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

[Mark Abraham]

On 24/08/2012 9:33 AM, Thomas Evangelidis 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 
> <http://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

In-source builds are not supported. See 
http://www.gromacs.org/Documentation/Installation_Instructions/Cmake?highlight=cmake#Configuring_with_default_settings. 
This page will need a lot of work before we can make a beta release. 
Probably you have some junk lying around from an old build, which is 
easier to get rid of if you haven't done an in-source build.

Mark

> 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
>     <mailto: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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