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Article ID: 107 - Last Modified: May 4, 2011

I have cluster nodes with two Intel Westmere 6 core CPUs and a PBS-like queuing system. How should I configure my schrodinger.hosts file for parallel applications like Desmond?

In this case, it might be easiest to define a few schrodinger.hosts file entries for the most common cpu requests. For example:

name: cores_16
host: head
queue: PBS
qargs: -q batch -l

name: cores_32
host: head
queue: PBS
qargs: -q batch -l nodes=2:ppn=12+nodes=1:ppn=8

In general, though, trying to minimize the number of nodes per job when each node contains 12 cores is going to be a bit awkward, since Desmond prefers jobs to be split across a number of processors that is a power of 2, and you will necessarily end up with an asymmetric load across nodes. From Suite 2011 on you can choose powers of 3 or 5 as well when starting jobs from Maestro or the command line, so a 2x2x3 distribution is possible for 12 cores.

Furthermore, the processes on each node with be contending for the same network interface, which will be a significant bottleneck, especially if you are using GigE. For Desmond, we generally recommend that if a job cannot be completely placed on a single node, then it is best to spread it across as many nodes as possible. With that in mind, you could also try something like this:

name: cores_N
host: head
queue: PBS
qargs: -q batch -l

Keywords: cpu toplogy westmere schrodinger.hosts

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