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

[Alan]

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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