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

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

Hi Carlos,

you are using NVIDIA GeForce RTX 3090 which is only supported by cryolo
1.8.

Have a look here:
https://cryolo.readthedocs.io/en/latest/installation.html#with-cuda-11

AFAIK, Scipion does not support this version yet.

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 2:20 PM Carlos HENRIQUE FERNANDES <
car...@so...> wrote:

> Dear Grigory,
>
> Thanks for all support. Cryolo training worked very well; however, I'm
> facing some problems with cryolo picking.
> I obtain this error:
> *Protocol failed: Command ' eval
> "$(/home/impmc/eman2-sphire-sparx/bin/conda shell.bash hook 2>
> /dev/null)"&& conda activate cryolo-1.7.6 && cryolo_predict.py -c
> Runs/002135_SphireProtCRYOLOPicking/extra/config.json -w
> /mnt/data2/charles/keops_scipion/keops_aout21/Runs/001993_SphireProtCRYOLOTraining/model.h5
> -i Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -o
> Runs/002135_SphireProtCRYOLOPicking/tmp/micrographs_1-27/ -t 0.300 -g 1 -nc
> 4 --otf' returned non-zero exit status 1*
>
> When I execute in bash *conda activate cryolo-1.7.6 && which
> cryolo_predict.py*, I obtain a normal response
> */home/impmc/eman2-sphire-sparx/envs/cryolo-1.7.6/bin/cryolo_predict.py*
>
> I'm sorry, I thought that the problems were solved...
> I attached the run.stderr and run.stdout files
> Thanks again for the support.
>
> ------------------------------
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"scipion-users" <sci...@li...>
> *Sent: *Thursday, September 30, 2021 2:08:45 PM
> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using
> Cryolo
>
> Oh, that's great that it worked!
> You are welcome!
> Best regards,
> Grigory
>
>
> --------------------------------------------------------------------------------
> Grigory Sharov, Ph.D.
>
> MRC Laboratory of Molecular Biology,
> Francis Crick Avenue,
> Cambridge Biomedical Campus,
> Cambridge CB2 0QH, UK.
> tel. +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