[gmx-users] MPICH2 and parallel Gromacs errors

[Art Poon]

Hi Richard,

I don't know about Gromacs specifically, but our users have had more  
luck getting MPI functionality for our software on Mac clusters/multi- 
core computers with OpenMPI.

Cheers,
- Art.


On Jun 20, 2008, at 9:43 AM, Casey,Richard wrote:

> Hello,
>
> This issue appears to have been encountered by many people.  We've  
> searched the discussion archives and tried every recommended  
> solution but no luck.
>
> We have MPICH2 v.1.0.7 installed on an Apple G5 cluster (64 CPU's).  
> And installed Gromacs v.3.3.3 with --enable-mpi option.
>
> Single CPU jobs run OK; parallel jobs always fail.  For parallel  
> jobs we use:
>
> grompp -v -np 2 -p topol.top (or other values for np for more cpu's)
>
> We launch MPD with:
>
> mpdboot -n 2 -f /common/mpich2/mpd.hosts
>
> We run jobs with:
>
> /common/mpich2/bin/mpiexec -l -n 2 \
> /common/gromacs/bin/mdrun_mpi -v -np 2 \
>  -s /Users/richardcasey/topol.tpr \
>  -g /Users/richardcasey/md.log \
>  -e /Users/richardcasey/ener.edr \
>  -o /Users/richardcasey/traj.trr \
>  -x /Users/richardcasey/traj.xtc \
>  -c /Users/richardcasey/confout.gro
>
>
> The output always says:
>
> -------------------------------------------------------
> 1: Program mdrun_mpi, VERSION 3.3.3
> 1: Source code file: init.c, line: 69
> 1:
> 1: Fatal error:
> 1: run input file /Users/richardcasey/topol.tpr was made for 2 nodes,
> 1: p0_29762:  p4_error: : -1
> 1:              while mdrun_mpi expected it to be for 1 nodes.
> 1: -------------------------------------------------------
>
>
> We've tried everything (many variations on the above and  
> recommendations from the discussion list) but for some reason  
> mdrun_mpi insists that it use a single-cpu version of the topology  
> file.  We've check environment variables and they appear to point to  
> the right directories. /common is NFS mounted on all nodes.
>
> Completely stumped - no idea what is wrong here.  Any suggestions?
>
>
>
> --------------------------------------------
> Richard Casey
>
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        ___,–––– Dr. Art FY Poon
     __/   `–– Division of Comparative Pathology and Medicine
___/  \____ Department of Pathology
    \___ University of California, San Diego