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At first pass, this does not seem to retain any of my environmet so it cannot find the genGCRHists executable. I 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
command and that did not work
(There was more here about libraries in an earlier version, but I traced that down to an error when I had begun making changes to switch to rhel7 before learning that things would not be built for rhel7 and I needed to use this container).
Currently the solution I found was to have my script write a script for each batch job I want to run. The commands in that script are just to source the setup script, and then run the genGCRHists command. The bsub command uses the "singularity exec..." command to run the new script for each joband 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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