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

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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*
>
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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