Dear Rossen,<br><br>Thanks for your reply.<br><br>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.<br>
<br>Bizzarely but gmx 4.5 beta were compiling ok.<br><br>I will try release-4-5-patches updated later.<br><br>Thanks,<br><br>Alan<br><br><div class="gmail_quote">On 13 September 2010 12:58, Rossen Apostolov <span dir="ltr"><<a href="mailto:rossen@kth.se">rossen@kth.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div bgcolor="#ffffff" text="#000000">
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<div><div></div><div class="h5"><br>
<br>
On 9/13/10 1:01 PM, Rossen Apostolov wrote:
<blockquote type="cite">
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 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 href="http://www.bio.cam.ac.uk/%7Eawd28" target="_blank">http://www.bio.cam.ac.uk/~awd28</a><<<br>
</div>
</div>
</blockquote>
<br>
<br>
<pre cols="72">--
-Rossen</pre>
</blockquote>
<br>
<br>
</div></div><pre cols="72">--
-Rossen</pre>
</div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><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 href="http://www.bio.cam.ac.uk/~awd28">http://www.bio.cam.ac.uk/~awd28</a><<<br>