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bsub

bsub

You use bsub to submit a job to the LSF batch system.

An extensive documentation on the bsub command can be found in the LSF documentation: "<a href="/lsf/lsf_users_guide/index.htm">Running Jobs with Platform LSF</a>".

Important parameters

There are some important parameters that are always required or at least recommended to use:

-q <queue> The queue your job should run in.
Available queues.
-n <processors> The number of job slots you need (=cores, if no affinity request is given).
-R 'span[ptile=64]'
-R 'span[hosts=1]'
Request to always get 64 processor together on one node, i.e. full nodes.
If you use 64 processors or less, use '-R 'span[hosts=1]' instead to ensure all processes running on one node.
-W <minutes>
-W <hour>:<min>
Set the runtime limit of your job (up to the maximum allowed by the selected queue). See the description for host model considerations.
-app <profile> Use an application profile to request an amount of memory for each process.
More details on memory reservation.
-I Run the job interactively, showing you its output directly in your shell session. Useful for debugging or short runs.
-J <jobname> Sets an arbitrary name for your job that is used for Email notifications and listing of jobs through bjobs.
See also our policy on jobnames.
-G <groupname> Specifies group or project name, such that a job is correctly accounted for the given group (important if more than one affiliation of a user is given).

To specify files for output, error and input consider the following:

-o <filename> Will direct stdout, stderr and the LSF job summary into one file.
-o <filename>.log -e <filename>.err Will direct stdout and the job summary to the log file and stderr to the error log file.
-N In addtition to -o will send the job summary seperately within a mail to the user.
-i <filename> Specifies additional input data.

Other important parameters / features on mogon include:

Using bsub

There are two ways to supply parameters and commands to bsub: Using the command line or using a bsub script.

Command line

On the command line, you simply attach all parameters to the bsub command and finish with your program:

$ bsub -q short -n 128 -R 'span[ptile=64]' -app Reserve1800M <mpirun/mpiexec> ./cpi

bsub script

In a bsub script, you list all your bsub parameters in a file as special comments like this:

job
#BSUB -q short
#BSUB -n 128
#BSUB -R 'span[ptile=64]'
#BSUB -app Reserve1800M
 
<mpirun/mpiexec> ./cpi

And then you pipe that file into the bsub command like this:

$ bsub < job

A good verification tool for shell scripts can be found here.

bsub.txt · Last modified: 2016/03/24 09:03 by meesters