RE: [AMBER-Developers] infinite ptraj.MPI, was: First AmberTools release candidate

From: Ross Walker <>
Date: Tue, 16 Mar 2010 22:35:12 -0700

> Slowdowns only - my tests compelte. Here are some timing results over
> an NFS
> filesystem for the first part of the ptraj_comprehensive test case (the
> part

If you are trying to run MPI/IO over NFS then I'm not surprised it runs
slower. NFS is utter junk for anything other than serial reads and write.
All you are doing is thrashing things. Probably even more so if the server
on the other end is not a nice spec raid system which can actually do
parallel read and writes properly without adding in 10ms of disk head seek
to every call. You really need a local (sata / SAS based) raid system or a
real parallel filesystem like luster or GPFS to see any benefit of running
ptraj, and thus the I/O in parallel.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Tue Mar 16 2010 - 23:00:03 PDT
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