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

[Rossen Apostolov]

  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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