Problem running datacat: (Tyrel)
Logged in on a centos7 machine, datacat (/afs/slac/g/glast/ground/bin/datacat) did not work within the container or with "singularity exec -B ...", I got the following errors:
/afs/slac/g/glast/ground/bin/datacat: line 2: /u/gl/glast/oracle/bin/setup-11gr2-j7.sh: No such file or directory
/afs/slac/g/glast/ground/bin/datacat: line 8: /bin/java: No such file or directory
I was able to run this from the machine itself and not using the container, so it may be a non-issue
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Need help modifying script to submit jobs to the farm: (Tyrel)
I'm trying to modify a script which submits jobs to the farm but relies on things which don't work on the centos7 machies. In the script I have the bsub command, which works fine on the rhel6-64 machines (done in a loop over i and with two inputs):
bsub -q long -W 20:00 -R rhel60 -o $PWD/gengcrhists_mod_$2_$i.output.txt genGCRHists -m ../../fit_protonCalib_calibOps_new_46runs.calMPD.txt -a ../fit_gcrhists_240m_244m_bigsum.gcr_asym_hist.txt ../../digitization-v4r0p2_077016861_digi_DIGI01.FLIGHT_GAIN.cidac2adc.txt digi_$2_$i.txt gcr_$2_$i.txt gcrhists_mod_$2_$i
When I try to update it to use the container as I understand it, I change it to the following:
bsub -q long -W 20:00 -R centos7 -o $PWD/gengcrhists_mod_$2_$i.output.txt singularity exec -B /nfs:/nfs -B /afs:/afs -B /gpfs:/gpfs $myimage genGCRHists -m ../../fit_protonCalib_calibOps_new_46runs.calMPD.txt -a ../fit_gcrhists_240m_244m_bigsum.gcr_asym_hist.txt ../../digitization-v4r0p2_077016861_digi_DIGI01.FLIGHT_GAIN.cidac2adc.txt digi_$2_$i.txt gcr_$2_$i.txt gcrhists_mod_$2_$i
At first pass, this does not seem to retain any of my environmet so it cannot find the genGCRHists executable. I tried explicitly sourcing the setup script before going into the loop and it can find the executable, but then it complains about not being able to find one of the libraries. I've checked and that library is in the $LD_LIBRARY_PATH of the setup script and should be accessible.
I tried calling the top level scripts with the container:
singularity exec -B /nfs:/nfs -B /afs:/afs -B /gpfs:/gpfs $myimage ../run_sing_gengcrhists_mod_jobs.sh 22 664m
and was given the error message "This machine is not licensed for LSF." so clearly something isn't correct about that usage. (Looking at Richard's slides from the last collaboration meeting this shows that there is definitely some subtlety I'm not understanding)
Am I using the container incorrectly with the bsub command? Why doesn't it inherit my setup (path, etc.) as before and instead need me to resource the script within the script? Do I need to compile a new version of the calibGenCalAnalysis within the container?
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