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

Thomas Evangelidis tevang3 at gmail.com
Fri Aug 24 01:33:33 CEST 2012

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
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
I removed that flag from everywhere:

for fname in $(grep -lR "\-fexcess\-precision=fast" *); do perl -pi -e
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
../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
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?


> 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
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