Syntax for submitting a qsub job without an actual job file?
pbs, python, qsub, sungridengine
Solution
You can pass the name of any executable script/file to `qsub` after you've provided all your options (`-d .`, etc.). Any arguments that come after the script name are treated as arguments for that script. For example, if I had the script test.py:
#!/usr/bin/python
from sys import argv
script, param = argv
print param
Then I can run
qsub test.py 2
and the output to my log will be `2`.
Two important things to note:
- Your Python script must be executable (e.g. `chmod +x test.py`).
- Your Python script must have a shebang (e.g. `#!/usr/bin/python`).
Problem
I would like to submit qsub jobs on the fly without creating discrete job files. So, let's say I have a python script called "get_time.py" that simply reports the time. Instead of making a submission script like this: ``` cat>job.sub<<eof #PBS -l walltime=1:00:00 cd $PBS_O_WORKDIR get_time.py eof ``` ...and then submitting the job: `qsub job.sub` I would like to be able to bypass the file creation step, and I'd image the construct would be something like this: `qsub -d . -e get_time.py` where `-e` is my imaginary parameter that tells qsub that the following is code to be sent to the scheduler, instead of using a discrete submission file. Am I crazy? It seems like there should already be a simple solution for this, but I couldn't find it anywhere. Thanks for any suggestions!