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CHARMM cpu usage on a cluster
#174 10/20/03 09:36 AM
Joined: Oct 2003
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tjaart Offline OP
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We are currently running CHARMM on a 32 cpu Linux cluster. When we check the workload of each node we see that CHARMM only uses about 1% of 31 nodes and almost a 100% of one node. Shouldn't the workload be distributed across all the nodes equally?
Can you change this workload by adjusting the priorities given to CHARMM jobs?

Thanks!!!


Tjaart de Beer
Re: CHARMM cpu usage on a cluster
tjaart #175 10/20/03 10:36 AM
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You should see an almost equal load on all nodes. Certain tasks are however not parallelized (see parallel.doc) and then you will see that only one node is being used. We typically run simulations (and sometimes also long minimizations) in parallel, leaving setup and analysis to be performed on a single CPU.
There is a penalty (communications overhead) for using more than one CPU, and you have to determine for yourself what is the optimum number to use with your system. Remember that in benchmarking parallel jobs it is the elapsed time, not the CPUtime that is important.


Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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