Documentation for VSC-1

Solutions for common problems can be found under Troubleshooting.

• Newsletter 10.6.2010
• Newsletter 11.10.2010

• Quick Start
• Advanced SGE topics
• Available software packages on VSC-1
• Copying back data from a temp. directory after a job is terminated: user defined epilog
• Notes on running Mathematica jobs
• Example for Matlab jobs
• Visualization software
• Notes on Gaussian09
• Cluster Monitoring: Ganglia
• Acknowledgement in publications
• Totalview: debugging software for parallel codes
• GPU CUDA: documentation
• MPI TUNING
• Using Intel Xeon Phi

1. Log in to your university's designated login server via SSH:
   

   # Uni Wien
   ssh <username>@vsc.univie.ac.at
   
   # TU Wien
   ssh <username>@vsc.tuwien.ac.at
   
   # Boku Wien
   ssh <username>@vsc.boku.ac.at

2. Transfer your programs and data/input files to your home directory.
3. (Re-)Compile your application. Please use the latest “Intel” MPI-Environment as described in MPI Environment.
4. Write a job script for your application:
   

   #$ -N <job_name>
   #$ -pe mpich <slots>
   #$ -V
   mpirun  -m $TMPDIR/machines -np $NSLOTS <executable>

   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:
   

   #$ -M <email address to notify of job events>
   #$ -m beas  # all job events sent via email

   It is often advisable to also specify the job's runtime as

   #$ -l h_rt=hh:mm:ss

   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:

   #$ -N hitchhiker
   #$ -pe mpich 32
   #$ -V
   #$ -M my.name@example.at
   #$ -m be
   #$ -l h_rt=03:00:00
   
   mpirun  -m $TMPDIR/machines -np $NSLOTS ./myjob

5. Submit your job:
   

   qsub <job_file>

   where “<job_file>” is the name of the file you just created.

6. Check if and where your job has been scheduled:
   

   qstat

7. 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:
   

   $ ls -l
   hitchhiker.o42
   hitchhiker.e42
   hitchhiker.po42
   hitchhiker.pe42

   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.

Ganglia is available via: http://ganglia.vsc.tuwien.ac.at

In publications, for which calculations have been performed on the VSC the following acknowledgment can be used:

1. “Die präsentierten Rechenergebnisse wurden [zum Teil] am Vienna Scientific Cluster (VSC) erzielt.”
2. “The computational results presented have been achieved [in part] using the Vienna Scientific Cluster (VSC).”