I did search for this answer, but it was not there exactly. What was there
i tried and it didn't work.
ubuntu 12.04
amber 12
openmpi
in .bashrc
export LD_LIBRARY_PATH=/usr/local/cuda/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
export AMBERHOME=/home/jonathan/amber12
export PATH=$PATH:/usr/local/cuda/bin
export CUDA_HOME=/usr/local/cuda
export PATH=$PATH:/$CUDA_HOME/bin
serial compile and test worked/passed
parallel compile and test worked/passed
cuda compile and test worked/passed (finally - thanks Ross, David case,
Jason and others)
(this uses the 'dac' method of editing of the config.h file moving
./cuda/cuda.a infront of the flags post configure, pre install)
finally while trying to compile the paralllel cuda version, I get the
following error.
make[3]: Entering directory `/home/jonathan/amber12/src/pmemd/src'
make -C ./cuda
make[4]: Entering directory `/home/jonathan/amber12/src/pmemd/src/cuda'
/usr/local/cuda/bin/nvcc -use_fast_math -O3 -gencode
arch=compute_13,code=sm_13 -gencode arch=compute_20,code=sm_20 -DCUDA -DMPI
-DMPICH_IGNORE_CXX_SEEK -I/usr/local/cuda/include -IB40C
-IB40C/KernelCommon -I/usr/include -c kForcesUpdate.cu
In file included from gpu.h:15:0,
from kForcesUpdate.cu:14:
gputypes.h:30:17: fatal error: mpi.h: No such file or directory
compilation terminated.
make[4]: *** [kForcesUpdate.o] Error 1
make[4]: Leaving directory `/home/jonathan/amber12/src/pmemd/src/cuda'
make[3]: *** [cuda/cuda.a] Error 2
make[3]: Leaving directory `/home/jonathan/amber12/src/pmemd/src'
make[2]: *** [cuda_parallel] Error 2
Here are the path's that are in place using whereis
mpi: /usr/include/mpi
openmpi: /etc/openmpi /usr/lib/openmpi /usr/include/openmpi
/usr/share/openmpi
mpif90: /usr/bin/mpif90.openmpi /usr/bin/mpif90 /usr/bin/X11/mpif90.openmpi
/usr/bin/X11/mpif90 /usr/share/man/man1/mpif90.1.gz
the one it can't find is at:
/usr/include/mpi/mpi.h
Previously it was suggested to add MPI_HOME. to the path /usr and I did try
that. no dice.
(export MPI_HOME=/usr)
-- also tried
(export PATH=$PATH:/$MPI_HOME/usr/bin/mpif90)
no dice
tried it without the mentioned edit in the config.h file, no dice
I did a full clean and recompiled parallel successfully and it passed all
tests.
parallel cuda compile (after that) still gives the same error.
jason mentioned adding the path to the nvcc flags, which I understand in
theory, but I'm not sure exactly of how the syntax is supposed to look. (if
someone could show me that would be great =))
any insight on fixing this would be appreciated!
Thanks,
Jonathan
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 01 2012 - 09:00:04 PDT
