I work at MSU's HPCC, and we are having issues with correct threading control of the tool. Specifically, it appears that the call out to BLASR has a hard-coded thread count of 4:
"I looked into this briefly. It appears the culprit is a call to blasr made by PBJelly. While most of the calls are nproc=1, there is one script: Valid.py - that makes a call using nproc=4:
Perhaps we can discuss this further. There is a difinitive problem, in that PBJelly is calling processes with non-controllable number of threads, made by blasr
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
This problem is fixed and will be available in the next PBSuite version - which I hope to release by the end of the month. If you don't wish to wait that long, copy this file:
I work at MSU's HPCC, and we are having issues with correct threading control of the tool. Specifically, it appears that the call out to BLASR has a hard-coded thread count of 4:
"I looked into this briefly. It appears the culprit is a call to blasr made by PBJelly. While most of the calls are nproc=1, there is one script: Valid.py - that makes a call using nproc=4:
/opt/software/PBSuite/14.7.14--GCC-4.4.5/bin/Valid.py
31: OLCAssembly.py input.fastq -nproc 4
34: OLCAssembly.py ../out.fasta ../out.qual -nproc 4
221: return exe("OLCAssembly.py %s --nproc 4 --fqOut --workDir %s" % (inputFq, workDir))"
You are correct that this is an error. However, the code 'Valid.py' is never used. So this won't create the error you might be seeing.
Perhaps we can discuss this further. There is a difinitive problem, in that PBJelly is calling processes with non-controllable number of threads, made by blasr
Hey Matthew,
This problem is fixed and will be available in the next PBSuite version - which I hope to release by the end of the month. If you don't wish to wait that long, copy this file:
https://sourceforge.net/p/pb-jelly/code-0/HEAD/tree/trunk/pbsuite/utils/CommandRunner.py
and overwrite $SWEETPATH/pbsuite/utils/CommandRunner.py in your installed version.