The filenames, paths, email addresses, and some values below are things you will probably need to change. In some cases, values/names have been used to demonstrate possibilities that you could employ (in a slightly different way). Apart from the
-l options, no option should appear on multiple lines.
Description of purpose
#PBS -c n
#PBS -c s
#PBS -c enabled
No checkpointing to be performed.
Checkpointing is to be done on a job at
Checkpointing is allowed but must be explicitly invoked by a
#PBS -d /fast/jc123456
Defines the working directory path to be used for the job.
#PBS -j oe
#PBS -o /tmp/output.$PBS_O_JOBID
Merge standard output and standard error streams into the named file.
#PBS -l pmem=4gb
#PBS -l nodes=1:ppn=2
#PBS -l walltime=24:00:00
Request that 4GB of memory per CPU core be reserved for the batch job.
Request that 2 CPU cores on 1 host be reserved for the batch job.
Advise the scheduler that this job will have completed within 24 hours.
#PBS -l nodes=2 -I -X
Request 2 CPU cores that can be used for interactive job(s).
Note: Our 2 login nodes each provide 18 CPU cores and 64GB of memory for running interactive jobs (without
#PBS -m ae
#PBS -M firstname.lastname@example.org
#PBS -M email@example.com
Send mail at batch job abort/exit to the Email address provided.
#PBS -N job_name
Assign a name (
job_name) to the batch job
#PBS -q normal
#PBS -q bigmem
Specify the queue into which your job will be placed.
bigmem queue targets two nodes only, long delays can be experienced before your job is run.
Export environment variables to the batch job
While defaults exist for many options, HPC staff ask researchers to specify CPU core, memory, and walltime requirements as accurately as possible.
-W option can be used for more complicated tasks such as job dependencies, stage-in and stage-out. Researchers may wish to consult with HPC staff with regard to use of the
-W options. A
man qsub will provide more information and more options than provided above.
Users interested in protecting there job runs with checkpointing should realize that this feature comes at a cost (I/O operations). Checkpoint restart of a job (using BLCR) will not work for all job types. HPC staff advise use to test this feature on a typical job first before using it on other similar jobs. Generally speaking, checkpointing will only be a real benefit to jobs that run for over a week.