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

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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
>> _______________________________________________
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>> sci...@li...
>> https://lists.sourceforge.net/lists/listinfo/scipion-users
>>
>
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> _______________________________________________
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> 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