Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo

SourceForge Headquarters 225 Broadway Suite 1600 San Diego, CA 92101 +1 (858) 422-6466

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
> _______________________________________________
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>

Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo

Image processing framework to integrate EM software packages.

Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo