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

[Szilárd Páll]

Hi Alan,

I assume this is still the same issue on the same issue (same
machine/os) as you reported last time.

Could you provide some details about the version of OS, compiler,
CUDA, OpenMM you're using?

I'll look into the problem and get back to you if I figure out something.

Cheers,
--
Szilárd



On Sat, Sep 11, 2010 at 12:56 AM, Alan <alanwilter at gmail.com> 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<<
>
> --
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