Good morning. I am trying to compile pmemd.cuda.MPI from Amber12 but I
am getting the error listed below. I followed a previous thread to
tackle the problem (
http://archive.ambermd.org/201203/0446.html) but I
was not able to make things work. I understand that the problem lies in
that the compiler does not knows were to look for mpi.h.
After typing: find -name mpi.h I get the following output:
./AmberTools/src/mpich2-1.4.1p1/src/include/mpi.h
./AmberTools/src/openmpi-1.5.5/ompi/include/mpi.h
./include/mpi.h
Can anyone point me out how to indicate the compiler were is mpi.h located?
Thank you very much in advance for the help,
best regards
Alfredo
Listed error:
***********************************
aquevedo.mini:~/Programas/Amber12/amber12$ make install
cd AmberTools/src && make install
make[1]: Entering directory
`/home/aquevedo/Programas/Amber12/amber12/AmberTools/src'
AmberTools12 has no CUDA-enabled components
(cd ../../src && make cuda_parallel )
make[2]: Entering directory `/home/aquevedo/Programas/Amber12/amber12/src'
Starting installation of Amber12 (cuda parallel) at Fri Apr 13 12:42:41
ART 2012.
cd pmemd && make cuda_parallel
make[3]: Entering directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd'
make -C src/ cuda_parallel
make[4]: Entering directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src'
make -C ./cuda
make[5]: Entering directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src/cuda'
/opt/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/opt/cuda/include -IB40C
-IB40C/KernelCommon
-I/home/aquevedo/Programas/Amber12/amber12/AmberTools/src/ompi//include
-c kForcesUpdate.cu
In file included from gpu.h:15:0,
from kForcesUpdate.cu:14:
gputypes.h:30:17: fatal error: mpi.h: No such file or directory
compilation terminated.
make[5]: *** [kForcesUpdate.o] Error 1
make[5]: Leaving directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src/cuda'
make[4]: *** [-L/opt/cuda/lib64] Error 2
make[4]: Leaving directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src'
make[3]: *** [cuda_parallel] Error 2
make[3]: Leaving directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory `/home/aquevedo/Programas/Amber12/amber12/src'
make[1]: [cuda_parallel] Error 2 (ignored)
make[1]: Leaving directory
`/home/aquevedo/Programas/Amber12/amber12/AmberTools/src'
make[1]: Entering directory `/home/aquevedo/Programas/Amber12/amber12/src'
Starting installation of Amber12 (cuda parallel) at Fri Apr 13 12:42:41
ART 2012.
cd pmemd && make cuda_parallel
make[2]: Entering directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd'
make -C src/ cuda_parallel
make[3]: Entering directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src/cuda'
/opt/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/opt/cuda/include -IB40C
-IB40C/KernelCommon
-I/home/aquevedo/Programas/Amber12/amber12/AmberTools/src/ompi//include
-c kForcesUpdate.cu
In file included from gpu.h:15:0,
from kForcesUpdate.cu:14:
gputypes.h:30:17: fatal error: mpi.h: No such file or directory
compilation terminated.
make[4]: *** [kForcesUpdate.o] Error 1
make[4]: Leaving directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src/cuda'
make[3]: *** [-L/opt/cuda/lib64] Error 2
make[3]: Leaving directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd/src'
make[2]: *** [cuda_parallel] Error 2
make[2]: Leaving directory
`/home/aquevedo/Programas/Amber12/amber12/src/pmemd'
make[1]: *** [cuda_parallel] Error 2
make[1]: Leaving directory `/home/aquevedo/Programas/Amber12/amber12/src'
make: *** [install] Error 2
************************
--
************************************************************************
Dr. Mario Alfredo Quevedo.-
Departamento de Farmacia.-
Facultad de Ciencias Químicas.-
Universidad Nacional Córdoba.-
5000 Córdoba, Argentina
TE: 54351 4334163 Ext: 106
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 13 2012 - 09:00:05 PDT
