[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

I installed it via:
cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
-DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
-DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
-DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
-DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
-DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON

then I was running it on login nodes via:

/lustre/beagle2/ams/gro/gromacs-4.6.7/build/bin/grompp -f
/lustre/beagle2/ruisun/MYCO/Set-1/input/grompp.mdp -c
/lustre/beagle2/ruisun/MYCO/Set-1/input/initial.gro -p
/lustre/beagle2/ruisun/MYCO/Set-1/input/topol.top -n
/lustre/beagle2/ruisun/MYCO/Set-1/input/index.ndx -o ttmeta1.tpr


but I didn't get .tpr file, and output was this:
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
Generated 1081 of the 1081 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 994 of the 1081 1-4 parameter combinations

-------------------------------------------------------
Program grompp, VERSION 4.6.7
Source code file:
/lustre/beagle2/ams/gro/gromacs-4.6.7/src/kernel/toppush.c, line: 1803

Fatal error:
[ file tip3p.itp, line 39 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.

can you please advise what should I do in this situation?

On Thu, Oct 22, 2015 at 11:06 AM, Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> so is it ok to try this?
> cmake ../ -DFFTWF_INCLUDE_DIR=/opt/fftw/3.3.4.0/abudhabi/include
> -DFFTWF_LIBRARY=/opt/fftw/3.3.4.0/abudhabi/lib/libfftw3f.a
> -DCMAKE_CXX_COMPILER=g++ -DCMAKE_C_COMPILER=gcc -DGMX_DOUBLE=OFF
> -DGMX_PREFER_STATIC_LIBS=ON -DGMX_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF -DCMAKE_SKIP_RPATH=ON
>
>
>
> On Thu, Oct 22, 2015 at 11:03 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Your blas and lapack were compiled with gfortran, but in a way that they
>> require that one links further dependencies to use them later on. So
>> compile them better, or use dynamic linking.
>>
>> But 99.9% of GROMACS users do not need to get involved with this, so just
>> leave GMX_BLAS_USER and GMX_BLAS_LAPACK unset and GROMACS will use its
>> internal versions.
>>
>> Mark
>>
>>
>