I haven't seen anything like this in my machines either. I have versions
compiled with the intel and gnu compilers both with OpenMPI 1.4.1 and MPICH2
1.2.1 (4 MPI's that are well-organized and do not trod on each others'
toes). I've gone up to 4 threads for each and not seen this problem. (I
also tested gnu compilers with the same 2 MPIs on Mac OS X).
The only times I can recall having problems is, I think, when I had an mpd
process (MPICH2) that had been running for days, and a quick mpdallexit;
mpdboot fixed my issues.
If none of your configurations match what I've tried, let me know what was
different and I'll see if I can reproduce it...
All the best,
Jason
On Fri, May 7, 2010 at 9:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> I personally havent seen this before. What compiler(s) are you using, and
> what MPI implementation?
>
> -Dan
>
> On Fri, May 7, 2010 at 2:14 PM, Gustavo Seabra <gustavo.seabra.gmail.com
> >wrote:
>
> > Hi All,
> >
> > I have compiled and tested Amber11 (release version) serial with no
> > problems on Ubuntu 9.10. Now, when I try the parallel version, it
> > compiles fine but some tests just stall. The processes keep running
> > (from "top" I can stil see the sander.MPI processes using all the
> > processor they need), but the calculation never advances.
> >
> > Which test will be a problem is random: I had with PIMD, then when I
> > try again it happens with QM tests, then something else, etc.
> >
> > I have found the following message on the archives:
> > http://structbio.vanderbilt.edu/archives/amber-archive/2009/5928.php
> >
> > But with no replies.
> >
> > Does anyone else experience such problems?
> >
> > Thanks,
> >
> > --
> > Gustavo Seabra
> > Professor Adjunto
> > Departamento de Química Fundamental
> > Universidade Federal de Pernambuco
> > Fone: +55-81-2126-7417
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Postdoctoral Associate
> SAS - Chemistry & Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri May 07 2010 - 19:30:03 PDT
