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| ===== Quick Start ===== | ====== Documentation for VSC-1 ====== |
| ==== Login ==== | |
| |
| | ===== Troubleshooting ===== |
| | Solutions for common problems [[doku:troubleshooting|can be found under Troubleshooting]]. |
| | |
| | ===== VSC Newsletter ===== |
| | *[[doku:newsletter20100610|Newsletter 10.6.2010]] |
| | *[[doku:newsletter20101011|Newsletter 11.10.2010]] |
| | |
| | ===== User Documentation ===== |
| | *[[vsc1#Quick Start|Quick Start]] |
| | *[[doku:advanced_sge|Advanced SGE topics]] |
| | *[[software_vsc1|Available software packages on VSC-1]] |
| | *[[doku:epilog|Copying back data from a temp. directory after a job is terminated: user defined epilog]] |
| | *[[doku:mathematica|Notes on running Mathematica jobs]] |
| | *[[doku:matlab|Example for Matlab jobs]] |
| | *[[doku:paraview|Visualization software]] |
| | *[[doku:gaussian09|Notes on Gaussian09]] |
| | *[[vsc1#Cluster Monitoring: Ganglia|Cluster Monitoring: Ganglia]] |
| | *[[vsc1#Acknowledgement in publications|Acknowledgement in publications]] |
| | *[[doku:totalview-tutorial|Totalview: debugging software for parallel codes]] |
| | *[[doku:gpu|GPU CUDA: documentation]] |
| | *[[doku:mpi_tuning|MPI TUNING]] |
| | *[[doku:xeonphi|Using Intel Xeon Phi]] |
| | ==== Quick Start ==== |
| - Log in to your university's designated login server via SSH: \\ <code># Uni Wien | - Log in to your university's designated login server via SSH: \\ <code># Uni Wien |
| ssh <username>@vsc.univie.ac.at | ssh <username>@vsc.univie.ac.at |
| 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> | |
| - (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]]. |
| | - Write a job script for your application: \\ <code>#$ -N <job_name> |
| ==== The job script ==== | |
| === header === | |
| <code>#$ -N <job_name> | |
| #$ -pe mpich <slots> | #$ -pe mpich <slots> |
| #$ -V | #$ -V |
| #$ -l h_rt=hh:mm:ss | 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> |
| #$ -M <email address to notify of job events> | #$ -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 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 |
| |
| mpirun -m $TMPDIR/machines -np $NSLOTS ./myjob</code> | mpirun -m $TMPDIR/machines -np $NSLOTS ./myjob</code> |
| | - Submit your job:\\ <code>qsub <job_file></code>where "<job_file>" is the name of the file you just created. |
| | |
| | |
| ====Submit your job:==== | |
| - <code>qsub <job_file></code>where "<job_file>" is the name of the file you just created. | |
| - Check if and where your job has been scheduled:\\ <code>qstat</code> | - Check if and where your job has been scheduled:\\ <code>qstat</code> |
| - Inspect the job output. Assuming your job was assigned the id "42" and your job's name was "hitchhiker", you should be able to find the following files in the directory you started it from: \\ <code>$ ls -l | - Inspect the job output. Assuming your job was assigned the id "42" and your job's name was "hitchhiker", you should be able to find the following files in the directory you started it from: \\ <code>$ ls -l |
| hitchhiker.po42 | hitchhiker.po42 |
| hitchhiker.pe42</code> In this example hitchhiker.o42 contains the output of your job. hitchhiker.e42 contains possible error messages. In hitchhiker.po42 and hitchhiker.pe42 you might find additional information related to the parallel computing environment. | hitchhiker.pe42</code> In this example hitchhiker.o42 contains the output of your job. hitchhiker.e42 contains possible error messages. In hitchhiker.po42 and hitchhiker.pe42 you might find additional information related to the parallel computing environment. |
| - Delete Jobs: <code>$ qdel <job_id></code> | |
| | ==== Cluster Monitoring: Ganglia ==== |
| | Ganglia is available via: |
| | http://ganglia.vsc.tuwien.ac.at |
| | |
| | ==== Acknowledgement in publications ===== |
| | In publications, for which calculations have been performed on the VSC the following acknowledgment can be used: |
| | |
| | - "Die präsentierten Rechenergebnisse wurden [zum Teil] am Vienna Scientific Cluster (VSC) erzielt." |
| | - "The computational results presented have been achieved [in part] using the Vienna Scientific Cluster (VSC)." |