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bsub

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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.

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
bsub.1454504281.txt.gz · Last modified: 2016/02/03 13:58 by meesters