[MITgcm-support] Parallel performance

[Patrick Heimbach]

Elena,

in your 'data' parameter file, in the namelist block PARM05
you can set
  mdsioLocalDir = '/mylocaldirectory/blabla'

This will write some output to this directory,
but not sure whether it's all output (I'd need to check again)
Can you try.

-Patrick



On Friday 17 June 2005 19:14, eyulaeva at ucsd.edu wrote:
  > Hello:
  > I  am running a 57b_post version of the MIT model (forward run) at linux
  > cluster and have the same problem of slow I/O
  > Is it possible to specify the path to the local (per node)  directory, so
  > that O/I files are written/read locally without modifying fortran code?
  >
  > Thanks
  > Elena
  >
  > > Hi Kevin,
  > > I had similar problems when I ported the code from an IBM SP4 to a
  > > linux cluster that seems similar to yours (Opteron 64, Rocks OS, Sun
  > > Grid Engine,
  > > ethernet network). Basically the bad performances when using multiple
  > > procs
  > > were due to I/O problems. SP4 has a very fast I/O scratch filesystem so
  > > I could make the model read and write files on that disk without
  > > problems (also using the GlobalFiles=.TRUE. option in PARM01 in the
  > > data file). The same configuration on the new cluster using NFS
  > > filesystem gave rise to very
  > > slow simulations. I solved the problem simply splitting the run on
  > > every CPU: before the beginnig of the simulation I copy the input files
  > > and the executable on each disk (via scp) then I start the run with
  > > GlobalFiles=.FALSE. and, at the end of the simulation, I copy the
  > > output back to the front-end node.
  > > Are you using the GlobalFiles=.TRUE. option in PARM01 in the data file?
  > > Maybe this is not the solution for your problem but a check on the I/O
  > > could
  > > be useful!
  > > Good luck!
  > >
  > > Stefano
  > >
  > > P.S.: updating the code to more recent versions is not so difficult and
  > > VERY
  > > useful, I suggest you to try a newer checkpoint (lots of new features
  > > and bugs fixed)!
  > >
  > >
  > > ----- Original Message -----
  > > From: "Kevin Oliver" <K.Oliver at uea.ac.uk>
  > > To: <mitgcm-support at mitgcm.org>
  > > Sent: Thursday, June 16, 2005 2:01 PM
  > > Subject: [MITgcm-support] Parallel performance
  > >
  > >> Hello,
  > >>
  > >> I wonder if anyone can help me with a problem I have regarding running
  > >> the
  > >> model in parallel. We
  > >> have just started running MIT model running on a new cluster: Opteron
  > >> 64 bit Susa 9.1, Sun Grid
  > >> Engine, linux platform, myrinet network (running release 1 patch 8 -
  > >> this
  > >> was the version I could
  > >> get to work on an older system). Presumably because not everything is
  > >> set
  > >> up optimally, we get
  > >> disappointing performance results running the MIT model in parallel.
  > >>
  > >> The experiment I have done uses a 120x120x40 domain. OLx and OLy are
  > >> both
  > >> 3 and all diffusion is
  > >> Laplacian. I've run it with 1x1 and 4x4 subgrids (and several other
  > >> combinations in between).
  > >> Through-put increases more-or-less monotonically with the number of
  > >> processers used, but the 4x4
  > >> expriment is only 20% faster than the 1x1 experiment. Delays due to
  > >> competition in the queue are not
  > >> an issue.
  > >>
  > >> Has looked at how the performance scales with multiple processors on a
  > >> similar setup, so we know
  > >> what we should be aiming for? Also, is there anything I need to look
  > >> out for in the code (e.g.
  > >> switches) which could affect performance?
  > >>
  > >> Many thanks for your time,
  > >>
  > >> Kevin
  > >>
  > >> _________________________
  > >> Dr Kevin Oliver
  > >> Senior Research Associate
  > >> School of Environmental Sciences
  > >> University of East Anglia
  > >> Norwich, NR4 7TJ
  > >> United Kingdom
  > >> ________________________
  > >>
  > >> _______________________________________________
  > >> MITgcm-support mailing list
  > >> MITgcm-support at mitgcm.org
  > >> http://mitgcm.org/mailman/listinfo/mitgcm-support
  > >
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  >
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-- 
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Patrick Heimbach     Massachusetts Institute of Technology
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