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| cluster:queuing-system [2012/03/02 19:23] – [The job-script] dreger | services:cluster:queuing-system [2012/10/18 17:26] – pneuser |
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| ====== Getting started with the HPC cluster ====== | ====== Introduction to the HPC cluster of the physics department ====== |
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| 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. |
| | walltime | seconds, or [[HH:]MM:]SS | Maximum amount of real time during which the job can be in the running state. The job will be terminated once this limit is reached. | **walltime=100:00:00** -> request 100 hours for this job | walltime=1:00:00 (1 hour) | | | walltime | seconds, or [[HH:]MM:]SS | Maximum amount of real time during which the job can be in the running state. The job will be terminated once this limit is reached. | **walltime=100:00:00** -> request 100 hours for this job | walltime=1:00:00 (1 hour) | |
| | pmem | size* | Maximum amount of physical memory used by any single process of the job. In our case this means per core. | **pmem=8gb** -> request 8gb RAM per core | pmem=2gb | | | pmem | size* | Maximum amount of physical memory used by any single process of the job. In our case this means per core. | **pmem=8gb** -> request 8gb RAM per core | pmem=2gb | |
| | file | size* | The amount of total **local disk space** requested for the job. The space can be accessed at /local_scratch/$PBS_JOBID | **file=10gb** -> request 10 gigabytes of local disk space on each compute node | none | | | file | size* | The amount of **local disk space per core per node** requested for the job. The space can be accessed at /local_scratch/$PBS_JOBID | **file=10gb** -> request 10 gigabytes of local disk space on each compute node for each core used | none | |
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| **size* format** = integer, optionally followed by a multiplier {b,kb,mb,gb,tb} meaning {bytes,kilobytes,megabytes,gigabytes,terabytes}. no suffix means bytes. | **size* format** = integer, optionally followed by a multiplier {b,kb,mb,gb,tb} meaning {bytes,kilobytes,megabytes,gigabytes,terabytes}. no suffix means bytes. |
| 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. |
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| === 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 === |
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| <code> | <code> |
