[gmx-developers] MPI_ERR_COMM on 4.5.5-patches
hess at kth.se
Tue Aug 28 22:41:23 CEST 2012
I think I might have found it already.
Could you try the fix below and report back if this solved the problem?
index 735c0e8..e00fa6f 100644
@@ -1814,8 +1814,11 @@ static void init_atomcomm(gmx_pme_t
pme,pme_atomcomm_t *atc, t_commrec *cr,
if (pme->nnodes > 1)
atc->mpi_comm = pme->mpi_comm_d[dimind];
+ if (atc->mpi_comm != MPI_COMM_NULL)
On 08/28/2012 10:34 PM, Berk Hess wrote:
> This seems to be a bug in Gromacs.
> As this is not in a Gromacs release yet, we could resolve this without
> a bug report.
> A you skilled enough that you can run this in a debugger and tell me
> which MPI_comm_size
> call in Gromacs is causing this?
> On 08/28/2012 07:39 PM, Alexander Schlaich wrote:
>> Dear Gromacs team,
>> I just tried to install the release-4.5.5_patches branch with
>> --enable-mpi on our cluster (OpemMPI-1.4.2), resulting in an error
>> when calling mdrun whith pme enabled:
>> Reading file topol.tpr, VERSION 4.5.5-dev-20120810-2859895 (single
>> [sheldon:22663] *** An error occurred in MPI_comm_size
>> [sheldon:22663] *** on communicator MPI_COMM_WORLD
>> [sheldon:22663] *** MPI_ERR_COMM: invalid communicator
>> [sheldon:22663] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
>> This seems to be related to a recent post on the list, however I
>> could not find a solution:
>> However, the 4.5.5 release version works fine.
>> Taking a closer look I found commit
>> dcf8b67e2801f994dae56374382b9e330833de30, "changed PME MPI_Comm
>> comparisions to MPI_COMM_NULL, fixes #931" (Berk Hess). Apparently
>> here the communicators were changed such that the initialization
>> fails on my system. Reverting this single commit on the head of the
>> release-4.5.5 branch solved the issue for me.
>> As I am no MPI expert I would like to know if my MPI implementation
>> is misbehaving here, if I made a configuration mistake or if I should
>> file a bug report?
>> Thanks for your help,
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