MPI is installed in a manner the configure script doesn't recognize. A
long-term fix is needed for this, but in the meantime, what Jason said will
work once you locate the correct mpi.h for whatever MPI (if any) is
installed on your machine.
Scott
On Sat, Mar 24, 2012 at 9:38 AM, Adam Jion <adamjion.yahoo.com> wrote:
> Hi,
>
> This was my command line:
> adam.adam-MS-7750:~/amber11/src$ make cuda_parallel
>
>
> And this is the error I got (last 30 lines):
> make -C ./cuda
> make[3]: Entering directory `/home/adam/amber11/src/pmemd/src/cuda'
> cpp -traditional -DMPI -P -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
> -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT -DCUDA -DMPI
> -DMPICH_IGNORE_CXX_SEEK cuda_info.fpp cuda_info.f90
> mpif90 -O3 -mtune=generic -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/include -c
> cuda_info.f90
> mpicc -O3 -mtune=generic -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/include -c
> gpu.cpp
> mpicc -O3 -mtune=generic -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI -DMPICH_IGNORE_CXX_SEEK
> -I/usr/local/cuda/include -IB40C -IB40C/KernelCommon -I/usr/include -c
> gputypes.cpp
> /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: fatal error: mpi.h: No such file or directory
> compilation terminated.
> make[3]: *** [kForcesUpdate.o] Error 1
> make[3]: Leaving directory `/home/adam/amber11/src/pmemd/src/cuda'
> make[2]: *** [-L/usr/local/cuda/lib64] Error 2
> make[2]: Leaving directory `/home/adam/amber11/src/pmemd/src'
> make[1]: *** [cuda_parallel] Error 2
> make[1]: Leaving directory `/home/adam/amber11/src/pmemd'
> make: *** [cuda_parallel] Error 2
>
> Very appreciative of your help,
> Adam
>
> ps. Amber 11 (Serial + Parallel) + Single GPU works well. So I'm really
> wondering what's going on...
>
>
>
>
> ________________________________
> From: Jason Swails <jason.swails.gmail.com>
> To: Adam Jion <adamjion.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Saturday, March 24, 2012 11:17 PM
> Subject: Re: [AMBER] Error Compiling pmemd.cuda.MPI (i.e. Multiple GPUs)
>
>
> It would help to see more of your error message (i.e. the compile line
> that failed, so we know what directories were searched for in the include
> path).
>
> Another option is to set MPI_HOME (such that mpif90 is in
> $MPI_HOME/bin/mpif90), and re-run configure
>
> (./configure -mpi -cuda [gnu|intel])
>
> This should have been grabbed by default inside configure, but it's
> possible you have a funky configuration.
>
> HTH,
> Jason
>
> P.S., alternatively, if you know where this include file lives, just add
> that directory to the NVCC compiler flags in config.h and just re-run "make"
>
>
> On Sat, Mar 24, 2012 at 9:03 AM, Adam Jion <adamjion.yahoo.com> wrote:
>
> Hi!
> >
> >I have problems compiling pmemd.cuda.MPI. (However, the single gpu
> version -pmemd.cuda - works)
> >The error log is:
> >
> >In file included from gpu.h:15,
> > from kForcesUpdate.cu:14:
> >gputypes.h:30: fatal error: mpi.h: No such file or directory
> >compilation terminated.
> >make[3]: *** [kForcesUpdate.o] Error 1
> >make[3]: Leaving directory `/home/adam/amber11/src/pmemd/src/cuda'
> >make[2]: *** [-L/usr/local/cuda/lib64] Error 2
> >make[2]: Leaving directory `/home/adam/amber11/src/pmemd/src'
> >make[1]: *** [cuda_parallel] Error 2
> >make[1]: Leaving directory `/home/adam/amber11/src/pmemd'
> >make: *** [cuda_parallel] Error 2
> >
> >
> >Any help will be much appreciated,
> >Adam
> >
> >ps. All the bugfixes have been applied. I have managed to combine both
> serial and parallel versions of Amber11 and AmberTools 1.5 without
> problems. My compilers are gcc-4.4, g++-4.4, gfortran-4.4.
> >_______________________________________________
> >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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Mar 24 2012 - 10:00:04 PDT
