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Just to add: the pre-built OpenMM-2.0 for Mac are compiled for
32bit. If you get an error as:<br>
<br>
Linking CXX shared library libopenmm_api_wrapper.dylib<br>
ld: warning: in /usr/local/openmm/lib/libOpenMM.dylib, file was
built for i386 which is not the architecture being linked (x86_64)<br>
Undefined symbols:<br>
"OpenMM::State::getVelocities() const", referenced from:<br>
.... snip .....<br>
<br>
then you can force compilation for 32bit by:<br>
<br>
$ export CFLAGS='-arch i386'<br>
$ export CXXFLAGS='-arch i386'<br>
<br>
or recompile the openmm from source.<br>
<br>
Rossen<br>
<br>
On 9/13/10 1:01 PM, Rossen Apostolov wrote:
<blockquote cite="mid:4C8E0482.8020001@kth.se" type="cite">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<title></title>
Hi Alan,<br>
<br>
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<br>
<br>
Rossen<br>
<br>
On 9/11/10 12:56 AM, Alan wrote:
<blockquote
cite="mid:AANLkTin=Di+LzwwXsfoz-6h2w=TtL+7TmJVmaSZ5yO--@mail.gmail.com"
type="cite"> I am doing, after compiling and installing the
normal grmx 4.5:
<div><br>
</div>
<div>
<div>rm -fr CMakeCache.txt</div>
<div>make clean</div>
<div>export OPENMM_ROOT_DIR=/usr/local/openmm</div>
<div>
<div>cmake -DGMX_OPENMM=ON ..</div>
<div>make mdrun</div>
</div>
<div>
<div>[ 1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_memtestG80_core.cu.o</div>
<div>[ 1%] Building NVCC (Device) object
src/kernel/gmx_gpu_utils/./gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div>Scanning dependencies of target gmx_gpu_utils</div>
<div>Linking CXX shared library libgmx_gpu_utils.dylib</div>
<div>Undefined symbols:</div>
<div> "_gmx_strncasecmp", referenced from:</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> "_debug", referenced from:</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> do_timed_memtest(int, int)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> do_full_memtest(int) in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> do_quick_memtest(int) in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> "_trim", referenced from:</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div> is_supported_cuda_gpu(int, char*)in
gmx_gpu_utils_generated_gmx_gpu_utils.cu.o</div>
<div>ld: symbol(s) not found</div>
<div>collect2: ld returned 1 exit status</div>
<div>make[3]: ***
[src/kernel/gmx_gpu_utils/libgmx_gpu_utils.dylib] Error 1</div>
<div>make[2]: ***
[src/kernel/gmx_gpu_utils/CMakeFiles/gmx_gpu_utils.dir/all]
Error 2</div>
<div>make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule]
Error 2</div>
<div>make: *** [mdrun] Error 2</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
-- <br>
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate<br>
Department of Biochemistry, University of Cambridge. <br>
80 Tennis Court Road, Cambridge CB2 1GA, UK.<br>
>><a moz-do-not-send="true"
href="http://www.bio.cam.ac.uk/%7Eawd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-Rossen</pre>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-Rossen</pre>
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