Post-processing jobs on PC-farms at Zeuthen

Using the PC-farms of the computing center of DESY Zeuthen is *not* possible by default. If you are member of DESY ask your local group administrator. Otherwise check with the APE administrators (apeadm@ifh.de) and provide the following information:

• For which period of time do you want to use the PC-farms?
• How many jobs will be submitted per day?
• How long will each job run on which type of PC?
• Are there any special needs (memory, disk space)?

Hints

1. The PC-farms queues are operated by a similar batch queueing system. However, a different 'cell' and (possibly) a different software version is used. You therefore have to re-define the following environment variables:

   	SGE_ROOT=/opt/products/gridengine/6.0u4
   	SGE_CELL=default
   

   Furthermore, you have to use the binaries located in

   	/opt/products/bin
   

   (e.g. ($SGE_ROOT/bin/qsub).
2. Check Batch System Usage for further information about the batch service for the PC-farms. In particular the hints for efficient data transfer should be taken into account.
3. It is currently not possible to submit jobs to APE from the PC-farm.

Example

Script for APEmille 'ape.job'

  #!/bin/zsh
  #$ -N test-ape
  #$ -P yourproject
  #$ -pe b* 1
  #$ -cwd

  # run APEmille program
  APErun -- your-ape-program.jex

  # submit post-processing job
  SGE_CELL=default SGE_ROOT=/opt/products/gridengine/6.0u4 /opt/products/bin/qsub pc.job

  # submit next APEmille job
  qsub ape.job

Script for job on PC-farm 'pc.job'

  #!/bin/zsh
  #$ -N test-pc
  #$ -l h_cpu=24:0:0	# define hard cpu limit of 24 hours
  #$ -cwd

  # run post-processing program
  ./your-pc-program.exe mydata.dat