[gmx-users] template parallelization

[Chandan Choudhury]

Dear gmx users,

I am trying to parallelize execute the template (gmx 4.6.3), but unable to
do so.

When I just include the header file of mpi
#include<mpi.h> in the header section of template, and then compile (export
CC=mpicc; make -f Makefile), it generates a lot of error:

Output:
mpicc  `pkg-config --cflags libgmx`  -c -o template.o template.c
In file included from template.c:46:0:
/opt/openmpi-1.6/include/mpi.h:319:37: error: conflicting types for
'MPI_Comm'
In file included from
/opt/apps/gmx/463/single/include/gromacs/types/commrec.h:46:0,
                 from /opt/apps/gmx/463/single/include/gromacs/futil.h:44,
                 from /opt/apps/gmx/463/single/include/gromacs/filenm.h:42,
                 from template.c:39:
/opt/apps/gmx/463/single/include/gromacs/types/../thread_mpi/mpi_bindings.h:66:28:
note: previous declaration of 'MPI_Comm' was here
In file included from template.c:46:0:
/opt/openmpi-1.6/include/mpi.h:320:33: error: conflicting types for
'MPI_Datatype'
In file included from
/opt/apps/gmx/463/single/include/gromacs/types/commrec.h:46:0,
                 from /opt/apps/gmx/463/single/include/gromacs/futil.h:44,
                 from /opt/apps/gmx/463/single/include/gromacs/filenm.h:42,


and many more.

I donot understand how to get rid of these errors and conflicts.
Does any one has experience in parallelizing the template or can someone
guide me to parallelize it.

Thanks
Chandan


-- 

Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India

*"All work and no play makes Jack a dull boy...”*