Hi,
Try adding your MPI distribution's include directory to the
environment variable CPATH, assuming you are using GNU compilers, e.g.
(bash)
export CPATH=$MPICH_DIR/include:$CPATH
(assuming MPICH_DIR is set). For intel compilers I think the variable
is C_INCLUDE PATH.
Hope this helps,
-Dan
On Fri, Apr 25, 2014 at 9:24 PM, zottisad <zottisad.iq.unesp.br> wrote:
> Dear Sirs,
>
> I am facing many installation problems with Amber12. My machine is a
> 64bit Linux Ubuntu 12.04. I do not know if it is the case, but it seems
> a problem with the compatibility with my NVidia GTX 650Ti when I try to
> install with mpi and cuda (./configure -cuda -mpi gnu). Running
> configure is ok, but make install returns errors. If this is the case,
> is still there any possibility to use cuda (my version is 5.5) with two
> graphics cards (GTX 650Ti)? Messages returned after command make install
> are as follow:
>
> mpif90 -DMPI -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC -DPUBFFT -O3 -mtune=native -DCUDA -DMPI
> -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -I/usr/local/cuda-5.5/include -IB40C
> -IB40C/KernelCommon -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi -c cuda_info.F90
> mpicc -O3 -mtune=native -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI
> -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -I/usr/local/cuda-5.5/include -IB40C
> -IB40C/KernelCommon -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi -c gpu.cpp
> In file included from gpu.cpp:29:0:
> gputypes.h:30:17: fatal error: mpi.h: No such file or directory
> compilation terminated.
> make[5]: *** [gpu.o] Error 1
> make[5]: Leaving directory
> `/home/aderson/Amber12/amber12/src/pmemd/src/cuda'
> make[4]: *** [cuda/cuda.a] Error 2
> make[4]: Leaving directory
> `/home/aderson/Amber12/amber12/src/pmemd/src'
> make[3]: *** [cuda_parallel] Error 2
> make[3]: Leaving directory `/home/aderson/Amber12/amber12/src/pmemd'
> make[2]: *** [cuda_parallel] Error 2
> make[2]: Leaving directory `/home/aderson/Amber12/amber12/src'
> make[1]: [cuda_parallel] Error 2 (ignored)
> make[1]: Leaving directory
> `/home/aderson/Amber12/amber12/AmberTools/src'
> make[1]: Entering directory `/home/aderson/Amber12/amber12/src'
> Starting installation of Amber12 (cuda parallel) at Fri Apr 25 16:12:38
> BRT 2014.
> cd pmemd && make cuda_parallel
> make[2]: Entering directory `/home/aderson/Amber12/amber12/src/pmemd'
> make -C src/ cuda_parallel
> make[3]: Entering directory
> `/home/aderson/Amber12/amber12/src/pmemd/src'
> make -C ./cuda
> make[4]: Entering directory
> `/home/aderson/Amber12/amber12/src/pmemd/src/cuda'
> mpicc -O3 -mtune=native -DMPICH_IGNORE_CXX_SEEK -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI -DCUDA -DMPI
> -DMPICH_IGNORE_CXX_SEEK -Duse_SPFP -I/usr/local/cuda-5.5/include -IB40C
> -IB40C/KernelCommon -I/usr/lib/openmpi/include
> -I/usr/lib/openmpi/include/openmpi -c gpu.cpp
> In file included from gpu.cpp:29:0:
> gputypes.h:30:17: fatal error: mpi.h: No such file or directory
> compilation terminated.
> make[4]: *** [gpu.o] Error 1
> make[4]: Leaving directory
> `/home/aderson/Amber12/amber12/src/pmemd/src/cuda'
> make[3]: *** [cuda/cuda.a] Error 2
> make[3]: Leaving directory
> `/home/aderson/Amber12/amber12/src/pmemd/src'
> make[2]: *** [cuda_parallel] Error 2
> make[2]: Leaving directory `/home/aderson/Amber12/amber12/src/pmemd'
> make[1]: *** [cuda_parallel] Error 2
> make[1]: Leaving directory `/home/aderson/Amber12/amber12/src'
> make: *** [install] Error 2
>
> Any suggestion on how to solve this would be very welcome.
> Thanks in advance.
>
> Aderson Zottis, PhD
> Department of Biochemistry and Technological Chemistry
> Araraquara Institute of Chemistry at UNESP
> Araraquara - Brazil
> email: zottisad.iq.unesp.br
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Apr 25 2014 - 21:30:03 PDT
