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Computational Cluster: How to Submit a Job

All jobs submitted to xray.bc.edu, regardless of program, must be submitted using Platform LSF (LSF for short). Currently, custom submission scripts have been written for Gaussian03, CNS and GAMESS.

General job submission:

bsub –q <queue_name> -J <job_name> -o <output_file_log> -R<resource_list> submission_scipt [submission_parameters]

Definitions:
bsub LSF command to submit a job
-q LSF switch to indicate the queue that will be used
<queue_name> replace with the name of the queue that will be used.
Possible
queue_names
short – for jobs that will run for less than
normal – for jobs that will run for less than 2 hr
long - for jobs that will run for more than 2 hr
-J LSF switch to indicate the name of the job
<job_name> replace with the name of the job
-o LSF switch to indicate that an output log file is to be recorded
<output_file_log> Replace with the name of the output log file
-R LSF switch to request a specific resource
<resource_list> Requested resources, see examples below
“linux” request linux node
“macg5” request macg5 node
“gaussian” request a node that can run Gaussian
“rusage[goldlicense=1]” request the system reserve one gold license
for submitted job
submission_script The script or program that will be run
[submission_parameters] Optional list of parameters required by program or script


Note: May other options are available. See the Platform LSF “Running Jobs with Platform LSF” manual

Currently available submission scripts:

gaussian_lsf submit <gaussian_input_file.com>

cns_lsf_submit <cns_input_file.inp>

gamess_lsf_submit <games_input_file.inp>

Examples:

Gaussian job:
bsub –q long –J first_g03_job –o g03_log.txt –R “gaussian” /progs/scripts/gaussian_lsf_submit test01.com
CNS job:
bsub –q normal –J first_cns_job –o cns_log.txt cns_lsf submit generate.inp
Gamess job:
bsub –q normal –J first_gamess_job –o gamess_log.txt gamess_lsf submit exam01.inp


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