[gmx-users] REMD and swaplist

Patricia Soto Becerra psoto at ultra.chem.ucsb.edu
Sun Aug 22 23:48:19 CEST 2004

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)

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

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!,


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
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intereses mas o menos legitimos**  Jesus A. Nunez Villaverde, 03-08-04


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