[gmx-developers] thread problem on AMD 12 core chips?

[Ake Sandgren]

On Thu, 2012-01-12 at 13:18 +0100, David van der Spoel wrote:
> On 2012-01-12 11:36, Berk Hess wrote:
> > On 01/12/2012 11:24 AM, David van der Spoel wrote:
> >> On 2012-01-12 11:17, Berk Hess wrote:
> >>> Which compiler is this?
> >>> We get lots of warnings with gcc4.6, but we run regularly on 32 and 64
> >>> core nodes.
> >>
> >> Thread model: posix
> >> gcc version 4.4.3 (Ubuntu 4.4.3-4ubuntu5)
> >>
> >> Is intel more reliable?
> > This is not a matter of platform I would think.
> > We have only used AMD platform with 32 or more MPI threads.
> > I would guess this is a thread-mpi bug or a compiler issue.
> Compiling with Intel C 12.0.3.174 gives the same error, but the same 
> pthread library is linked in.
> 
> Other tips for debugging this?
> 
> >
> > Berk
> >>>
> >>> Berk
> >>>
> >>> On 01/12/2012 11:04 AM, David van der Spoel wrote:
> >>>> Hi,
> >>>>
> >>>> I'm trying to compile and install gromacs release-4-5-patches on a new
> >>>> cluster with four 12-core AMD chips (abisko in Umea, Sweden). However
> >>>> the threaded code bails out with the following message:
> >>>>
> >>>> Reading file topol.tpr, VERSION 4.5.5-dev-20120111-9181e (double
> >>>> precision)
> >>>> Starting 32 threads
> >>>> tMPI error: tMPI Initialization error (in valid comm)
> >>>>
> >>>> First, I'm a bit confused why the code detects only 32 cores, second
> >>>> it shows above error and quits.
> >>>>
> >>>> Any clues?


Abisko's current nodes are 4-socket 8-core (the 12-cores are still under
test)

If you are using openmpi it does not have support for MPI threads
compiled in (the openib part of openmpi doesn't support this yet) that
probably explains your problem.