Difference between revisions of "Cluster:Using the F@C PBS script"
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* The F@C PBS script lives in <tt>/cluster/generic/bin/fatc_pbs.sh</tt>. To use it, you have to specify the number of nodes, the processors per node, the molecule, the database table name, and the test set label. You should also set redirection files for STDOUT and STDERR. Do so like this: | * The F@C PBS script lives in <tt>/cluster/generic/bin/fatc_pbs.sh</tt>. To use it, you have to specify the number of nodes, the processors per node, the molecule, the database table name, and the test set label. You should also set redirection files for STDOUT and STDERR. Do so like this: | ||
| − | qsub -l nodes=n:ppn=m -v MOLECULE=molecule_name,TABLE_NAME=table,TEST_SET_LABEL=label -o out.txt -e err.txt /cluster/generic/bin/fatc_pbs.sh | + | <tt>qsub -l nodes=n:ppn=m -v MOLECULE=molecule_name,TABLE_NAME=table,TEST_SET_LABEL=label -o out.txt -e err.txt /cluster/generic/bin/fatc_pbs.sh</tt> |
* Make the submission from the head node (probably a0, b0, or c0) of that cluster. Make sure that your current working directory is inside a fatc directory. | * Make the submission from the head node (probably a0, b0, or c0) of that cluster. Make sure that your current working directory is inside a fatc directory. | ||
* The log parsing is done from within the submission script, and is stuck in the fatc-testing database. | * The log parsing is done from within the submission script, and is stuck in the fatc-testing database. | ||
| + | |||
| + | * For general information on using PBS/Maui, see [[Using PBS/Maui|here]]. | ||
Revision as of 14:46, 20 July 2005
- The F@C PBS script lives in /cluster/generic/bin/fatc_pbs.sh. To use it, you have to specify the number of nodes, the processors per node, the molecule, the database table name, and the test set label. You should also set redirection files for STDOUT and STDERR. Do so like this:
qsub -l nodes=n:ppn=m -v MOLECULE=molecule_name,TABLE_NAME=table,TEST_SET_LABEL=label -o out.txt -e err.txt /cluster/generic/bin/fatc_pbs.sh
- Make the submission from the head node (probably a0, b0, or c0) of that cluster. Make sure that your current working directory is inside a fatc directory.
- The log parsing is done from within the submission script, and is stuck in the fatc-testing database.
- For general information on using PBS/Maui, see here.
