Can you post your config.h file here? The C compiler for pmemd _should_ be
mpicc, which should provide the proper include paths so that "mpi.h" should
be found. Furthermore, the CUDA compilers should get the MPI include path
as well, so you should see a line that looks like
PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
-I/mpi/intel-12.1.0/mpich2-1.4.1p1/include
in your config.h. The key component is the last one, which is
"-I/path/to/mpi/include" so that the CUDA source files know about the MPI
header file. If something went wrong, then it'll look like
PMEMD_CU_INCLUDES=-I$(CUDA_HOME)/include -IB40C -IB40C/KernelCommon
-I/include
which I think indicates that you have not applied the bug fixes (which you
should definitely do).
HTH,
Jason
On Wed, Jan 25, 2012 at 2:53 PM, Massimiliano Porrini <M.Porrini.ed.ac.uk>wrote:
> Hi all,
>
> After having applied all the bugfixes for AT1.5 and Amber11, I've just
> finished successfully
> installing and testing AT1.5 (serial and parallel), Amber11 (serial
> and parallel) and pmemd.cuda
> (and it worked fine on all the 3 GPUs I have in my machine),
> but when I try to install the parallel version of it (pmemd.cuda.MPI):
>
> cd $AMBERHOME/AmberTools/src/
> make clean
> ./configure -cuda -mpi gnu
> cd ../../
> ./AT15_Amber.py
> cd src/
> make clean
> make cuda_parallel
>
> I get the following error (the last excerpt is reported):
>
>
> ##############################################################################
> *****
> *****
> *****
> gputypes.h:1249: warning: ‘_gpuContext::pbImageSoluteAtomID’ will be
> initialized after
> gputypes.h:1217: warning: ‘GpuBuffer<unsigned int>*
> _gpuContext::pbNLExclusionList’
> gputypes.cpp:438: warning: when initialized here
> gputypes.h:1229: warning: ‘_gpuContext::pbNLPosition’ will be initialized
> after
> gputypes.h:1219: warning: ‘GpuBuffer<uint2>*
> _gpuContext::pbNLNonbondCellStartEnd’
> gputypes.cpp:438: warning: when initialized here
> gputypes.h:1269: warning: ‘_gpuContext::pbConstraintSolventConstraint’
> will be initialized after
> gputypes.h:1195: warning: ‘PMEDouble _gpuContext::ee_plasma’
> gputypes.cpp:438: warning: when initialized here
> /usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode
> arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA
> -DMPI -DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C
> -IB40C/KernelCommon -I/usr/include -c kForcesUpdate.cu
> In file included from gpu.h:15,
> from kForcesUpdate.cu:14:
> gputypes.h:30:17: error: mpi.h: No such file or directory
> make[3]: *** [kForcesUpdate.o] Error 1
> make[3]: Leaving directory `/home/max/amber11/src/pmemd/src/cuda'
> make[2]: *** [-L/usr/local/cuda/lib64] Error 2
> make[2]: Leaving directory `/home/max/amber11/src/pmemd/src'
> make[1]: *** [cuda_parallel] Error 2
> make[1]: Leaving directory `/home/max/amber11/src/pmemd'
> make: *** [cuda_parallel] Error 2
>
> ##############################################################################
>
>
> Thanks as always for any prospective hints about this issue.
>
> Best,
>
> Il 21 gennaio 2012 15:28, Jason Swails <jason.swails.gmail.com> ha
> scritto:
> > If that is the same config.h file as before, then AT15_Amber11.py has
> not been run (which also means that not all of the AmberTools bug fixes
> have been applied.
> >
> > Either run that script or apply all of the bug fixes for both Amber 11
> and AmberTools 1.5.
> >
> > You can see detailed instructions at http://jswails.wikidot.com where
> there is a page dedicated to installing Amber 11 and AmberTools 1.5.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
> > On Jan 21, 2012, at 7:35 AM, Massimiliano Porrini <mozz76.gmail.com>
> wrote:
> >
> >> Sorry, here is the config.h file.
> >> Cheers,
> >>
> >>
> >> Dr Massimiliano Porrini
> >> Institute for Condensed Matter and Complex Systems
> >> School of Physics & Astronomy
> >> The University of Edinburgh
> >> James Clerk Maxwell Building
> >> The King's Buildings
> >> Mayfield Road
> >> Edinburgh EH9 3JZ
> >>
> >> Tel +44-(0)131-650-5229
> >>
> >> E-mails : M.Porrini.ed.ac.uk
> >> mozz76.gmail.com
> >> maxp.iesl.forth.gr
> >>
> >> Begin forwarded message:
> >>
> >>> From: max.complexity1.site
> >>> Date: 21 January 2012 12:17:31 GMT
> >>> To: mozz76.gmail.com
> >>> Subject: Amber11 cuda config file
> >>>
> >>> Amber11 cuda config file created via ./config cuda gnu
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
>
> Tel +44-(0)131-650-5229
>
> E-mails : M.Porrini.ed.ac.uk
> mozz76.gmail.com
> maxp.iesl.forth.gr
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jan 25 2012 - 12:30:05 PST
