[gmx-users] template parallelization

[Mark Abraham]

Hi,

It would seem your GROMACS installation was originally configured to build
with thread-MPI, which definitely would produce the errors you're seeing.
Whether you can successfully build an MPI program from the template is
unknown (nobody's tried), but installing GROMACS configured to use the same
MPI library as you intend to use with the template would probably be
needed. I would suggest you not attempt to parallelize your program until
you know you need to - most analysis tasks are I/O bound, not compute bound.

Mark

On Tue, Mar 10, 2015 at 5:16 PM, Chandan Choudhury <iitdckc at gmail.com>
wrote:

> 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...”*
> --
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