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

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

Dear Grigory, 

Thanks again for all your help. 
I wish you all the best. 
Best regards, 
Carlos. 

From: "Grigory Sharov" <sha...@gm...> 
To: "scipion-users" <sci...@li...> 
Sent: Thursday, September 30, 2021 4:18:28 PM 
Subject: Re: [scipion-users] Problems with CONDA_ACTIVATION_CMD using Cryolo 

Yes you are correct. You can only use cryolo 1.8 outside Scipion. 

Best regards, 
Grigory 

-------------------------------------------------------------------------------- 
Grigory Sharov, Ph.D. 

MRC Laboratory of Molecular Biology, 
Francis Crick Avenue, 
Cambridge Biomedical Campus, 
Cambridge CB2 0QH, UK. 
tel. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Thu, Sep 30, 2021 at 3:17 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

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" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Thu, Sep 30, 2021 at 2:39 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

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" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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 | 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. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Thu, Sep 30, 2021 at 2:20 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

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" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Thu, Sep 30, 2021 at 1:04 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

Dear Grigory, 

Thanks so so much! 
Cryolo is running now in Scipion. 
Best regards, 
Carlos. 

From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Thu, Sep 30, 2021 at 11:11 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

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" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Thu, Sep 30, 2021 at 10:47 AM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

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" < [ mailto:pc...@cn... | pc...@cn... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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: 

BQ_BEGIN

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. [ tel:+44%201223%20267228 | +44 (0)
                                      1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Wed, Sep 29, 2021 at 5:37 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

Dear Grigory, 

The files that you requested are attached. 
Thanks so much again 

From: "Grigory Sharov" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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. [ tel:+44%201223%20267228 | +44
                                                (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Wed, Sep 29, 2021 at 5:15 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

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/ | http://scipion.i2pc.es/getplugins/ ] 
SCIPION_SOFTWARE = ${SCIPION_HOME}/software 
SCIPION_SUPPORT_EMAIL = [ mailto:sc...@cn... | sc...@cn... ] 
SCIPION_TESTS = ${SCIPION_HOME}/data/tests 
SCIPION_TESTS_CMD = scipion3 tests 
SCIPION_TESTS_OUTPUT = ~/ScipionUserData/Tests 
SCIPION_TMP = ~/ScipionUserData/tmp 
SCIPION_URL = [ http://scipion.cnb.csic.es/downloads/scipion | http://scipion.cnb.csic.es/downloads/scipion ] 
SCIPION_URL_SOFTWARE = [ http://scipion.cnb.csic.es/downloads/scipion/software | http://scipion.cnb.csic.es/downloads/scipion/software ] 
SCIPION_URL_TESTDATA = [ http://scipion.cnb.csic.es/downloads/scipion/data/tests | http://scipion.cnb.csic.es/downloads/scipion/data/tests ] 
SCIPION_USER_DATA = ~/ScipionUserData 
WIZARD_MASK_COLOR = [0.125, 0.909, 0.972] 
CONDA_ACTIVATION_CMD = eval "$(/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" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Wed, Sep 29, 2021 at 4:47 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

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.org/simple ] , [ https://pypi.ngc.nvidia.com/ | 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 | 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" < [ mailto:sha...@gm... | sha...@gm... ] > 
To: "scipion-users" < [ mailto:sci...@li... | 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. [ tel:+44%201223%20267228 | +44 (0) 1223 267228 ] 
e-mail: [ mailto:gs...@mr... | gs...@mr... ] 

On Wed, Sep 29, 2021 at 4:03 PM Carlos HENRIQUE FERNANDES < [ mailto:car...@so... | car...@so... ] > wrote: 

BQ_BEGIN

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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-- 
Pablo Conesa - Madrid [ http://scipion.i2pc.es/ | Scipion ] team 

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

Image processing framework to integrate EM software packages.

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