| Both sides previous revision Previous revision Next revision | Previous revision |
| doku:testquickstart [2014/06/17 11:57] – [Login] ir | doku:testquickstart [Unknown date] (current) – external edit (Unknown date) 127.0.0.1 |
|---|
| ssh <username>@vsc.boku.ac.at | ssh <username>@vsc.boku.ac.at |
| </code> | </code> |
| - Transfer your programs and data/input files to your home directory. <code> scp filename username@vsc.univie.ac.at:~/ | - Transfer your programs and data/input files to your home directory. <code> scp <filename> <username>@vsc.univie.ac.at:~/ |
| </code> | </code> |
| - (Re-)Compile your application. Please use the latest "Intel" MPI-Environment as described in [[doku:mpi|MPI Environment]]. | - (Re-)Compile your application. Please use the latest "Intel" MPI-Environment as described in [[doku:mpi|MPI Environment]]. |
| |
| ==== The job script ==== | ==== The job script ==== |
| - Write a job script for your application: \\ <code>#$ -N <job_name> | === header === |
| | <code>#$ -N <job_name> |
| #$ -pe mpich <slots> | #$ -pe mpich <slots> |
| #$ -V | #$ -V |
| mpirun -m $TMPDIR/machines -np $NSLOTS <executable></code> where "<job_name>" is a freely chosen descriptive name and "<slots>" is the number of processor cores that you want to use for the calculation. To ensure exclusive reservation of the computenodes for your job you have to give a multiple of 8 as value for "<slots>". Substitute the path to your MPI-enabled application for <executable> and you are ready to run!\\ To receive E-Mail notifications concerning job events (b .. beginning, e .. end, a .. abort or reschedule, s .. suspend), use these lines in your job script: \\ <code>#$ -M <email address to notify of job events> | #$ -l h_rt=hh:mm:ss |
| #$ -m beas # all job events sent via email</code> It is often advisable to also specify the job's runtime as <code>#$ -l h_rt=hh:mm:ss</code> in particular when you know that your job will run only for several hours or even minutes. That way one can "backfill" the queue, thus avoiding very long waiting times, which may be due to a highly parallel job waiting for free resources. \\ Here is an example job-script, requesting 32 processor cores, which will run for a maximum of 3 hours and sends emails at the beginning and at the end of the job: <code> | #$ -M <email address to notify of job events> |
| | #$ -m beas # all job events sent via email </code> |
| | - "<job_name>" is a freely chosen descriptive name, |
| | - "<slots>" is the number of processor cores that you want to use for the calculation. To ensure exclusive reservation of the compute nodes for your job, the value for "<slots>" has to be a multiple of 8. |
| | - "-V" declares that all environment variables in the qsub command's environment are to be exported to the batch job. |
| | - "-l" specifies the job's runtime. This explicit specification is in particular advisable for jobs with short run times, i.e., several hours or even minutes. In order to **reduce the time in the queue**, see also the section on [[doku:runtime|maximum runtime specification.]] |
| | - "-M <email address>; -m beas" request E-Mail notifications concerning job events (b .. beginning, e .. end, a .. abort or reschedule, s .. suspend). |
| | |
| | === run executable === |
| | The job can be started in several ways, |
| | - as single core job on one core (no MPI) task <code>./<executable></code> |
| | - as parallel single core job (no MPI) on parallel cores (see also [[doku:sequential-codes|Sequential code]]) |
| | - as MPI-enabled application <code> |
| | mpirun -m $TMPDIR/machines -np $NSLOTS <executable></code> |
| | |
| | "<executable>" is substituted by the path of the MPI-enabled application. |
| | |
| | |
| | ==== example ==== |
| | Here is an example job-script, requesting 32 processor cores, which will run for a maximum of 3 hours and sends emails at the beginning and at the end of the job: <code> |
| #$ -N hitchhiker | #$ -N hitchhiker |
| #$ -pe mpich 32 | #$ -pe mpich 32 |
| |
| |
| [[doku:runtime|In order to reduce the time in the queue, see the section on maximum runtime specification.]] | |
| |
| ====Submit your job:==== | ====Submit your job:==== |