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

[Jose M. de la R. T. <del...@gm...>]

Hi Caroline,

I think the problem with 3090 cards is more specific to cryolo and topaz
due to the cuda version requirements and also the dependency with
tensorflow library. Other plugins should work.

Best,
José Miguel


On Thu, Sep 30, 2021, 10:54 AM Caroline Ingeborg Jegerschöld <ci...@kt...>
wrote:

> Dear all,
>
> Is it so that for all plugins-versions within scipion3 one has to check
> what hardware that is both necessary and possible to use? Before buying
> e.g. such a computer with a card like nvidia 3090? Or just live with not
> using some software.
>
> I was looking for some hardware suggestions for scipion3 but might not be
> possible to do to accommodate all plugins?
>
> Best regards,
>
> Caroline
>
>
>
> *From:* Carlos HENRIQUE FERNANDES [mailto:
> car...@so...]
> *Sent:* Thursday, 30 September 2021 16:17
> *To:* scipion-users <sci...@li...>
> *Subject:* Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using
> Cryolo
>
>
>
> Dear Grigory,
>
> Yes, you indeed said that, I realized now.
> Thus, we have two problems, scipion does not support cryolo 1.8 and my
> NVIDIA GeForce is not supported by cryolo 1.7.
> So, as I understand, we can not solve this for now.
> Thanks again.
> Best regards,
> Carlos.
> ------------------------------
>
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"scipion-users" <sci...@li...>
> *Sent: *Thursday, September 30, 2021 3:52:48 PM
> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using
> Cryolo
>
>
>
> Hi,
>
> As I said earlier, the sphire plugin does not support cryolo 1.8, you
> cannot install or/and use it inside Scipion.
>
>
> 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 2:39 PM Carlos HENRIQUE FERNANDES <
> car...@so...> wrote:
>
> Dear Grigory,
>
> So, should I remove cryolo-1.7.6 and reinstall cryolo 1.8 (I removed it
> using pip uninstall cryolo) and put it to work inside Scipion?
> I tried to no use GPUs on cryolo picking, but I obtained the same error.
> Thanks again for the help.
> Best regards, Carlos.
> ------------------------------
>
> *From: *"Grigory Sharov" <sha...@gm...>
> *To: *"scipion-users" <sci...@li...>
> *Sent: *Thursday, September 30, 2021 3:26:53 PM
> *Subject: *Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using
> Cryolo
>
>
>
> 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.
>
>
>
> _______________________________________________
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>
>
>
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>
> _______________________________________________
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>
>
>
> _______________________________________________
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>
> _______________________________________________
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>
>
>
> _______________________________________________
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>
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>
>
>
>
> _______________________________________________
>
> scipion-users mailing list
>
> sci...@li...
>
> https://lists.sourceforge.net/lists/listinfo/scipion-users
>
> --
> Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
>
>
>
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>
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>
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>
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>
>
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>
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>
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>
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