Job script template
From FarmShare
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#!/bin/bash | #!/bin/bash | ||
# the above line is called a 'hashbang' and sets which shell you run under; you probably want bash | # the above line is called a 'hashbang' and sets which shell you run under; you probably want bash | ||
| + | # it's not real hashbang but is parsed by qsub for the '-S' option | ||
# | # | ||
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# | # | ||
# set the maximum memory usage (per slot) | # set the maximum memory usage (per slot) | ||
| - | #$ -l mem_free= | + | #$ -l mem_free=2G |
# | # | ||
| + | # on other clusters this memory resource may have a different name | ||
# | # | ||
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#$ -pe shm 1 | #$ -pe shm 1 | ||
# | # | ||
| + | # on other clusters this pe may have a different name | ||
# | # | ||
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# | # | ||
| - | # pass the current environment variables | + | ##We strongly discourage users from exporting their environment onto the compute node. |
| - | #$ -V | + | ##Doing this pretty much means the job is non-reproductible, |
| + | ##because all the required settings are not captured in the job script. | ||
| + | ## | ||
| + | ## pass the current environment variables | ||
| + | ##$ -V | ||
| + | ## | ||
| + | |||
| + | # join the stdout and stderr streams into one file | ||
| + | #$ -j y | ||
# | # | ||
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Of course, you can just use the equivalent command line: | Of course, you can just use the equivalent command line: | ||
| - | qsub -S /bin/bash -N example_job -l mem_free= | + | qsub -S /bin/bash -N example_job -l mem_free=2G -pe shm 1 -m ea -M $USER@stanford.edu -w e -j y /full/path/to/command arg1 arg2 arg3 |
You may need to also have '-b y' if the command is a binary and not a script. | You may need to also have '-b y' if the command is a binary and not a script. | ||
Latest revision as of 12:19, 5 November 2014
This is meant to be a script you can copy and adapt to get up and running quickly. A similar one appears at the bottom of the man page for 'qsub'.
#!/bin/bash # the above line is called a 'hashbang' and sets which shell you run under; you probably want bash # it's not real hashbang but is parsed by qsub for the '-S' option # # set the name of the job; this will appear in the job listing #$ -N example_job # # # set the maximum memory usage (per slot) #$ -l mem_free=2G # # on other clusters this memory resource may have a different name # # set the number of slots, replace '1' with a larger number if needed #$ -pe shm 1 # # on other clusters this pe may have a different name # # set the maximum run time, hh:mm:ss, default is 48hrs on FarmShare #$ -l h_rt=12:00:00 # # # send mail when job ends or aborts #$ -m ea # # # specify an email address #$ -M $USER@stanford.edu # # check for errors in the job submission options #$ -w e # ##We strongly discourage users from exporting their environment onto the compute node. ##Doing this pretty much means the job is non-reproductible, ##because all the required settings are not captured in the job script. ## ## pass the current environment variables ##$ -V ## # join the stdout and stderr streams into one file #$ -j y # /full/path/to/command arg1 arg2 arg3 ... #make sure that the command above actually doesn't use more memory or CPU than you specified.
Of course, you can just use the equivalent command line:
qsub -S /bin/bash -N example_job -l mem_free=2G -pe shm 1 -m ea -M $USER@stanford.edu -w e -j y /full/path/to/command arg1 arg2 arg3
You may need to also have '-b y' if the command is a binary and not a script.
