Just to add: the pre-built OpenMM-2.0 for Mac are compiled for 32bit.
If you get an error as:
Linking CXX shared library libopenmm_api_wrapper.dylib
ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was built
for i386 which is not the architecture being linked (x86_64)
Undefined symbols:
"OpenMM::State::getVelocities() const", referenced from:
.... snip .....
then you can force compilation for 32bit by:
$ export CFLAGS='-arch i386'
$ export CXXFLAGS='-arch i386'
or recompile the openmm from source.
Rossen
On 9/13/10 1:01 PM, Rossen Apostolov wrote:
Hi Alan,
There was a missing dependency for building gmx_gpu_utils, but for
some reason compilation didn't break on linux:) This is now fixed in
release-4-5-patches. Pay attention though that the prebuilt
OpenMM-2.0 libraries from the SimTK website are for MacOSX 10.6
Rossen
On 9/11/10 12:56 AM, Alan wrote:
I am doing, after compiling and installing the normal grmx 4.5:
rm -fr CMakeCache.txt
make clean
export OPENMM_ROOT_DIR=/usr/local/openmm
cmake -DGMX_OPENMM=ON ..
make mdrun
[ 1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o
[ 1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
Scanning dependencies of target gmx_gpu_utils
Linking CXX shared library libgmx_gpu_utils.dylib
Undefined symbols:
"_gmx_strncasecmp", referenced from:
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
"_debug", referenced from:
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
do_timed_memtest(int, int)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
do_full_memtest(int) in gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
do_quick_memtest(int) in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
"_trim", referenced from:
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[3]: *** [src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1
make[2]: ***
[src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all] Error 2
make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
make: *** [mdrun] Error 2
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
--
-Rossen
--
-Rossen
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
