This document describes how to run your simulations on the CCS oneSIS cluster.
You cannot run simulations directly on the compute nodes. To use the cluster, ssh into the head node ares, then submit your jobs using the PBS queuing system command qsub. Both ares and the compute nodes share /scratch00 and /scratch02 through NFS.
The program qsub allocates compute nodes and runs programs on the compute CPUs. Each compute node can run 2 to 16 simulations depending on the number of CPU cores it has. Memory usage is also a consideration when requesting CPUs during job submission.
NOTE: THE COMPUTE NODES CAN ONLY WRITE TO /scratch00 and /scratch02!! Keep this in mind when writing your scripts.
The compute nodes have no shared libraries and no executables. Any executable you run on the compute nodes must be statically linked for this reason. Here is a sample compile to run on the oneSIS cluster:
>module load intel
>icc -static program.c -o a.out
>mkdir -p /scratch00/john/run1
>cp ./a.out /scratch00/john/run1/
>cp ./data.txt /scratch00/john/run1/
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