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

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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.
>>>>
>>>>
>>>> _______________________________________________
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>>>> 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