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cluster:queuing-system [2012/03/02 19:09] – dregerservices:cluster:queuing-system [2012/03/20 09:51] – dreger
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-====== Getting started with the HPC cluster ======+====== Introduction to the HPC cluster of the physics department ======
  
 The login node of the HPC cluster is ''sheldon.physik.fu-berlin.de''. You can connect to it from anywhere using ssh, e.g. by issuing ''ssh sheldon.physik.fu-berlin.de'' on the command line or using putty from windows. The login node of the HPC cluster is ''sheldon.physik.fu-berlin.de''. You can connect to it from anywhere using ssh, e.g. by issuing ''ssh sheldon.physik.fu-berlin.de'' on the command line or using putty from windows.
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 ===== Submitting a job to the HPC cluster ===== ===== Submitting a job to the HPC cluster =====
  
-In oder to do any calculations on the HPC cluster **you have to submit your jobs to the queuing system** using the ''qsub'' command. You may not login to a compute node and start interactive calculations at any time.+In order to do any calculations on the HPC cluster **you have to submit your jobs to the queuing system** using the ''qsub'' command. You may not login to a compute node and start interactive calculations at any time.
  
 You submit jobs to the queuing system by writing a job-script which tells the queuing system about the resources your job needs and about the programs which are to be run. Basically the job-script is a shell script with some magic comments at the top (lines starting with ''#PBS'') which are parsed by the queuing system. You submit jobs to the queuing system by writing a job-script which tells the queuing system about the resources your job needs and about the programs which are to be run. Basically the job-script is a shell script with some magic comments at the top (lines starting with ''#PBS'') which are parsed by the queuing system.
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 Please try to use local disk space on the compute nodes whenever possible. Since access to local storage is faster than access to your $PBS_O_WORKDIR, this will most likely speed up your compute jobs. At the same time it reduces the load on the central home-server. However, do not forget to copy back data from the compute nodes to $PBS_O_WORKDIR after the job has finised, since the local disk space will be cleared once your job-script ha finished. The following advanced job-script is using local disk space. Please try to use local disk space on the compute nodes whenever possible. Since access to local storage is faster than access to your $PBS_O_WORKDIR, this will most likely speed up your compute jobs. At the same time it reduces the load on the central home-server. However, do not forget to copy back data from the compute nodes to $PBS_O_WORKDIR after the job has finised, since the local disk space will be cleared once your job-script ha finished. The following advanced job-script is using local disk space.
  
-=== Complicated job-script example running CP2K using MPI on 12 nodes with 8 cores each ===+=== Advanced job-script example running CP2K using MPI on 12 nodes with 8 cores each ===
  
 <code> <code>
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 export seq=`cat seq` export seq=`cat seq`
 awk 'BEGIN{printf "%2.2d\n",ENVIRON["seq"]+1}' > seq awk 'BEGIN{printf "%2.2d\n",ENVIRON["seq"]+1}' > seq
- 
  
 infile=${flag}.inp infile=${flag}.inp
services/cluster/queuing-system.txt · Last modified: 2014/06/11 14:40 by dreger
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