<br><br><div class="gmail_quote">On Thu, Aug 23, 2012 at 7:33 PM, Thomas Evangelidis <span dir="ltr"><<a href="mailto:tevang3@gmail.com" target="_blank">tevang3@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<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></div></div></blockquote><div>if you want to get the new native gpu feature you need no special cmake flags so </div><div>cmake .</div><div>should work. But I got confused when claiming you should get release-4-6. Instead you need to get:</div>
<div>git fetch <a href="https://gerrit.gromacs.org/gromacs">https://gerrit.gromacs.org/gromacs</a> refs/changes/84/1284/14 && git checkout FETCH_HEAD</div><div>(for other download options see <a href="https://gerrit.gromacs.org/#/c/1284/">https://gerrit.gromacs.org/#/c/1284/</a>)</div>
<div>It will be in 4.6 but is not (quite) in it yet.</div><div>As far as I know the OpenMM GPU option hasn't been updated for 4.6 and thus for OpenMM you could as well use the 4.5 version.</div><div><br></div><div>I never had problems with in-source build. Mark, why do you say in-source build is not supported?</div>
<div><br></div><div>Roland</div><div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="gmail_quote">
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>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"><div><br>
make: *** [mdrun] Error 2<br>
<br>
<br>
</div></div>
The same happens if I use -DGMX_OPENMM=OFF with cmake.<br>
Any idea what went wrong?<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
Thomas</font></span><div class="im"><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>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>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></div>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>