[gmx-users] please help, cannot compile gmx 4.5 openmm

[Alan]

Dear Rossen,

Thanks for your reply.

For your info I use Mac 10.6 with Fink in 64 bits. I have access to svn
Openmm dev source code so I am compiling it in 64 bits. It could be a source
of issues, but all others programmes I have running that depends on openmm
(e.g. sander_openmm) were working fine except GMX.

Bizzarely but gmx 4.5 beta were compiling ok.

I will try release-4-5-patches updated later.

Thanks,

Alan

On 13 September 2010 12:58, Rossen Apostolov <rossen at kth.se> wrote:

>  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
>
>
> --
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-- 
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<<
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