psubmit

Set of shell scripts to submit batch jobs on various HPC systems in a generalized way.

File psubmit.opt is expected to be filled in. See psubmit.opt.example for the ideas on creating your own files.

The command line options that add or override settings of psubmit.opt:

• -x -- print debug trace (rather verbose)
• -o psubmit_opt_file_name -- use an alternative file name for the options file
• -n NNODES -- number of cluster nodes (assumed 1 if omitted)
• -p PPN -- number of MPI ranks per node
• -t NTHREADS -- number of OpenMP threads per rank
• -e BINARY -- override the TARGET_BIN settings of psubmit.opt
• -a ARGS -- arguments (as a single string literal) to pass to BINARY
• -b preproc_script -- override the BEFORE setting of psubmit.opt
• -f postproc_script -- override the AFTER setting of psubmit.opt
• -l key=value:key=value:.. -- set up some parameters using key/value pair syntax
• -u DIR -- set up the subdirectory for psubmit.opt and TARGET_BINARY files
• -s -- omit the procedure of looking for stack trace files after execution

Please note, that options -n, -p and -t not only override the values given in psubmit.opt file, but also the values set in the -l option.

The parameters that can be set in a key-value form:

• nnodes=NUM -- overrides NNODES setting of psubmit.opt (but -n NUM option is of higher priority)
• ppn=NUM -- overrides PPN setting of psubmit.opt (but -p NUM option is of higher priority)
• nth=NUM -- overrides NTH setting of psubmit.opt (but -t NUM option is of higher priority)
• ngpus=NUM -- overrides NGPUS setting of psubmit.opt
• queue=STRING -- overrides QUEUE setting of psubmit.opt
• constraint=STRING -- overrides CONSTRAINT setting of psubmit.opt
• account=STRING -- overrides ACCOUNT setting of psubmit.opt
• nodetype=STRING -- overrides NODETYPE setting of psubmit.opt
• time=NUM -- overrides TIME_LIMIT setting of psubmit.opt
• gres=STRING -- overrides GENERIC_RESOURCES setting of psubmit.opt
• mpiexec=STRING -- overrides MPIEXEC setting of psubmit.opt
• batch=STRING -- overrides BATCH setting of psubmit.opt
• before=STRING -- overrides BEFORE setting of psubmit.opt
• after=STRING -- overrides AFTER setting of psubmit.opt
• subdir=STRING -- overrides the command line option -u DIR