fourier_accel` -i Runs/008120_XmippProtValidateOverfitting/extra/Nfraction_alignment00_00_00.xmd -o Runs/008120_XmippProtValidateOverfitting/extra/Nfraction00_00_00.vol --sym c2 --max_resolution 0.500 --padding 2 --thr 1 --sampling 0.961270' returned non-zero exit status 1.
[31mProtocol failed: Command ' mpirun -np 8 `which xmipp_mpi_reconstruct_fourier_accel` -i Runs/008120_XmippProtValidateOverfitting/extra/Nfraction_alignment00_00_00.xmd -o Runs/008120_XmippProtValidateOverfitting/extra/Nfraction00_00_00.vol --sym c2 --max_resolution 0.500 --padding 2 --thr 1 --sampling 0.961270' returned non-zero exit status 1.[0m
Any ideas?
Thank you
Sincerely,
Dmitry
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From: Anastasina, M. <mar...@he...> - 2021-09-30 09:12:41
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Hi Grigory, Thank you for looking into my files. Yes, this job is a continuation of another one where 25 iterations were completed, but CreateOutput step failed with exactly the same error message. This is why I put 0 iterations in the job, hoping that it will just manage to create the output (or was it a wrong idea?). Since the original job with 25 iterations also filed, it seems that the source of error is something else, or maybe was a problem with that original job that migrated to the next one (sorry if it sounds confusing)?. Just in case, I attach here .stderr and .stdout files form the original job too. There all 25 iterations were completed, but the CreateOutput failed. Best, Maria On 30. Sep 2021, at 11.50, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Hello Maria, srun `which relion_refine_mpi` --norm --scale --o Runs/012188_ProtRelionClassify3D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 4.0 --iter 25 --pad 2 --skip_gridding --healpix_order 4 --offset_range 5.0 --offset_step 2.0 --continue Runs/011346_ProtRelionClassify3D/extra/relion_it025_optimiser.star --dont_combine_weights_via_disc --pool 3 --gpu --j 4 You are running a job that will not do anything, continuing from iteration 25 until 25. Did you put 0 in number of iterations in the protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228<tel:+44%201223%20267228> e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 6:07 PM Anastasina, Maria <mar...@he...<mailto:mar...@he...>> wrote: Dear Grigory, Here they go Best, Maria [masha@puhti-login2 ~]$ scipion3 config -p relion Scipion v3.0.8 - Eugenius Variables defined by plugin 'relion': RELION_HOME = /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.1 RELION_CUDA_LIB = /appl/spack/install-tree/gcc-8.3.0/cuda-10.1.168-mrdepn/lib64 These variables can be added/edited in '/appl/soft/math/scipion/3.0.7/config/scipion.conf' On 29. Sep 2021, at 18.28, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Dear Maria, could you please 1) post here the output of "scipion3 config -p relion" 2) attach run.stdout and run.stderr files from the failed protocol Thank you. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria <mar...@he...<mailto:mar...@he...>> wrote: > > Hello, > > All my recent Relion 3D classification jobs the I run in Scipion fail at CreateOutput step with the error message "Protocol failed: 'Class3D' object has no attribute ‘_rlnClassDistribution’”. > > Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used to finish successfully. I’m not aware of any changes or updates that have been done at our HPC server or Scipion installation (we use Scipion 3.0.8). > > Do you know what could be the reason for this error? > > Best regards, > Maria > _______________________________________________ > scipion-users mailing list > sci...@li...<mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-30 08:51:05
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Hello Maria, srun `which relion_refine_mpi` --norm --scale --o Runs/012188_ProtRelionClassify3D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 4.0 --iter 25 --pad 2 --skip_gridding --healpix_order 4 --offset_range 5.0 --offset_step 2.0 --continue Runs/011346_ProtRelionClassify3D/extra/relion_it025_optimiser.star --dont_combine_weights_via_disc --pool 3 --gpu --j 4 You are running a job that will not do anything, continuing from iteration 25 until 25. Did you put 0 in number of iterations in the protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Sep 29, 2021 at 6:07 PM Anastasina, Maria < mar...@he...> wrote: > Dear Grigory, > > Here they go > > Best, > Maria > > [masha@puhti-login2 ~]$ scipion3 config -p relion > Scipion v3.0.8 - Eugenius > Variables defined by plugin 'relion': > > RELION_HOME = /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.1 > RELION_CUDA_LIB = > /appl/spack/install-tree/gcc-8.3.0/cuda-10.1.168-mrdepn/lib64 > > These variables can be added/edited in > '/appl/soft/math/scipion/3.0.7/config/scipion.conf' > > > On 29. Sep 2021, at 18.28, Grigory Sharov <sha...@gm...> > wrote: > > Dear Maria, > > could you please > > 1) post here the output of "scipion3 config -p relion" > 2) attach run.stdout and run.stderr files from the failed protocol > > Thank you. > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria < > mar...@he...> wrote: > > > > Hello, > > > > All my recent Relion 3D classification jobs the I run in Scipion fail at > CreateOutput step with the error message "Protocol failed: 'Class3D' > object has no attribute ‘_rlnClassDistribution’”. > > > > Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used > to finish successfully. I’m not aware of any changes or updates that have > been done at our HPC server or Scipion installation (we use Scipion 3.0.8). > > > > Do you know what could be the reason for this error? > > > > Best regards, > > Maria > > _______________________________________________ > > scipion-users mailing list > > sci...@li... > > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Pablo C. <pc...@cn...> - 2021-09-30 08:29:30
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I agree with Grigory, using eman2 conda is not a good practice. Probably he did not decided that but Scipion installer used the available one, and probably that one was eman2 one. If you want to undo this you will need to install miniconda, and have it available instead of eman2 one. "which conda" will tell you the available one. On 29/9/21 18:54, Grigory Sharov wrote: > Thanks! In run.stderr you can see the reason it has failed: > > 2021-09-30 02:14:42.492074: W > tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could > not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: > cannot open shared object file: No such file or directory; > LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib > > For some reason it's looking for libcudnn.so.8 but the cryolo package > should have installed libcudnn.so.7.1.2 for you. Can you check that > a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I > dont know where is your env is installed. You can activate conda and > "check conda list env" > b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct > path for cryolo env. The previous command should tell you where it > should be > > In general, my advice would be to not use eman2 conda for anything > except eman. You'd be better off using a separate miniconda3 > installation. Which conda did you use for cryolo 1.8? From eman? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > The files that you requested are attached. > Thanks so much again > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 6:18:12 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD > using Cryolo > > Hi, > The config files look ok. Could you attach run.stderr and > run.stdout for the failed protocol? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thank you so much, fixing this space solved the problem with > cryolo_1.7.6_installing (shame on me for this). > However, I tried to run the cryolo training and I obtained the > same previous error: > > eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash > hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && > cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 > --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py > -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned > non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 > 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ > <http://scipion.i2pc.es/getplugins/> > SCIPION_SOFTWARE = ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = sc...@cn... > <mailto:sc...@cn...> > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion > <http://scipion.cnb.csic.es/downloads/scipion> > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > <http://scipion.cnb.csic.es/downloads/scipion/software> > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > <http://scipion.cnb.csic.es/downloads/scipion/data/tests> > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 > MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 5:51:06 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Hello Carlos, > > to start, you are missing a space between eval and the rest in: > CONDA_ACTIVATION_CMD = eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> wrote: > > Dear Grigory, > > Thanks for the message. The all output is bellow: > > Scipion v3.0.9 - Eugenius > Building scipion-em-sphire ... > /home/impmc/scipion/.scipion3/bin/python -m pip install > scipion-em-sphire==3.0.7 > Looking in indexes: https://pypi.org/simple > <https://pypi.org/simple>, https://pypi.ngc.nvidia.com > <https://pypi.ngc.nvidia.com> > Requirement already satisfied: scipion-em-sphire==3.0.7 in > ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) > Requirement already satisfied: scipion-em in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em-sphire==3.0.7) (3.0.13) > Requirement already satisfied: biopython==1.76 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (1.76) > Requirement already satisfied: tifffile in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) > Requirement already satisfied: scipion-pyworkflow>=3.0.15 > in ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (3.0.17) > Requirement already satisfied: numpy in > ./scipion/.scipion3/lib/python3.8/site-packages (from > biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) > (1.18.4) > Requirement already satisfied: mpi4py<=3.0.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.0.3) > Requirement already satisfied: configparser<=5.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.0.0) > Requirement already satisfied: psutil<=5.8.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (5.7.0) > Requirement already satisfied: pillow<=8.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.2.0) > Requirement already satisfied: requests<=2.25.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.25.1) > Requirement already satisfied: matplotlib==3.2.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (3.2.2) > Requirement already satisfied: tkcolorpicker<=2.1.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.1.3) > Requirement already satisfied: cycler>=0.10 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.10.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.8.1) > Requirement already satisfied: > pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.4.7) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.3.1) > Requirement already satisfied: future>=0.16.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.18.2) > Requirement already satisfied: six in > ./scipion/.scipion3/lib/python3.8/site-packages (from > cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.16.0) > Requirement already satisfied: certifi>=2017.4.17 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2020.12.5) > Requirement already satisfied: urllib3<1.27,>=1.21.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.26.4) > Requirement already satisfied: chardet<5,>=3.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (4.0.0) > Requirement already satisfied: idna<3,>=2.5 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.10) > Done (0.84 seconds) > Building cryolo-1.7.6 ... > Skipping command: wget -nv -c -O > /home/impmc/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > <http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz> > mv -v /home/impmc/scipion/software/em/void.tgz.part > /home/impmc/scipion/software/em/void.tgz > All targets exist. > Skipping command: mkdir > /home/impmc/scipion/software/em/cryolo-1.7.6 > All targets exist. > Skipping command: tar -xf void.tgz -C cryolo-1.7.6 > All targets exist. > cd /home/impmc/scipion/software/em/cryolo-1.7.6 > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash > hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 > numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 > &&conda activate cryolo-1.7.6 &&pip install > cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed > /bin/sh: 1: evalexport > CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' > export _CE_M='' > export _CE_CONDA='' > export > CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' > > # Copyright (C) 2012 Anaconda, Inc > # SPDX-License-Identifier: BSD-3-Clause > > __add_sys_prefix_to_path() { > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then > SYSP=$(\dirname "${CONDA_EXE}") > else > SYSP=$(\dirname "${CONDA_EXE}") > SYSP=$(\dirname "${SYSP}") > fi > > if [ -n "${WINDIR+x}" ]; then > PATH="${SYSP}/bin:${PATH}" > PATH="${SYSP}/Scripts:${PATH}" > PATH="${SYSP}/Library/bin:${PATH}" > PATH="${SYSP}/Library/usr/bin:${PATH}" > PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" > PATH="${SYSP}:${PATH}" > else > PATH="${SYSP}/bin:${PATH}" > fi > \export PATH > } > > __conda_exe() ( > __add_sys_prefix_to_path > "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" > ) > > __conda_hashr() { > if [ -n "${ZSH_VERSION:+x}" ]; then > \rehash > elif [ -n "${POSH_VERSION:+x}" ]; then > : # pass > else > \hash -r > fi > } > > __conda_activate() { > if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then > # Handle transition from shell activated with > conda <= 4.3 to a subsequent activation > # after conda updated to >= 4.4. See issue #6173. > PS1="$CONDA_PS1_BACKUP" > \unset CONDA_PS1_BACKUP > fi > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix > "$@")" || \return > \eval "$ask_conda" > __conda_hashr > } > > __conda_reactivate() { > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix > reactivate)" || \return > \eval "$ask_conda" > __conda_hashr > } > > conda() { > \local cmd="${1-__missing__}" > case "$cmd" in > activate|deactivate) > __conda_activate "$@" > ;; > install|update|upgrade|remove|uninstall) > __conda_exe "$@" || \return > __conda_reactivate > ;; > *) > __conda_exe "$@" > ;; > esac > } > > if [ -z "${CONDA_SHLVL+x}" ]; then > \export CONDA_SHLVL=0 > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then > PATH="$(\dirname > "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" > else > PATH="$(\dirname "$(\dirname > "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" > fi > \export PATH > > # We're not allowing PS1 to be unbound. It must at > least be set. > # However, we're not exporting it, which can cause > problems when starting a second shell > # via a first shell (i.e. starting zsh from bash). > if [ -z "${PS1+x}" ]; then > PS1= > fi > fi > > conda activate base: not found > Traceback (most recent call last): > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 > intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > Error at main: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running > 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 > cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 > intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > > ------------------------------------------------------------------------ > *From: *"Grigory Sharov" <sha...@gm... > <mailto:sha...@gm...>> > *To: *"scipion-users" <sci...@li... > <mailto:sci...@li...>> > *Sent: *Wednesday, September 29, 2021 5:33:09 PM > *Subject: *Re: [scipion-users] Problems with > CONDA_ACTIVATION_CMD using Cryolo > > Dear Carlos, > given the fact that the installation has failed, could you > attach all output after "scipion3 installp -p > scipion-em-sphire" command? > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... > <mailto:gs...@mr...> > > > On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES > <car...@so... > <mailto:car...@so...>> > wrote: > > Dear all, > > I'm facing some problems using cryolo training at Scipion. > I found the following error: > *Protocol failed: Command ' source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& > conda activate cryolo-1.7.6 && cryolo_train.py -c > config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' > returned non-zero exit status 127. > * > * > * > I saw some discussion about that at Scipion lists, but > I'm still little lost in how to fix it. > In my scipion.conf file, I inserted > /CONDA_ACTIVATION_CMD = source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh /// > or even > CONDA_ACTIVATION_CMD = > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)"// > (I saw these pathways in my bash.rc) > > Moreover, when I try to install cryolo using command > line (scipion3 installp -p scipion-em-sphire), the > following error apears: > *AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' > not built (after running 'source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda > create -y -n cryolo-1.7.6 -c conda-forge -c anaconda > python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate > cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed')* > > I am not sure if these errors are related and hinder > performing cryolo in Scipion. > I have conda installed in the computer and I'm able to > use cryolo 1.8 outside from Scipion in the same > computer (using /source activate cryolo /command). > > Anyone know what I'm doing wrong? Thanks in advance, > Carlos. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Anastasina, M. <mar...@he...> - 2021-09-29 17:06:39
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Dear Grigory, Here they go Best, Maria [masha@puhti-login2 ~]$ scipion3 config -p relion Scipion v3.0.8 - Eugenius Variables defined by plugin 'relion': RELION_HOME = /appl/soft/math/scipion/3.0.7/software/em/relion-3.1.1 RELION_CUDA_LIB = /appl/spack/install-tree/gcc-8.3.0/cuda-10.1.168-mrdepn/lib64 These variables can be added/edited in '/appl/soft/math/scipion/3.0.7/config/scipion.conf' On 29. Sep 2021, at 18.28, Grigory Sharov <sha...@gm...<mailto:sha...@gm...>> wrote: Dear Maria, could you please 1) post here the output of "scipion3 config -p relion" 2) attach run.stdout and run.stderr files from the failed protocol Thank you. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 e-mail: gs...@mr...<mailto:gs...@mr...> On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria <mar...@he...<mailto:mar...@he...>> wrote: > > Hello, > > All my recent Relion 3D classification jobs the I run in Scipion fail at CreateOutput step with the error message "Protocol failed: 'Class3D' object has no attribute ‘_rlnClassDistribution’”. > > Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used to finish successfully. I’m not aware of any changes or updates that have been done at our HPC server or Scipion installation (we use Scipion 3.0.8). > > Do you know what could be the reason for this error? > > Best regards, > Maria > _______________________________________________ > scipion-users mailing list > sci...@li...<mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-29 16:55:03
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Thanks! In run.stderr you can see the reason it has failed: 2021-09-30 02:14:42.492074: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudnn.so.8'; dlerror: libcudnn.so.8: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /usr/local/cuda/lib64::/home/impmc/scipion/software/lib For some reason it's looking for libcudnn.so.8 but the cryolo package should have installed libcudnn.so.7.1.2 for you. Can you check that a) you do have libcudnn8 in cryolo-1.7.6 environment lib folder? I dont know where is your env is installed. You can activate conda and "check conda list env" b) /home/impmc/.local/bin/cryolo_train.py does not look like a correct path for cryolo env. The previous command should tell you where it should be In general, my advice would be to not use eman2 conda for anything except eman. You'd be better off using a separate miniconda3 installation. Which conda did you use for cryolo 1.8? From eman? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > The files that you requested are attached. > Thanks so much again > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 6:18:12 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Hi, > The config files look ok. Could you attach run.stderr and run.stdout for > the failed protocol? > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> Thank you so much, fixing this space solved the problem with >> cryolo_1.7.6_installing (shame on me for this). >> However, I tried to run the cryolo training and I obtained the same >> previous error: >> >> eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune >> 00022: Protocol failed: Command ' eval >> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json >> -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. >> 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 >> 02:14:42.822982 >> >> Bellow, it is my current scipion.conf file >> [PYWORKFLOW] >> SCIPION_DOMAIN = pwem >> SCIPION_FONT_NAME = Helvetica >> SCIPION_GUI_REFRESH_IN_THREAD = False >> SCIPION_LOG = ~/ScipionUserData/logs/scipion.log >> SCIPION_LOGO = scipion_logo.gif >> SCIPION_LOGS = ~/ScipionUserData/logs >> SCIPION_NOTES_FILE = notes.txt >> SCIPION_NOTIFY = True >> SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ >> SCIPION_SOFTWARE = ${SCIPION_HOME}/software >> SCIPION_SUPPORT_EMAIL = sc...@cn... >> SCIPION_TESTS = ${SCIPION_HOME}/data/tests >> SCIPION_TESTS_CMD = scipion3 tests >> SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests >> SCIPION_TMP = ~/ScipionUserData/tmp >> SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion >> SCIPION_URL_SOFTWARE = >> http://scipion.cnb.csic.es/downloads/scipion/software >> SCIPION_URL_TESTDATA = >> http://scipion.cnb.csic.es/downloads/scipion/data/tests >> SCIPION_USER_DATA = ~/ScipionUserData >> WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] >> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >> shell.bash hook 2> /dev/null)" >> >> [PLUGINS] >> CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 >> CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 >> CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta >> CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 >> CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 >> CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 >> CRYOLO_GENERIC_DENOISED_MODEL = >> %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 >> CRYOLO_GENERIC_MODEL = >> %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 >> CRYOLO_NS_GENERIC_MODEL = >> %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 >> CRYOSPARC_HOME = /home/impmc/ >> CRYO_PROJECTS_DIR = scipion_projects >> CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 >> EMAN2SCRATCHDIR = /tmp >> EMAN2_HOME = %(EM_ROOT)s/eman-2.91 >> EM_ROOT = software/em >> JANNI_GENERIC_MODEL = >> %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 >> MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 >> MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 >> MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 >> MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 >> PHENIX_HOME = %(EM_ROOT)s/phenix- >> RELION_CUDA_LIB = /usr/local/cuda/lib64 >> RELION_HOME = %(EM_ROOT)s/relion-3.1.2 >> XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src >> XMIPP_HOME = %(EM_ROOT)s/xmipp >> >> >> Thanks again. >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Wednesday, September 29, 2021 5:51:06 PM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Hello Carlos, >> >> to start, you are missing a space between eval and the rest in: >> CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda >> shell.bash hook)" >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear Grigory, >>> >>> Thanks for the message. The all output is bellow: >>> >>> Scipion v3.0.9 - Eugenius >>> Building scipion-em-sphire ... >>> /home/impmc/scipion/.scipion3/bin/python -m pip install >>> scipion-em-sphire==3.0.7 >>> Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com >>> Requirement already satisfied: scipion-em-sphire==3.0.7 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >>> Requirement already satisfied: scipion-em in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-em-sphire==3.0.7) (3.0.13) >>> Requirement already satisfied: biopython==1.76 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-em->scipion-em-sphire==3.0.7) (1.76) >>> Requirement already satisfied: tifffile in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >>> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >>> Requirement already satisfied: numpy in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >>> Requirement already satisfied: mpi4py<=3.0.3 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >>> Requirement already satisfied: configparser<=5.0.2 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >>> Requirement already satisfied: psutil<=5.8.0 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >>> Requirement already satisfied: pillow<=8.2.0 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >>> Requirement already satisfied: bibtexparser<=1.2.0 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >>> Requirement already satisfied: requests<=2.25.1 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >>> Requirement already satisfied: matplotlib==3.2.2 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >>> Requirement already satisfied: tkcolorpicker<=2.1.3 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >>> Requirement already satisfied: cycler>=0.10 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (0.10.0) >>> Requirement already satisfied: python-dateutil>=2.1 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (2.8.1) >>> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 >>> in ./scipion/.scipion3/lib/python3.8/site-packages (from >>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (2.4.7) >>> Requirement already satisfied: kiwisolver>=1.0.1 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (1.3.1) >>> Requirement already satisfied: future>=0.16.0 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (0.18.2) >>> Requirement already satisfied: six in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (1.16.0) >>> Requirement already satisfied: certifi>=2017.4.17 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (2020.12.5) >>> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (1.26.4) >>> Requirement already satisfied: chardet<5,>=3.0.2 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (4.0.0) >>> Requirement already satisfied: idna<3,>=2.5 in >>> ./scipion/.scipion3/lib/python3.8/site-packages (from >>> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >>> (2.10) >>> Done (0.84 seconds) >>> Building cryolo-1.7.6 ... >>> Skipping command: wget -nv -c -O >>> /home/impmc/scipion/software/em/void.tgz.part >>> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >>> mv -v /home/impmc/scipion/software/em/void.tgz.part >>> /home/impmc/scipion/software/em/void.tgz >>> All targets exist. >>> Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 >>> All targets exist. >>> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >>> All targets exist. >>> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >>> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >>> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >>> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >>> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >>> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >>> /bin/sh: 1: evalexport >>> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >>> export _CE_M='' >>> export _CE_CONDA='' >>> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >>> >>> # Copyright (C) 2012 Anaconda, Inc >>> # SPDX-License-Identifier: BSD-3-Clause >>> >>> __add_sys_prefix_to_path() { >>> # In dev-mode CONDA_EXE is python.exe and on Windows >>> # it is in a different relative location to condabin. >>> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >>> SYSP=$(\dirname "${CONDA_EXE}") >>> else >>> SYSP=$(\dirname "${CONDA_EXE}") >>> SYSP=$(\dirname "${SYSP}") >>> fi >>> >>> if [ -n "${WINDIR+x}" ]; then >>> PATH="${SYSP}/bin:${PATH}" >>> PATH="${SYSP}/Scripts:${PATH}" >>> PATH="${SYSP}/Library/bin:${PATH}" >>> PATH="${SYSP}/Library/usr/bin:${PATH}" >>> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >>> PATH="${SYSP}:${PATH}" >>> else >>> PATH="${SYSP}/bin:${PATH}" >>> fi >>> \export PATH >>> } >>> >>> __conda_exe() ( >>> __add_sys_prefix_to_path >>> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >>> ) >>> >>> __conda_hashr() { >>> if [ -n "${ZSH_VERSION:+x}" ]; then >>> \rehash >>> elif [ -n "${POSH_VERSION:+x}" ]; then >>> : # pass >>> else >>> \hash -r >>> fi >>> } >>> >>> __conda_activate() { >>> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >>> # Handle transition from shell activated with conda <= 4.3 to a >>> subsequent activation >>> # after conda updated to >= 4.4. See issue #6173. >>> PS1="$CONDA_PS1_BACKUP" >>> \unset CONDA_PS1_BACKUP >>> fi >>> \local ask_conda >>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return >>> \eval "$ask_conda" >>> __conda_hashr >>> } >>> >>> __conda_reactivate() { >>> \local ask_conda >>> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || >>> \return >>> \eval "$ask_conda" >>> __conda_hashr >>> } >>> >>> conda() { >>> \local cmd="${1-__missing__}" >>> case "$cmd" in >>> activate|deactivate) >>> __conda_activate "$@" >>> ;; >>> install|update|upgrade|remove|uninstall) >>> __conda_exe "$@" || \return >>> __conda_reactivate >>> ;; >>> *) >>> __conda_exe "$@" >>> ;; >>> esac >>> } >>> >>> if [ -z "${CONDA_SHLVL+x}" ]; then >>> \export CONDA_SHLVL=0 >>> # In dev-mode CONDA_EXE is python.exe and on Windows >>> # it is in a different relative location to condabin. >>> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >>> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >>> else >>> PATH="$(\dirname "$(\dirname >>> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >>> fi >>> \export PATH >>> >>> # We're not allowing PS1 to be unbound. It must at least be set. >>> # However, we're not exporting it, which can cause problems when >>> starting a second shell >>> # via a first shell (i.e. starting zsh from bash). >>> if [ -z "${PS1+x}" ]; then >>> PS1= >>> fi >>> fi >>> >>> conda activate base: not found >>> Traceback (most recent call last): >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>> line 470, in <module> >>> main() >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >>> line 293, in main >>> installPluginMethods() >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >>> line 232, in installPluginMethods >>> plugin.installBin({'args': ['-j', numberProcessor]}) >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >>> line 166, in installBin >>> environment.execute() >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 748, in execute >>> self._executeTargets(targetList) >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 690, in _executeTargets >>> tgt.execute() >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 221, in execute >>> command.execute() >>> File >>> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >>> line 161, in execute >>> assert glob(t), ("target '%s' not built (after " >>> AssertionError: target >>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>> Error at main: target >>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >>> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >>> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >>> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >>> >>> ------------------------------ >>> *From: *"Grigory Sharov" <sha...@gm...> >>> *To: *"scipion-users" <sci...@li...> >>> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >>> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >>> Cryolo >>> >>> Dear Carlos, >>> given the fact that the installation has failed, could you attach all >>> output after "scipion3 installp -p scipion-em-sphire" command? >>> >>> Best regards, >>> Grigory >>> >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <+44%201223%20267228> >>> e-mail: gs...@mr... >>> >>> >>> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >>> car...@so...> wrote: >>> >>>> Dear all, >>>> >>>> I'm facing some problems using cryolo training at Scipion. >>>> I found the following error: >>>> >>>> *Protocol failed: Command ' source >>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>>> --fine_tune' returned non-zero exit status 127.* >>>> >>>> I saw some discussion about that at Scipion lists, but I'm still little >>>> lost in how to fix it. >>>> In my scipion.conf file, I inserted >>>> *CONDA_ACTIVATION_CMD = source >>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>>> or even >>>> CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>>> shell.bash hook)" >>>> (I saw these pathways in my bash.rc) >>>> >>>> Moreover, when I try to install cryolo using command line (scipion3 >>>> installp -p scipion-em-sphire), the following error apears: >>>> *AssertionError: target >>>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>>> built (after running 'source >>>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>>> cryolo_1.7.6_installed')* >>>> >>>> I am not sure if these errors are related and hinder performing cryolo >>>> in Scipion. >>>> I have conda installed in the computer and I'm able to use cryolo 1.8 >>>> outside from Scipion in the same computer (using *source activate >>>> cryolo *command). >>>> >>>> Anyone know what I'm doing wrong? >>>> Thanks in advance, >>>> Carlos. >>>> >>>> >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>>> >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos H. F. <car...@so...> - 2021-09-29 16:37:09
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Dear Grigory, The files that you requested are attached. Thanks so much again From: "Grigory Sharov" <sha...@gm...> To: "scipion-users" <sci...@li...> Sent: Wednesday, September 29, 2021 6:18:12 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hi, The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: Dear Grigory, Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this). However, I tried to run the cryolo training and I obtained the same previous error: eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune 00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982 Bellow, it is my current scipion.conf file [PYWORKFLOW] SCIPION_DOMAIN = pwem SCIPION_FONT_NAME = Helvetica SCIPION_GUI_REFRESH_IN_THREAD = False SCIPION_LOG = ~/ScipionUserData/logs/scipion.log SCIPION_LOGO = scipion_logo.gif SCIPION_LOGS = ~/ScipionUserData/logs SCIPION_NOTES_FILE = notes.txt SCIPION_NOTIFY = True SCIPION_PLUGIN_REPO_URL = [ http://scipion.i2pc.es/getplugins/ | http://scipion.i2pc.es/getplugins/ ] SCIPION_SOFTWARE = ${SCIPION_HOME}/software SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ] SCIPION_TESTS = ${SCIPION_HOME}/data/tests SCIPION_TESTS_CMD = scipion3 tests SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests SCIPION_TMP = ~/ScipionUserData/tmp SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ] SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ] SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ] SCIPION_USER_DATA = ~/ScipionUserData WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" [PLUGINS] CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 CRYOSPARC_HOME = /home/impmc/ CRYO_PROJECTS_DIR = scipion_projects CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 EMAN2SCRATCHDIR = /tmp EMAN2_HOME = %(EM_ROOT)s/eman-2.91 EM_ROOT = software/em JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 PHENIX_HOME = %(EM_ROOT)s/phenix- RELION_CUDA_LIB = /usr/local/cuda/lib64 RELION_HOME = %(EM_ROOT)s/relion-3.1.2 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp Thanks again. From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:51:06 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hello Carlos, to start, you are missing a space between eval and the rest in: CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear Grigory, Thanks for the message. The all output is bellow: Scipion v3.0.9 - Eugenius Building scipion-em-sphire ... /home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7 Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ] Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13) Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76) Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17) Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1) Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2) Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0) Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10) Done (0.84 seconds) Building cryolo-1.7.6 ... Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ] mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz All targets exist. Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 All targets exist. Skipping command: tar -xf void.tgz -C cryolo-1.7.6 All targets exist. cd /home/impmc/scipion/software/em/cryolo-1.7.6 eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' export _CE_M='' export _CE_CONDA='' export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' # Copyright (C) 2012 Anaconda, Inc # SPDX-License-Identifier: BSD-3-Clause __add_sys_prefix_to_path() { # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then SYSP=$(\dirname "${CONDA_EXE}") else SYSP=$(\dirname "${CONDA_EXE}") SYSP=$(\dirname "${SYSP}") fi if [ -n "${WINDIR+x}" ]; then PATH="${SYSP}/bin:${PATH}" PATH="${SYSP}/Scripts:${PATH}" PATH="${SYSP}/Library/bin:${PATH}" PATH="${SYSP}/Library/usr/bin:${PATH}" PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" PATH="${SYSP}:${PATH}" else PATH="${SYSP}/bin:${PATH}" fi \export PATH } __conda_exe() ( __add_sys_prefix_to_path "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" ) __conda_hashr() { if [ -n "${ZSH_VERSION:+x}" ]; then \rehash elif [ -n "${POSH_VERSION:+x}" ]; then : # pass else \hash -r fi } __conda_activate() { if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then # Handle transition from shell activated with conda <= 4.3 to a subsequent activation # after conda updated to >= 4.4. See issue #6173. PS1="$CONDA_PS1_BACKUP" \unset CONDA_PS1_BACKUP fi \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return \eval "$ask_conda" __conda_hashr } __conda_reactivate() { \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return \eval "$ask_conda" __conda_hashr } conda() { \local cmd="${1-__missing__}" case "$cmd" in activate|deactivate) __conda_activate "$@" ;; install|update|upgrade|remove|uninstall) __conda_exe "$@" || \return __conda_reactivate ;; *) __conda_exe "$@" ;; esac } if [ -z "${CONDA_SHLVL+x}" ]; then \export CONDA_SHLVL=0 # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" else PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" fi \export PATH # We're not allowing PS1 to be unbound. It must at least be set. # However, we're not exporting it, which can cause problems when starting a second shell # via a first shell (i.e. starting zsh from bash). if [ -z "${PS1+x}" ]; then PS1= fi fi conda activate base: not found Traceback (most recent call last): File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:33:09 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Carlos, given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-29 16:18:54
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Hi, The config files look ok. Could you attach run.stderr and run.stdout for the failed protocol? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > Thank you so much, fixing this space solved the problem with > cryolo_1.7.6_installing (shame on me for this). > However, I tried to run the cryolo training and I obtained the same > previous error: > > eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune > 00022: Protocol failed: Command ' eval > "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json > -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. > 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 > 02:14:42.822982 > > Bellow, it is my current scipion.conf file > [PYWORKFLOW] > SCIPION_DOMAIN = pwem > SCIPION_FONT_NAME = Helvetica > SCIPION_GUI_REFRESH_IN_THREAD = False > SCIPION_LOG = ~/ScipionUserData/logs/scipion.log > SCIPION_LOGO = scipion_logo.gif > SCIPION_LOGS = ~/ScipionUserData/logs > SCIPION_NOTES_FILE = notes.txt > SCIPION_NOTIFY = True > SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ > SCIPION_SOFTWARE = ${SCIPION_HOME}/software > SCIPION_SUPPORT_EMAIL = sc...@cn... > SCIPION_TESTS = ${SCIPION_HOME}/data/tests > SCIPION_TESTS_CMD = scipion3 tests > SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests > SCIPION_TMP = ~/ScipionUserData/tmp > SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion > SCIPION_URL_SOFTWARE = > http://scipion.cnb.csic.es/downloads/scipion/software > SCIPION_URL_TESTDATA = > http://scipion.cnb.csic.es/downloads/scipion/data/tests > SCIPION_USER_DATA = ~/ScipionUserData > WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)" > > [PLUGINS] > CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 > CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 > CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta > CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 > CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 > CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 > CRYOLO_GENERIC_DENOISED_MODEL = > %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 > CRYOLO_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 > CRYOLO_NS_GENERIC_MODEL = > %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 > CRYOSPARC_HOME = /home/impmc/ > CRYO_PROJECTS_DIR = scipion_projects > CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 > EMAN2SCRATCHDIR = /tmp > EMAN2_HOME = %(EM_ROOT)s/eman-2.91 > EM_ROOT = software/em > JANNI_GENERIC_MODEL = > %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 > MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 > MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 > MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 > MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 > PHENIX_HOME = %(EM_ROOT)s/phenix- > RELION_CUDA_LIB = /usr/local/cuda/lib64 > RELION_HOME = %(EM_ROOT)s/relion-3.1.2 > XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src > XMIPP_HOME = %(EM_ROOT)s/xmipp > > > Thanks again. > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 5:51:06 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Hello Carlos, > > to start, you are missing a space between eval and the rest in: > CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear Grigory, >> >> Thanks for the message. The all output is bellow: >> >> Scipion v3.0.9 - Eugenius >> Building scipion-em-sphire ... >> /home/impmc/scipion/.scipion3/bin/python -m pip install >> scipion-em-sphire==3.0.7 >> Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com >> Requirement already satisfied: scipion-em-sphire==3.0.7 in >> ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) >> Requirement already satisfied: scipion-em in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em-sphire==3.0.7) (3.0.13) >> Requirement already satisfied: biopython==1.76 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em->scipion-em-sphire==3.0.7) (1.76) >> Requirement already satisfied: tifffile in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) >> Requirement already satisfied: scipion-pyworkflow>=3.0.15 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-em->scipion-em-sphire==3.0.7) (3.0.17) >> Requirement already satisfied: numpy in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) >> Requirement already satisfied: mpi4py<=3.0.3 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) >> Requirement already satisfied: configparser<=5.0.2 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) >> Requirement already satisfied: psutil<=5.8.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) >> Requirement already satisfied: pillow<=8.2.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) >> Requirement already satisfied: bibtexparser<=1.2.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) >> Requirement already satisfied: requests<=2.25.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) >> Requirement already satisfied: matplotlib==3.2.2 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) >> Requirement already satisfied: tkcolorpicker<=2.1.3 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) >> Requirement already satisfied: cycler>=0.10 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (0.10.0) >> Requirement already satisfied: python-dateutil>=2.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2.8.1) >> Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 >> in ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2.4.7) >> Requirement already satisfied: kiwisolver>=1.0.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (1.3.1) >> Requirement already satisfied: future>=0.16.0 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (0.18.2) >> Requirement already satisfied: six in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (1.16.0) >> Requirement already satisfied: certifi>=2017.4.17 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2020.12.5) >> Requirement already satisfied: urllib3<1.27,>=1.21.1 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (1.26.4) >> Requirement already satisfied: chardet<5,>=3.0.2 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (4.0.0) >> Requirement already satisfied: idna<3,>=2.5 in >> ./scipion/.scipion3/lib/python3.8/site-packages (from >> requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) >> (2.10) >> Done (0.84 seconds) >> Building cryolo-1.7.6 ... >> Skipping command: wget -nv -c -O >> /home/impmc/scipion/software/em/void.tgz.part >> http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz >> mv -v /home/impmc/scipion/software/em/void.tgz.part >> /home/impmc/scipion/software/em/void.tgz >> All targets exist. >> Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 >> All targets exist. >> Skipping command: tar -xf void.tgz -C cryolo-1.7.6 >> All targets exist. >> cd /home/impmc/scipion/software/em/cryolo-1.7.6 >> eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> >> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda >> python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 >> intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install >> cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed >> /bin/sh: 1: evalexport >> CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' >> export _CE_M='' >> export _CE_CONDA='' >> export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' >> >> # Copyright (C) 2012 Anaconda, Inc >> # SPDX-License-Identifier: BSD-3-Clause >> >> __add_sys_prefix_to_path() { >> # In dev-mode CONDA_EXE is python.exe and on Windows >> # it is in a different relative location to condabin. >> if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then >> SYSP=$(\dirname "${CONDA_EXE}") >> else >> SYSP=$(\dirname "${CONDA_EXE}") >> SYSP=$(\dirname "${SYSP}") >> fi >> >> if [ -n "${WINDIR+x}" ]; then >> PATH="${SYSP}/bin:${PATH}" >> PATH="${SYSP}/Scripts:${PATH}" >> PATH="${SYSP}/Library/bin:${PATH}" >> PATH="${SYSP}/Library/usr/bin:${PATH}" >> PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" >> PATH="${SYSP}:${PATH}" >> else >> PATH="${SYSP}/bin:${PATH}" >> fi >> \export PATH >> } >> >> __conda_exe() ( >> __add_sys_prefix_to_path >> "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" >> ) >> >> __conda_hashr() { >> if [ -n "${ZSH_VERSION:+x}" ]; then >> \rehash >> elif [ -n "${POSH_VERSION:+x}" ]; then >> : # pass >> else >> \hash -r >> fi >> } >> >> __conda_activate() { >> if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then >> # Handle transition from shell activated with conda <= 4.3 to a >> subsequent activation >> # after conda updated to >= 4.4. See issue #6173. >> PS1="$CONDA_PS1_BACKUP" >> \unset CONDA_PS1_BACKUP >> fi >> \local ask_conda >> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return >> \eval "$ask_conda" >> __conda_hashr >> } >> >> __conda_reactivate() { >> \local ask_conda >> ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || >> \return >> \eval "$ask_conda" >> __conda_hashr >> } >> >> conda() { >> \local cmd="${1-__missing__}" >> case "$cmd" in >> activate|deactivate) >> __conda_activate "$@" >> ;; >> install|update|upgrade|remove|uninstall) >> __conda_exe "$@" || \return >> __conda_reactivate >> ;; >> *) >> __conda_exe "$@" >> ;; >> esac >> } >> >> if [ -z "${CONDA_SHLVL+x}" ]; then >> \export CONDA_SHLVL=0 >> # In dev-mode CONDA_EXE is python.exe and on Windows >> # it is in a different relative location to condabin. >> if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then >> PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" >> else >> PATH="$(\dirname "$(\dirname >> "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" >> fi >> \export PATH >> >> # We're not allowing PS1 to be unbound. It must at least be set. >> # However, we're not exporting it, which can cause problems when >> starting a second shell >> # via a first shell (i.e. starting zsh from bash). >> if [ -z "${PS1+x}" ]; then >> PS1= >> fi >> fi >> >> conda activate base: not found >> Traceback (most recent call last): >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >> line 470, in <module> >> main() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", >> line 293, in main >> installPluginMethods() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", >> line 232, in installPluginMethods >> plugin.installBin({'args': ['-j', numberProcessor]}) >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", >> line 166, in installBin >> environment.execute() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 748, in execute >> self._executeTargets(targetList) >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 690, in _executeTargets >> tgt.execute() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 221, in execute >> command.execute() >> File >> "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", >> line 161, in execute >> assert glob(t), ("target '%s' not built (after " >> AssertionError: target >> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >> Error at main: target >> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >> built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >> shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c >> conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython >> wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip >> install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') >> >> ------------------------------ >> *From: *"Grigory Sharov" <sha...@gm...> >> *To: *"scipion-users" <sci...@li...> >> *Sent: *Wednesday, September 29, 2021 5:33:09 PM >> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using >> Cryolo >> >> Dear Carlos, >> given the fact that the installation has failed, could you attach all >> output after "scipion3 installp -p scipion-em-sphire" command? >> >> Best regards, >> Grigory >> >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <+44%201223%20267228> >> e-mail: gs...@mr... >> >> >> On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < >> car...@so...> wrote: >> >>> Dear all, >>> >>> I'm facing some problems using cryolo training at Scipion. >>> I found the following error: >>> >>> *Protocol failed: Command ' source >>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >>> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >>> --fine_tune' returned non-zero exit status 127.* >>> >>> I saw some discussion about that at Scipion lists, but I'm still little >>> lost in how to fix it. >>> In my scipion.conf file, I inserted >>> *CONDA_ACTIVATION_CMD = source >>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >>> or even >>> CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >>> shell.bash hook)" >>> (I saw these pathways in my bash.rc) >>> >>> Moreover, when I try to install cryolo using command line (scipion3 >>> installp -p scipion-em-sphire), the following error apears: >>> *AssertionError: target >>> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >>> built (after running 'source >>> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >>> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >>> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >>> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >>> cryolo_1.7.6_installed')* >>> >>> I am not sure if these errors are related and hinder performing cryolo >>> in Scipion. >>> I have conda installed in the computer and I'm able to use cryolo 1.8 >>> outside from Scipion in the same computer (using *source activate >>> cryolo *command). >>> >>> Anyone know what I'm doing wrong? >>> Thanks in advance, >>> Carlos. >>> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... >>> https://lists.sourceforge.net/lists/listinfo/scipion-users >>> >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Carlos H. F. <car...@so...> - 2021-09-29 16:14:50
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Dear Grigory, Thank you so much, fixing this space solved the problem with cryolo_1.7.6_installing (shame on me for this). However, I tried to run the cryolo training and I obtained the same previous error: eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune 00022: Protocol failed: Command ' eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 1 -nc 4 -e 10 --fine_tune' returned non-zero exit status 1. 00023: FAILED: cryoloModelingStep, step 3, time 2021-09-30 02:14:42.822982 Bellow, it is my current scipion.conf file [PYWORKFLOW] SCIPION_DOMAIN = pwem SCIPION_FONT_NAME = Helvetica SCIPION_GUI_REFRESH_IN_THREAD = False SCIPION_LOG = ~/ScipionUserData/logs/scipion.log SCIPION_LOGO = scipion_logo.gif SCIPION_LOGS = ~/ScipionUserData/logs SCIPION_NOTES_FILE = notes.txt SCIPION_NOTIFY = True SCIPION_PLUGIN_REPO_URL = http://scipion.i2pc.es/getplugins/ SCIPION_SOFTWARE = ${SCIPION_HOME}/software SCIPION_SUPPORT_EMAIL = sc...@cn... SCIPION_TESTS = ${SCIPION_HOME}/data/tests SCIPION_TESTS_CMD = scipion3 tests SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests SCIPION_TMP = ~/ScipionUserData/tmp SCIPION_URL = http://scipion.cnb.csic.es/downloads/scipion SCIPION_URL_SOFTWARE = http://scipion.cnb.csic.es/downloads/scipion/software SCIPION_URL_TESTDATA = http://scipion.cnb.csic.es/downloads/scipion/data/tests SCIPION_USER_DATA = ~/ScipionUserData WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)" [PLUGINS] CCP4_HOME = %(EM_ROOT)s/ccp4-7.0.056 CHIMERA_HOME = %(EM_ROOT)s/chimerax-1.2.5 CISTEM_HOME = %(EM_ROOT)s/cistem-1.0.0-beta CRYOLO_CUDA_LIB = /usr/local/cuda/lib64 CRYOLO_ENV_ACTIVATION = conda activate cryolo-1.7.6 CRYOLO_ENV_ACTIVATION_CPU = conda activate cryolo-1.7.6 CRYOLO_GENERIC_DENOISED_MODEL = %(EM_ROOT)s/cryolo_model-202005_nn_N63_c17/gmodel_phosnet_202005_nn_N63_c17.h5 CRYOLO_GENERIC_MODEL = %(EM_ROOT)s/cryolo_model-202005_N63_c17/gmodel_phosnet_202005_N63_c17.h5 CRYOLO_NS_GENERIC_MODEL = %(EM_ROOT)s/cryolo_negstain_model-20190226/gmodel_phosnet_negstain_20190226.h5 CRYOSPARC_HOME = /home/impmc/ CRYO_PROJECTS_DIR = scipion_projects CTFFIND4_HOME = %(EM_ROOT)s/ctffind4-4.1.14 EMAN2SCRATCHDIR = /tmp EMAN2_HOME = %(EM_ROOT)s/eman-2.91 EM_ROOT = software/em JANNI_GENERIC_MODEL = %(EM_ROOT)s/janni_model-20190703/gmodel_janni_20190703.h5 MAXIT_HOME = %(EM_ROOT)s/maxit-10.1 MOTIONCOR2_BIN = MotionCor2_1.4.0_Cuda101 MOTIONCOR2_CUDA_LIB = /usr/local/cuda/lib64 MOTIONCOR2_HOME = %(EM_ROOT)s/motioncor2-1.4.0 PHENIX_HOME = %(EM_ROOT)s/phenix- RELION_CUDA_LIB = /usr/local/cuda/lib64 RELION_HOME = %(EM_ROOT)s/relion-3.1.2 XMIPP2_HOME = %(EM_ROOT)s/Xmipp-2.4-src XMIPP_HOME = %(EM_ROOT)s/xmipp Thanks again. From: "Grigory Sharov" <sha...@gm...> To: "scipion-users" <sci...@li...> Sent: Wednesday, September 29, 2021 5:51:06 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Hello Carlos, to start, you are missing a space between eval and the rest in: CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2- sphire-sparx/bin/conda shell.bash hook)" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: Dear Grigory, Thanks for the message. The all output is bellow: Scipion v3.0.9 - Eugenius Building scipion-em-sphire ... /home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7 Looking in indexes: [ https://pypi.org/simple | https://pypi.org/simple ] , [ https://pypi.ngc.nvidia.com/ | https://pypi.ngc.nvidia.com ] Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13) Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76) Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17) Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1) Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2) Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0) Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10) Done (0.84 seconds) Building cryolo-1.7.6 ... Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part [ http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz | http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz ] mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz All targets exist. Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 All targets exist. Skipping command: tar -xf void.tgz -C cryolo-1.7.6 All targets exist. cd /home/impmc/scipion/software/em/cryolo-1.7.6 eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' export _CE_M='' export _CE_CONDA='' export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' # Copyright (C) 2012 Anaconda, Inc # SPDX-License-Identifier: BSD-3-Clause __add_sys_prefix_to_path() { # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then SYSP=$(\dirname "${CONDA_EXE}") else SYSP=$(\dirname "${CONDA_EXE}") SYSP=$(\dirname "${SYSP}") fi if [ -n "${WINDIR+x}" ]; then PATH="${SYSP}/bin:${PATH}" PATH="${SYSP}/Scripts:${PATH}" PATH="${SYSP}/Library/bin:${PATH}" PATH="${SYSP}/Library/usr/bin:${PATH}" PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" PATH="${SYSP}:${PATH}" else PATH="${SYSP}/bin:${PATH}" fi \export PATH } __conda_exe() ( __add_sys_prefix_to_path "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" ) __conda_hashr() { if [ -n "${ZSH_VERSION:+x}" ]; then \rehash elif [ -n "${POSH_VERSION:+x}" ]; then : # pass else \hash -r fi } __conda_activate() { if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then # Handle transition from shell activated with conda <= 4.3 to a subsequent activation # after conda updated to >= 4.4. See issue #6173. PS1="$CONDA_PS1_BACKUP" \unset CONDA_PS1_BACKUP fi \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return \eval "$ask_conda" __conda_hashr } __conda_reactivate() { \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return \eval "$ask_conda" __conda_hashr } conda() { \local cmd="${1-__missing__}" case "$cmd" in activate|deactivate) __conda_activate "$@" ;; install|update|upgrade|remove|uninstall) __conda_exe "$@" || \return __conda_reactivate ;; *) __conda_exe "$@" ;; esac } if [ -z "${CONDA_SHLVL+x}" ]; then \export CONDA_SHLVL=0 # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" else PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" fi \export PATH # We're not allowing PS1 to be unbound. It must at least be set. # However, we're not exporting it, which can cause problems when starting a second shell # via a first shell (i.e. starting zsh from bash). if [ -z "${PS1+x}" ]; then PS1= fi fi conda activate base: not found Traceback (most recent call last): File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > To: "scipion-users" < [ mailto:sci...@li... | sci...@li... ] > Sent: Wednesday, September 29, 2021 5:33:09 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Carlos, given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: BQ_BEGIN Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] BQ_END _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-29 15:52:41
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Hello Carlos, to start, you are missing a space between eval and the rest in: CONDA_ACTIVATION_CMD = eval "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear Grigory, > > Thanks for the message. The all output is bellow: > > Scipion v3.0.9 - Eugenius > Building scipion-em-sphire ... > /home/impmc/scipion/.scipion3/bin/python -m pip install > scipion-em-sphire==3.0.7 > Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com > Requirement already satisfied: scipion-em-sphire==3.0.7 in > ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) > Requirement already satisfied: scipion-em in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em-sphire==3.0.7) (3.0.13) > Requirement already satisfied: biopython==1.76 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (1.76) > Requirement already satisfied: tifffile in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) > Requirement already satisfied: scipion-pyworkflow>=3.0.15 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-em->scipion-em-sphire==3.0.7) (3.0.17) > Requirement already satisfied: numpy in > ./scipion/.scipion3/lib/python3.8/site-packages (from > biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) > Requirement already satisfied: mpi4py<=3.0.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) > Requirement already satisfied: configparser<=5.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) > Requirement already satisfied: psutil<=5.8.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) > Requirement already satisfied: pillow<=8.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) > Requirement already satisfied: bibtexparser<=1.2.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) > Requirement already satisfied: requests<=2.25.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) > Requirement already satisfied: matplotlib==3.2.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) > Requirement already satisfied: tkcolorpicker<=2.1.3 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) > Requirement already satisfied: cycler>=0.10 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.10.0) > Requirement already satisfied: python-dateutil>=2.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.8.1) > Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.4.7) > Requirement already satisfied: kiwisolver>=1.0.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.3.1) > Requirement already satisfied: future>=0.16.0 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (0.18.2) > Requirement already satisfied: six in > ./scipion/.scipion3/lib/python3.8/site-packages (from > cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.16.0) > Requirement already satisfied: certifi>=2017.4.17 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2020.12.5) > Requirement already satisfied: urllib3<1.27,>=1.21.1 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (1.26.4) > Requirement already satisfied: chardet<5,>=3.0.2 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (4.0.0) > Requirement already satisfied: idna<3,>=2.5 in > ./scipion/.scipion3/lib/python3.8/site-packages (from > requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) > (2.10) > Done (0.84 seconds) > Building cryolo-1.7.6 ... > Skipping command: wget -nv -c -O > /home/impmc/scipion/software/em/void.tgz.part > http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz > mv -v /home/impmc/scipion/software/em/void.tgz.part > /home/impmc/scipion/software/em/void.tgz > All targets exist. > Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 > All targets exist. > Skipping command: tar -xf void.tgz -C cryolo-1.7.6 > All targets exist. > cd /home/impmc/scipion/software/em/cryolo-1.7.6 > eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> > /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda > python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 > intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install > cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed > /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' > export _CE_M='' > export _CE_CONDA='' > export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' > > # Copyright (C) 2012 Anaconda, Inc > # SPDX-License-Identifier: BSD-3-Clause > > __add_sys_prefix_to_path() { > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then > SYSP=$(\dirname "${CONDA_EXE}") > else > SYSP=$(\dirname "${CONDA_EXE}") > SYSP=$(\dirname "${SYSP}") > fi > > if [ -n "${WINDIR+x}" ]; then > PATH="${SYSP}/bin:${PATH}" > PATH="${SYSP}/Scripts:${PATH}" > PATH="${SYSP}/Library/bin:${PATH}" > PATH="${SYSP}/Library/usr/bin:${PATH}" > PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" > PATH="${SYSP}:${PATH}" > else > PATH="${SYSP}/bin:${PATH}" > fi > \export PATH > } > > __conda_exe() ( > __add_sys_prefix_to_path > "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" > ) > > __conda_hashr() { > if [ -n "${ZSH_VERSION:+x}" ]; then > \rehash > elif [ -n "${POSH_VERSION:+x}" ]; then > : # pass > else > \hash -r > fi > } > > __conda_activate() { > if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then > # Handle transition from shell activated with conda <= 4.3 to a > subsequent activation > # after conda updated to >= 4.4. See issue #6173. > PS1="$CONDA_PS1_BACKUP" > \unset CONDA_PS1_BACKUP > fi > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return > \eval "$ask_conda" > __conda_hashr > } > > __conda_reactivate() { > \local ask_conda > ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || > \return > \eval "$ask_conda" > __conda_hashr > } > > conda() { > \local cmd="${1-__missing__}" > case "$cmd" in > activate|deactivate) > __conda_activate "$@" > ;; > install|update|upgrade|remove|uninstall) > __conda_exe "$@" || \return > __conda_reactivate > ;; > *) > __conda_exe "$@" > ;; > esac > } > > if [ -z "${CONDA_SHLVL+x}" ]; then > \export CONDA_SHLVL=0 > # In dev-mode CONDA_EXE is python.exe and on Windows > # it is in a different relative location to condabin. > if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then > PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" > else > PATH="$(\dirname "$(\dirname > "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" > fi > \export PATH > > # We're not allowing PS1 to be unbound. It must at least be set. > # However, we're not exporting it, which can cause problems when > starting a second shell > # via a first shell (i.e. starting zsh from bash). > if [ -z "${PS1+x}" ]; then > PS1= > fi > fi > > conda activate base: not found > Traceback (most recent call last): > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 470, in <module> > main() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", > line 293, in main > installPluginMethods() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", > line 232, in installPluginMethods > plugin.installBin({'args': ['-j', numberProcessor]}) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", > line 166, in installBin > environment.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 748, in execute > self._executeTargets(targetList) > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 690, in _executeTargets > tgt.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 221, in execute > command.execute() > File > "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", > line 161, in execute > assert glob(t), ("target '%s' not built (after " > AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > Error at main: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c > conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython > wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip > install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') > > ------------------------------ > *From: *"Grigory Sharov" <sha...@gm...> > *To: *"scipion-users" <sci...@li...> > *Sent: *Wednesday, September 29, 2021 5:33:09 PM > *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using > Cryolo > > Dear Carlos, > given the fact that the installation has failed, could you attach all > output after "scipion3 installp -p scipion-em-sphire" command? > > Best regards, > Grigory > > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <+44%201223%20267228> > e-mail: gs...@mr... > > > On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < > car...@so...> wrote: > >> Dear all, >> >> I'm facing some problems using cryolo training at Scipion. >> I found the following error: >> >> *Protocol failed: Command ' source >> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate >> cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 >> --fine_tune' returned non-zero exit status 127.* >> >> I saw some discussion about that at Scipion lists, but I'm still little >> lost in how to fix it. >> In my scipion.conf file, I inserted >> *CONDA_ACTIVATION_CMD = source >> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * >> or even >> CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda >> shell.bash hook)" >> (I saw these pathways in my bash.rc) >> >> Moreover, when I try to install cryolo using command line (scipion3 >> installp -p scipion-em-sphire), the following error apears: >> *AssertionError: target >> '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not >> built (after running 'source >> /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n >> cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 >> numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate >> cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch >> cryolo_1.7.6_installed')* >> >> I am not sure if these errors are related and hinder performing cryolo in >> Scipion. >> I have conda installed in the computer and I'm able to use cryolo 1.8 >> outside from Scipion in the same computer (using *source activate cryolo >> *command). >> >> Anyone know what I'm doing wrong? >> Thanks in advance, >> Carlos. >> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... >> https://lists.sourceforge.net/lists/listinfo/scipion-users >> > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
|
From: Carlos H. F. <car...@so...> - 2021-09-29 15:47:01
|
Dear Grigory, Thanks for the message. The all output is bellow: Scipion v3.0.9 - Eugenius Building scipion-em-sphire ... /home/impmc/scipion/.scipion3/bin/python -m pip install scipion-em-sphire==3.0.7 Looking in indexes: https://pypi.org/simple, https://pypi.ngc.nvidia.com Requirement already satisfied: scipion-em-sphire==3.0.7 in ./scipion/.scipion3/lib/python3.8/site-packages (3.0.7) Requirement already satisfied: scipion-em in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em-sphire==3.0.7) (3.0.13) Requirement already satisfied: biopython==1.76 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (1.76) Requirement already satisfied: tifffile in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (2021.4.8) Requirement already satisfied: scipion-pyworkflow>=3.0.15 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-em->scipion-em-sphire==3.0.7) (3.0.17) Requirement already satisfied: numpy in ./scipion/.scipion3/lib/python3.8/site-packages (from biopython==1.76->scipion-em->scipion-em-sphire==3.0.7) (1.18.4) Requirement already satisfied: mpi4py<=3.0.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.0.3) Requirement already satisfied: configparser<=5.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.0.0) Requirement already satisfied: psutil<=5.8.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (5.7.0) Requirement already satisfied: pillow<=8.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (7.1.2) Requirement already satisfied: bibtexparser<=1.2.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.2.0) Requirement already satisfied: requests<=2.25.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.25.1) Requirement already satisfied: matplotlib==3.2.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (3.2.2) Requirement already satisfied: tkcolorpicker<=2.1.3 in ./scipion/.scipion3/lib/python3.8/site-packages (from scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.1.3) Requirement already satisfied: cycler>=0.10 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.10.0) Requirement already satisfied: python-dateutil>=2.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.8.1) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.4.7) Requirement already satisfied: kiwisolver>=1.0.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.3.1) Requirement already satisfied: future>=0.16.0 in ./scipion/.scipion3/lib/python3.8/site-packages (from bibtexparser<=1.2.0->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (0.18.2) Requirement already satisfied: six in ./scipion/.scipion3/lib/python3.8/site-packages (from cycler>=0.10->matplotlib==3.2.2->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.16.0) Requirement already satisfied: certifi>=2017.4.17 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2020.12.5) Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (1.26.4) Requirement already satisfied: chardet<5,>=3.0.2 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (4.0.0) Requirement already satisfied: idna<3,>=2.5 in ./scipion/.scipion3/lib/python3.8/site-packages (from requests<=2.25.1->scipion-pyworkflow>=3.0.15->scipion-em->scipion-em-sphire==3.0.7) (2.10) Done (0.84 seconds) Building cryolo-1.7.6 ... Skipping command: wget -nv -c -O /home/impmc/scipion/software/em/void.tgz.part http://scipion.cnb.csic.es/downloads/scipion/software/em/void.tgz mv -v /home/impmc/scipion/software/em/void.tgz.part /home/impmc/scipion/software/em/void.tgz All targets exist. Skipping command: mkdir /home/impmc/scipion/software/em/cryolo-1.7.6 All targets exist. Skipping command: tar -xf void.tgz -C cryolo-1.7.6 All targets exist. cd /home/impmc/scipion/software/em/cryolo-1.7.6 eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed /bin/sh: 1: evalexport CONDA_EXE='/home/impmc/eman2-sphire-sparx/bin/conda' export _CE_M='' export _CE_CONDA='' export CONDA_PYTHON_EXE='/home/impmc/eman2-sphire-sparx/bin/python' # Copyright (C) 2012 Anaconda, Inc # SPDX-License-Identifier: BSD-3-Clause __add_sys_prefix_to_path() { # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA}" ] && [ -n "${WINDIR+x}" ]; then SYSP=$(\dirname "${CONDA_EXE}") else SYSP=$(\dirname "${CONDA_EXE}") SYSP=$(\dirname "${SYSP}") fi if [ -n "${WINDIR+x}" ]; then PATH="${SYSP}/bin:${PATH}" PATH="${SYSP}/Scripts:${PATH}" PATH="${SYSP}/Library/bin:${PATH}" PATH="${SYSP}/Library/usr/bin:${PATH}" PATH="${SYSP}/Library/mingw-w64/bin:${PATH}" PATH="${SYSP}:${PATH}" else PATH="${SYSP}/bin:${PATH}" fi \export PATH } __conda_exe() ( __add_sys_prefix_to_path "$CONDA_EXE" $_CE_M $_CE_CONDA "$@" ) __conda_hashr() { if [ -n "${ZSH_VERSION:+x}" ]; then \rehash elif [ -n "${POSH_VERSION:+x}" ]; then : # pass else \hash -r fi } __conda_activate() { if [ -n "${CONDA_PS1_BACKUP:+x}" ]; then # Handle transition from shell activated with conda <= 4.3 to a subsequent activation # after conda updated to >= 4.4. See issue #6173. PS1="$CONDA_PS1_BACKUP" \unset CONDA_PS1_BACKUP fi \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix "$@")" || \return \eval "$ask_conda" __conda_hashr } __conda_reactivate() { \local ask_conda ask_conda="$(PS1="${PS1:-}" __conda_exe shell.posix reactivate)" || \return \eval "$ask_conda" __conda_hashr } conda() { \local cmd="${1-__missing__}" case "$cmd" in activate|deactivate) __conda_activate "$@" ;; install|update|upgrade|remove|uninstall) __conda_exe "$@" || \return __conda_reactivate ;; *) __conda_exe "$@" ;; esac } if [ -z "${CONDA_SHLVL+x}" ]; then \export CONDA_SHLVL=0 # In dev-mode CONDA_EXE is python.exe and on Windows # it is in a different relative location to condabin. if [ -n "${_CE_CONDA:+x}" ] && [ -n "${WINDIR+x}" ]; then PATH="$(\dirname "$CONDA_EXE")/condabin${PATH:+":${PATH}"}" else PATH="$(\dirname "$(\dirname "$CONDA_EXE")")/condabin${PATH:+":${PATH}"}" fi \export PATH # We're not allowing PS1 to be unbound. It must at least be set. # However, we're not exporting it, which can cause problems when starting a second shell # via a first shell (i.e. starting zsh from bash). if [ -z "${PS1+x}" ]; then PS1= fi fi conda activate base: not found Traceback (most recent call last): File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 470, in <module> main() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/__main__.py", line 293, in main installPluginMethods() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/install_plugin.py", line 232, in installPluginMethods plugin.installBin({'args': ['-j', numberProcessor]}) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/plugin_funcs.py", line 166, in installBin environment.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 748, in execute self._executeTargets(targetList) File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 690, in _executeTargets tgt.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 221, in execute command.execute() File "/home/impmc/scipion/.scipion3/lib/python3.8/site-packages/scipion/install/funcs.py", line 161, in execute assert glob(t), ("target '%s' not built (after " AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') Error at main: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2> /dev/null)"&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') From: "Grigory Sharov" <sha...@gm...> To: "scipion-users" <sci...@li...> Sent: Wednesday, September 29, 2021 5:33:09 PM Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo Dear Carlos, given the fact that the installation has failed, could you attach all output after " scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] e-mail: [ mailto:gs...@mr... | gs...@mr... ] On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. _______________________________________________ scipion-users mailing list [ mailto:sci...@li... | sci...@li... ] [ https://lists.sourceforge.net/lists/listinfo/scipion-users | https://lists.sourceforge.net/lists/listinfo/scipion-users ] _______________________________________________ scipion-users mailing list sci...@li... https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Grigory S. <sha...@gm...> - 2021-09-29 15:34:26
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Dear Carlos, given the fact that the installation has failed, could you attach all output after "scipion3 installp -p scipion-em-sphire" command? Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 <+44%201223%20267228> e-mail: gs...@mr... On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < car...@so...> wrote: > Dear all, > > I'm facing some problems using cryolo training at Scipion. > I found the following error: > > *Protocol failed: Command ' source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate > cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 > --fine_tune' returned non-zero exit status 127.* > > I saw some discussion about that at Scipion lists, but I'm still little > lost in how to fix it. > In my scipion.conf file, I inserted > *CONDA_ACTIVATION_CMD = source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh * > or even > CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda > shell.bash hook)" > (I saw these pathways in my bash.rc) > > Moreover, when I try to install cryolo using command line (scipion3 > installp -p scipion-em-sphire), the following error apears: > *AssertionError: target > '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not > built (after running 'source > /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n > cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 > numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate > cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch > cryolo_1.7.6_installed')* > > I am not sure if these errors are related and hinder performing cryolo in > Scipion. > I have conda installed in the computer and I'm able to use cryolo 1.8 > outside from Scipion in the same computer (using *source activate cryolo * > command). > > Anyone know what I'm doing wrong? > Thanks in advance, > Carlos. > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
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From: Grigory S. <sha...@gm...> - 2021-09-29 15:29:44
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Dear Maria, could you please 1) post here the output of "scipion3 config -p relion" 2) attach run.stdout and run.stderr files from the failed protocol Thank you. Best regards, Grigory -------------------------------------------------------------------------------- Grigory Sharov, Ph.D. MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. tel. +44 (0) 1223 267228 e-mail: gs...@mr... On Wed, Sep 29, 2021 at 4:08 PM Anastasina, Maria < mar...@he...> wrote: > > Hello, > > All my recent Relion 3D classification jobs the I run in Scipion fail at CreateOutput step with the error message "Protocol failed: 'Class3D' object has no attribute ‘_rlnClassDistribution’”. > > Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used to finish successfully. I’m not aware of any changes or updates that have been done at our HPC server or Scipion installation (we use Scipion 3.0.8). > > Do you know what could be the reason for this error? > > Best regards, > Maria > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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From: Anastasina, M. <mar...@he...> - 2021-09-29 15:07:55
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Hello, All my recent Relion 3D classification jobs the I run in Scipion fail at CreateOutput step with the error message "Protocol failed: 'Class3D' object has no attribute ‘_rlnClassDistribution’”. Jobs that I ran earlier (e.g. 10 days ago) in identical conditions used to finish successfully. I’m not aware of any changes or updates that have been done at our HPC server or Scipion installation (we use Scipion 3.0.8). Do you know what could be the reason for this error? Best regards, Maria |
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From: Carlos H. F. <car...@so...> - 2021-09-29 15:02:50
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Dear all, I'm facing some problems using cryolo training at Scipion. I found the following error: Protocol failed: Command ' source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&& conda activate cryolo-1.7.6 && cryolo_train.py -c config.json -w 5 -g 0 -nc 4 -e 10 --fine_tune' returned non-zero exit status 127. I saw some discussion about that at Scipion lists, but I'm still little lost in how to fix it. In my scipion.conf file, I inserted CONDA_ACTIVATION_CMD = source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh or even CONDA_ACTIVATION_CMD = eval"$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook)" (I saw these pathways in my bash.rc) Moreover, when I try to install cryolo using command line (scipion3 installp -p scipion-em-sphire), the following error apears: AssertionError: target '/home/impmc/scipion/software/em/cryolo-1.7.6/cryolo_1.7.6_installed' not built (after running 'source /home/impmc/eman2-sphire-sparx/etc/profile.d/conda.sh&&conda create -y -n cryolo-1.7.6 -c conda-forge -c anaconda python=3.6 pyqt=5 cudnn=7.1.2 numpy==1.14.5 cython wxPython==4.0.4 intel-openmp==2019.4 &&conda activate cryolo-1.7.6 &&pip install cryolo[gpu]==1.7.6 &&touch cryolo_1.7.6_installed') I am not sure if these errors are related and hinder performing cryolo in Scipion. I have conda installed in the computer and I'm able to use cryolo 1.8 outside from Scipion in the same computer (using source activate cryolo command). Anyone know what I'm doing wrong? Thanks in advance, Carlos. |
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From: Pablo C. <pc...@cn...> - 2021-09-27 15:29:51
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I haven't seen much use of them. In theory, you may denoise mics to to a "better picking" in case picking is bad. And then extract the particles on the non denoised mics. On 27/9/21 16:54, Dmitry Semchonok wrote: > Dear colleagues, > > Small question about demonising protocol — what is your practice to use it in SPA? > > > Thank you > > Sincerely, > Dmitry > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
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From: Dmitry S. <Sem...@gm...> - 2021-09-27 14:54:36
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Dear colleagues, Small question about demonising protocol — what is your practice to use it in SPA? Thank you Sincerely, Dmitry |
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From: Dmitry S. <Sem...@gm...> - 2021-09-27 12:04:07
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Ah, ok, undestand. Thank you! Sincerely, Dmitry > On 27. Sep 2021, at 14:02, Grigory Sharov <sha...@gm...> wrote: > > I don't understand what you are trying to do :) > > The plugin v4.0b2 can work with both 3.1.2 and 4.0 Relion binaries. The 4.0 binaries are not provided by Scipion, you have to install them yourself. > > Best regards, > Grigory > > -------------------------------------------------------------------------------- > Grigory Sharov, Ph.D. > > MRC Laboratory of Molecular Biology, > Francis Crick Avenue, > Cambridge Biomedical Campus, > Cambridge CB2 0QH, UK. > tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> > e-mail: gs...@mr... <mailto:gs...@mr...> > > > On Mon, Sep 27, 2021 at 12:58 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: > Yes, it exists. > > I installed relion 3.1.2 via the plugin and currently it runs fine. > > > But there is still a riddle - how to run the relion 4.0b2? > > Sincerely, > Dmitry > > >> On 27. Sep 2021, at 13:53, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >> >> Thank you. You don't have to update as the new plugin should work with relion 3. >> >> Does /home/user/Data/Software/scipion3/software/em/relion-3.1.2 exist? >> >> Best regards, >> Grigory >> >> -------------------------------------------------------------------------------- >> Grigory Sharov, Ph.D. >> >> MRC Laboratory of Molecular Biology, >> Francis Crick Avenue, >> Cambridge Biomedical Campus, >> Cambridge CB2 0QH, UK. >> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >> e-mail: gs...@mr... <mailto:gs...@mr...> >> >> >> On Mon, Sep 27, 2021 at 12:51 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >> Dear Grigory, >> >> [user@dataanalysisserver1 ~]$ scipion3 config -p relion >> Scipion v3.0.9 - Eugenius >> Variables defined by plugin 'relion': >> >> RELION_HOME = /home/user/Data/Software/scipion3/software/em/relion-3.1.2 >> RELION_CUDA_LIB = /usr/local/cuda/lib64 >> RELION_PYTHON = None >> >> These variables can be added/edited in '/home/user/Data/Software/scipion3/config/scipion.conf’ >> >> >> >> >> So it seems to be 3.1.2. >> >> Shall I update for the 4.0 via the plugin command? >> >> Sincerely, >> Dmitry >> >> >> >> >> >>> On 27. Sep 2021, at 13:47, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >>> >>> You can see the version via scipion config -p relion >>> >>> Best regards, >>> Grigory >>> >>> -------------------------------------------------------------------------------- >>> Grigory Sharov, Ph.D. >>> >>> MRC Laboratory of Molecular Biology, >>> Francis Crick Avenue, >>> Cambridge Biomedical Campus, >>> Cambridge CB2 0QH, UK. >>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >>> e-mail: gs...@mr... <mailto:gs...@mr...> >>> >>> >>> On Mon, Sep 27, 2021 at 12:44 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>> Dear Grigory, >>> >>> Sorry, but how to verify the version? >>> >>> I the plugin I see scipion-em-relion >>> Relion-3.1.3 >>> >>> >>> Shall I also update for relion-4.0? >>> >>> Sincerely, >>> >>> Dmitry >>> >>> >>> >>>> On 27. Sep 2021, at 13:40, Grigory Sharov <sha...@gm... <mailto:sha...@gm...>> wrote: >>>> >>>> Hi Dmitry, >>>> >>>> you are looking at a wrong tab, check run.stderr. Also, are you running relion 3.1? >>>> >>>> Best regards, >>>> Grigory >>>> >>>> -------------------------------------------------------------------------------- >>>> Grigory Sharov, Ph.D. >>>> >>>> MRC Laboratory of Molecular Biology, >>>> Francis Crick Avenue, >>>> Cambridge Biomedical Campus, >>>> Cambridge CB2 0QH, UK. >>>> tel. +44 (0) 1223 267228 <tel:+44%201223%20267228> >>>> e-mail: gs...@mr... <mailto:gs...@mr...> >>>> >>>> >>>> On Mon, Sep 27, 2021 at 12:18 PM Dmitry Semchonok <Sem...@gm... <mailto:Sem...@gm...>> wrote: >>>> Dear Grigory & colleagues, >>>> >>>> Error running updated relion plugin. >>>> >>>> >>>> Any ideas? >>>> >>>> Thank you >>>> >>>> Sincerely, >>>> Dmitry >>>> >>>> >>>> >>>> >>>> File 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't existFile 'Runs/004970_ProtRelionClassify2D/logs/run.stdout' doesn't exist00001: Logging configured. STDOUT --> Runs/004970_ProtRelionClassify2D/logs/run.stdout , STDERR --> Runs/004970_ProtRelionClassify2D/logs/run.stderr >>>> 00002: RUNNING PROTOCOL ----------------- >>>> 00003: Protocol starts >>>> 00004: Hostname: localhost4.localdomain4 >>>> 00005: PID: 99422 >>>> 00006: pyworkflow: 3.0.17 >>>> 00007: plugin: relion >>>> 00008: plugin v: 4.0b2 >>>> 00009: currentDir: /home/user/Data/ScipionUserData/projects/Quentin__august__PSI >>>> 00010: workingDir: Runs/004970_ProtRelionClassify2D >>>> 00011: runMode: Continue >>>> 00012: MPI: 6 >>>> 00013: threads: 4 >>>> 00014: Starting at step: 1 >>>> 00015: Running steps >>>> 00016: STARTED: convertInputStep, step 1, time 2021-09-27 13:14:18.891805 >>>> 00017: Converting set from 'Runs/001948_ProtUserSubSet/particles.sqlite' into 'Runs/004970_ProtRelionClassify2D/input_particles.star' >>>> 00018: convertBinaryFiles: creating soft links. >>>> 00019: Root: Runs/004970_ProtRelionClassify2D/extra/input -> Runs/001072_ProtRelionExtractParticles/extra >>>> 00020: FINISHED: convertInputStep, step 1, time 2021-09-27 13:14:20.274397 >>>> 00021: STARTED: runRelionStep, step 2, time 2021-09-27 13:14:20.279078 >>>> 00022: mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4 >>>> 00023: Protocol failed: Command ' mpirun -np 6 `which relion_refine_mpi` --i Runs/004970_ProtRelionClassify2D/input_particles.star --particle_diameter 346 --ctf --zero_mask --K 24 --norm --scale --o Runs/004970_ProtRelionClassify2D/extra/relion --oversampling 1 --flatten_solvent --tau2_fudge 2.0 --iter 25 --offset_range 5.0 --offset_step 2.0 --psi_step 12.0 --dont_combine_weights_via_disc --pool 3 --gpu --j 4' returned non-zero exit status 213. >>>> 00024: FAILED: runRelionStep, step 2, time 2021-09-27 13:14:20.303854 >>>> 00025: *** Last status is failed >>>> 00026: ------------------- PROTOCOL FAILED (DONE 2/3) >>>> _______________________________________________ >>>> scipion-users mailing list >>>> sci...@li... <mailto:sci...@li...> >>>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >>> _______________________________________________ >>> scipion-users mailing list >>> sci...@li... <mailto:sci...@li...> >>> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> >> _______________________________________________ >> scipion-users mailing list >> sci...@li... <mailto:sci...@li...> >> https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > > _______________________________________________ > scipion-users mailing list > sci...@li... <mailto:sci...@li...> > https://lists.sourceforge.net/lists/listinfo/scipion-users <https://lists.sourceforge.net/lists/listinfo/scipion-users> > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users |
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