7. Batch Jobs
An introduction to bsub
LSF
is the batch system utilised by the CSAR machines. The command used
to submit jobs to LSF is bsub. In order to submit to fermat
and green you should issue commands on wren. Jobs to be run on newton
can be submitted by logging into newton and running commands.
You must give LSF options to inform it about
the needs of your job. The basic options are described below.
- Number of cpus: requested
using the
-n flag.
- Wall clock time: requested
with the
-W flag. This means that your job will automatically
finish after that amount of time is used up if it has not already
finished. Measured and specified in minutes.
- Total CPU time: specified
with the
-c option and is similar to -W
in that it is a way of restricting the amount of time your job runs
for. However -c is the total amount of CPU time used.
Measured and specified in minutes.
- Where to run the job: to specify where your job
runs can be achieved with the
-q and -m
options. The -m option specifies which machine to run
on such as green. The -q option tells it which queue
to run on for that particular machine.
- Job name: to give your job a name which can be
useful to identify which of your jobs are running when using some
of the LSF monitoring commands use the
-J option.
- Output: the stderr and stdout can be controlled
with the
-e and -o options. The -e
options specifies where the stderr should be put and the -o
option specifies where the stdout should be put. If neither option
is specified the output should be emailed to you, if only the -o
option is specified the stdout and stderr are merged into the specified
file. It is also useful to put "%J" at the end of the filename
as this will create a unique file for each job output.
Submission script example
The following script can be submitted which will run
a.out on 8 processors asking for one hour of green and
writing the output to a file called output and calling the job my_job.
It should be submitted using bsub < scriptname
#BSUB -n 8
#BSUB -W 1:00
#BSUB -m green
#BSUB -J my_job
#BSUB -q normal
#BSUB -o output
mpirun -np 8 ./a.out
Command line example
bsub -n 8 -W 1:00 -m
green -J my_job -q normal -o output scriptname
Only the mpirun -np 8 ./a.out then needs
to be in the script.
Further Information
Note that the IRIX machines and the Altix do differ
slightly. Please consult the following webpages for more detailed information:
Job Submission (inc machine specific pages): http://www.csar.cfs.ac.uk/user_information/job_info/
LSF: http://www.csar.cfs.ac.uk/user_information/lsf/
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