actually, at my group, we have pmemd.cuda.mpi working with openmpi:
the solution:
> When compiling pmemd.cuda.MPI, we have to manually add to PMEMD_CU_LIBS in
> config.h the -lmpi_cxx flag:
>
> PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib
> -lcurand -lcufft -lcudart
>
> changed to:
>
> PMEMD_CU_LIBS=./cuda/cuda.a -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib
> -lcurand -lcufft -lcudart -lmpi_cxx
>
i hope this is helpful!
igor
Igor Marques, *Researcher*
MSc in Pharmaceutical Biomedicine
BSc in Biomedical Sciences
Molecular Modeling Group – University of Aveiro
http://molecular-modeling.dq.ua.pt/
Mobile phone: +351 918 567 294
Phone: +351 234 370 200 Ext: 22102
Campus Universitario de Santiago
Edificio III
3810-193 Aveiro
Portugal
On Fri, Apr 12, 2013 at 4:05 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> >Did you follow the above advice? It looks like you are using openMPI;
> >which
> >case, I'm not sure whether or not it will work with pmemd.cuda.MPI. You
> >will
> >need at least version 1.5 or later (and, in fact, even that might not
> >actually
> >work. If anyone on the list has current knowledge of how openMPI is or
> >is not
> >compatible with pmemd.cuda.MPI, please post some info.)
>
> I have never been successful in getting OpenMPI to work with the GPU code
> - as far as I can tell it is NOT completely MPI v2 compatible. I gave up a
> while ago on it and switched to MPICH2 and/or MVAPICH2. It is a shame that
> all the various Linux installations choose to include OpenMPI as their
> default (and in the PATH :-( ) MPI.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
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Received on Fri Apr 12 2013 - 11:00:03 PDT
