[gmx-developers] (no subject)

David spoel at xray.bmc.uu.se
Thu Jun 16 21:30:24 CEST 2005

On Thu, 2005-06-16 at 14:48 -0400, Ken Rotondi wrote:
> Dear Gromacs community,
> Well, it appears we've stumbled across some genuine weirdness here. The 
> CVS version of GROMACS runs on our SGI supercomputer:
> SGI Origin 3800, 128 processor R14000 500 MHz
> SGI Message Passing Toolkit 1.6 (this is SGI's tuned MPI libraries)
> FFTW version 2.1.3 (single-precision, shared libraries, MPI-enabled)
> The issue is, it won't run on more than 24 processors without 
> generating an MPI error, which may be an issue with GROMACS or an issue 
> with something on the SGI.
What kind of system are you testing?

> This is the error message when it dies using more than 24 processors:
> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
> MPI: Received signal 10

This is a USR1 signal, which is very weird, because it can only be
issued by the user. Have you checked md0.log, since processor 0 appears
to be the culprit. 
#define SIGUSR1         10      /* User-defined signal 1 (POSIX).  */

You can also try mdrun -debug (if you have enough disk space)...

> It dumps a nasty core file which doesn't contain usable symbols (We 
> probably need to recompile without stripping the binaries). I've 
> noticed that it also takes a long time to set up before dying compared 
> to the set up and successful run using 24 processors.
> Sorry to post to both developers and users, but I thought it might be a 
> CVS issue.
> Thanks for any insight/help,
> Ken
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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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