[gmx-users] REMD and swaplist

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 23 09:55:09 CEST 2004

On Sun, 2004-08-22 at 23:48, Patricia Soto Becerra wrote:
> Hi List!
> I am trying the code of REMD in gromacs3.1.4 designed by Luca and Walter.
> I have tried it in an *old* cluster and it runs very nice!!
> But when I run it on a new cluster under scali, the simulation gets
> *frozen* after ~ 5 minutes of being running.
> It stops at the point where (to my understanding) the communication
> between nodes takes place:
> ***** Master says: this is the IDTswaplist
> (the simulation is reported to be running but does not do anything else
> after this point)

check with the system administrator, or if you are the system
administrator, check with Scali. I have had lots of problems where
arbitrary calculations using Scali would cause kernel panics on
machines, due to bugs in either the Scali hardware or the mpi library.

> What is more strange is that the simulation has already had communication
> between nodes (i.e. swaping has taken place before).
> Has anybody faced this problem? I am not familiar with mpi programming but
> I wonder whether this is a problem of the code or a problem of scali (of
> course the system manager of my group claims that scali is working
> properly...)
> Standard parallel jobs of gromacs 3.2.1 run on that new cluster (with
> scali) without any problem!
> Does anybody have any suggestion for this problem??
> thanks in advance!,
> patricia.
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. Patricia Soto
> Post-doctoral Researcher
> Department of Chemistry and Biochemistry
> University of California, Santa Barbara CA 93106 - 9510 
> United States
> **Como bien nos ensena la vida, la verdad es una aspiracion inalcanzable
> que, en todo caso, habita al otro lado del muro que forman las
> innumerables verdades que cada uno sostenemos por convencimiento o por
> intereses mas o menos legitimos**  Jesus A. Nunez Villaverde, 03-08-04
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone:  +46 18 471 4205  fax: +46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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