[scipion-users] scipion3, own special scipion conda - cluster submission problems/question

[Lugmayr, W. <w.l...@uk...>]

Hi,

I have re-installed recently scipion3 with its own conda environment. Mainly for the reason that the plugins could overwrite my conda installation e.g. mine is cryolo-1.7 and the scipion plugin creates a cryolo-1.7.2

My new scipion3 conda looks now like:
base                  *  /beegfs/cssb/software/em/scipion/3.0/anaconda3
.scipion3env             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env
cryolo-1.7.2             /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryolo-1.7.2
cryoloCPU-1.7.2          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/cryoloCPU-1.7.2
xmipp_DLTK_v0.3          /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_DLTK_v0.3
xmipp_MicCleaner         /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/xmipp_MicCleaner

If I run everything locally via scipion3 the task runs fine.

The task script for the cluster contains:
:
source /beegfs/cssb/software/em/scipion/3.0/anaconda3/etc/profile.d/conda.sh
conda activate .scipion3env
which python3
################################
python3 /beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py "/home/lugmayr/ScipionUserData/projects/Scipion3_TestSuite" "Runs/000146_XmippProtMovieCorr/logs/run.db" 146

Now I get the following error:
### jobid : 5452483  ###
/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/bin/python3
Traceback (most recent call last):
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/apps/pw_protocol_run.py", line 39, in <module>
    runProtocolMain(projPath, dbPath, protId)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2167, in runProtocolMain
    protocol = getProtocolFromDb(projectPath, protDbPath, protId, chdir=True)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/protocol/protocol.py", line 2249, in getProtocolFromDb
    project.load(dbPath=os.path.join(projectPath, protDbPath), chdir=chdir,
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 244, in load
    self._loadDb(dbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 302, in _loadDb
    self.mapper = self.createMapper(absDbPath)
  File "/beegfs/cssb/software/em/scipion/3.0/anaconda3/envs/.scipion3env/lib/python3.8/site-packages/pyworkflow/project/project.py", line 211, in createMapper
    classesDict.update(self._domain.getMapperDict())
AttributeError: 'NoneType' object has no attribute 'getMapperDict'

Before when my base conda included all other scipion conda envs the cluster submission was fine.
I have set autoactivation for my base to off in my .condarc.

I have to use the python3 from the .scipion3env otherwise there would not be the pyworkflow package.
What else could I change for submission?

Cheers,
Wolfgang

-- 
Universitätsklinikum Hamburg-Eppendorf (UKE)
@ Centre for Structral Systems Biology (CSSB)
@ Deutsches Elektronen-Synchrotron (DESY)
Notkestrasse 85 Gebäude 15
22607 Hamburg, Germany
Tel.: +49 40 8998-87652
Email: wol...@cs...
http://www.cssb-hamburg.de/