Difference between revisions of "Cluster:Using the F@C PBS script"

Revision as of 14:07, 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=4:ppn=2 -v MOLECULE=villin,TABLE_NAME=results_skylar,TEST_SET_LABEL=Parse_Test -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.

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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=4:ppn=2 -v MOLECULE=villin,TABLE_NAME=results_skylar,TEST_SET_LABEL=Parse_Test -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.
+* 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.