<br><br><div class="gmail_quote">Hi Roland,<br><br>Many thanks for the swift reply. I am sorry, it's confusing with all these instructions in the website and the INSTALL files...<br><br>This time I did:<br>git clone git://<a href="http://git.gromacs.org/gromacs.git" target="_blank">git.gromacs.org/gromacs.git</a> gromacs-4.6<br>
cd gromacs-4.6<br>git checkout --track -b release-4-6 origin/release-4-6<br>cmake . -DGMX_OPENMM=ON -DGMX_THREADS=OFF<br>make mdrun<br><br>The first time I ran "make mdrun" I got the following error:<br><br>cc1plus: error: unrecognized command line option "-fexcess-precision=fast"<br>
<br>and as described at <a href="http://verahill.blogspot.gr/2012/01/debian-testing-64-wheezy-compiling_20.html" target="_blank">http://verahill.blogspot.gr/2012/01/debian-testing-64-wheezy-compiling_20.html</a> , I removed that flag from everywhere:<br>
<br>for fname in $(grep -lR "\-fexcess\-precision=fast" *); do perl -pi -e "s/\-fexcess\-precision=fast//<div id=":nz">g" $fname; done<br><br>and then reran "cmake" and "make mdrun", and at the end I got an error about openmm:<br>
</div><br>Scanning dependencies of target mdrun<br>
[ 97%] Building C object src/kernel/CMakeFiles/mdrun.dir/gctio.c.o<br>[ 97%] Building C object src/kernel/CMakeFiles/mdrun.dir/ionize.c.o<br>[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/runner.c.o<br>[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/do_gct.c.o<br>
[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/repl_ex.c.o<br>[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/xutils.c.o<br>[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/md.c.o<br>[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/mdrun.c.o<br>
[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/genalg.c.o<br>[ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/membed.c.o<br>[100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o<br>Linking CXX executable mdrun-openmm<br>
../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_thread_num'<br>../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_num_threads'<br>../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_parallel_start'<br>
../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_loop_end_nowait'<br>../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_loop_ordered_static_start'<br>../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_parallel_end'<br>
../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_barrier'<br>../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_loop_ordered_static_next'<br>collect2: error: ld returned 1 exit status<br>make[3]: *** [src/kernel/mdrun-openmm] Error 1<br>
make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2<br>make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2<div class="im"><br>make: *** [mdrun] Error 2<br><br><br></div>The same happens if I use -DGMX_OPENMM=OFF with cmake.<br>
Any idea what went wrong?<br>
<br><br>Thomas<br><br><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br><div class="gmail_quote"><div><div class="h5">On 24 August 2012 01:48, Roland Schulz <span dir="ltr"><<a href="mailto:roland@utk.edu" target="_blank">roland@utk.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi,<div><br></div><div>you don't need OpenMM for the new GPU feature in 4.6. It has build in GPU/Cuda support. Also you seem to have downloaded the master branch and not 4.6. If you got the code by git you can use "git checkout release-4-6" to get 4.6.</div>
<div>You seem to have found a problem with OpenMM and the master branch. I don't know whether we are planning to support OpenMM for 5.0 so I'm not sure this is something important to fix.</div><div><br></div><div>
Roland<br></div></div></div></blockquote></div></blockquote><div> </div></div>