[AMBER] amber12's performance on AMD

From: <wl2290.columbia.edu>
Date: Thu, 18 Jul 2013 15:36:20 -0400

We are having problem running Amber12/pmemd.MPI on a 512 core (16
computing nodes) cluster.

We installed amber12 using openmpi 1.6.5, and running pmemd.MPI on a
Linux cluster (OS is OpenSuse 11.4). Each node has 32 cores, and the
CPU type and system info is as below:
model name: AMD Opteron Processor 6274
cpu 2200 MHz
cache size 2048 KB
memory size: 64 GB.

Network is 1 gigabit ethernet.

Our benchmarks showed that the performance only using one node (32
cores) almost matched the speed on an 8yr old cluster (4core AMD
Opteron 8GB ram on each node, using a total of 68 cores). But when
used more than 2 nodes (64, 128, ..., or 512 cores), the performance
is several times slower than using only one node (32 cores).

We tried using different numbers of nodes, or core per nodes, but have
no success so far.

The new cluster has no problem with other program such as MDFF, which
scales almost linearly.

Thank you!

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Received on Thu Jul 18 2013 - 13:00:03 PDT
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