[gmx-developers] GROMACS 4.6 error in file src/gromacs/analysisdata/analysisdata.cpp:45:0

[Roland Schulz]

On Thu, Aug 23, 2012 at 7:33 PM, Thomas Evangelidis <tevang3 at gmail.com>wrote:

>
>
> Hi Roland,
>
> Many thanks for the swift reply. I am sorry, it's confusing with all these
> instructions in the website and the INSTALL files...
>
> This time I did:
> git clone git://git.gromacs.org/gromacs.git gromacs-4.6
> cd gromacs-4.6
> git checkout --track -b release-4-6 origin/release-4-6
> cmake . -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>
if you want to get the new native gpu feature you need no special cmake
flags so
cmake .
should work. But I got confused when claiming you should get release-4-6.
Instead you need to get:
git fetch https://gerrit.gromacs.org/gromacs refs/changes/84/1284/14 && git
checkout FETCH_HEAD
(for other download options see https://gerrit.gromacs.org/#/c/1284/)
It will be in 4.6 but is not (quite) in it yet.
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.

I never had problems with in-source build. Mark, why do you say in-source
build is not supported?

Roland




> make mdrun
>
> The first time I ran "make mdrun" I got the following error:
>
> cc1plus: error: unrecognized command line option "-fexcess-precision=fast"
>
> and as described at
> http://verahill.blogspot.gr/2012/01/debian-testing-64-wheezy-compiling_20.html, I removed that flag from everywhere:
>
> for fname in $(grep -lR "\-fexcess\-precision=fast" *); do perl -pi -e
> "s/\-fexcess\-precision=fast//
> g" $fname; done
>
> and then reran "cmake" and "make mdrun", and at the end I got an error
> about openmm:
>
> Scanning dependencies of target mdrun
> [ 97%] Building C object src/kernel/CMakeFiles/mdrun.dir/gctio.c.o
> [ 97%] Building C object src/kernel/CMakeFiles/mdrun.dir/ionize.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/runner.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/do_gct.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/repl_ex.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/xutils.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/md.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/mdrun.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/genalg.c.o
> [ 98%] Building C object src/kernel/CMakeFiles/mdrun.dir/membed.c.o
> [100%] Building C object src/kernel/CMakeFiles/mdrun.dir/md_openmm.c.o
> Linking CXX executable mdrun-openmm
> ../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_thread_num'
> ../mdlib/libmd_openmm.so.6: undefined reference to `omp_get_num_threads'
> ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_parallel_start'
> ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_loop_end_nowait'
> ../mdlib/libmd_openmm.so.6: undefined reference to
> `GOMP_loop_ordered_static_start'
> ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_parallel_end'
> ../mdlib/libmd_openmm.so.6: undefined reference to `GOMP_barrier'
> ../mdlib/libmd_openmm.so.6: undefined reference to
> `GOMP_loop_ordered_static_next'
> collect2: error: ld returned 1 exit status
> make[3]: *** [src/kernel/mdrun-openmm] Error 1
> make[2]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/rule] Error 2
>
> make: *** [mdrun] Error 2
>
>
>  The same happens if I use -DGMX_OPENMM=OFF with cmake.
> Any idea what went wrong?
>
>
> Thomas
>
>
>
>
>>  On 24 August 2012 01:48, Roland Schulz <roland at utk.edu> wrote:
>>
>>>  Hi,
>>>
>>>  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.
>>> 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.
>>>
>>>  Roland
>>>
>>
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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