[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

where with "complete run" means I would run it later on compute nodes.

On Thu, Oct 22, 2015 at 11:58 AM, Ana Marija <sokovic.anamarija at gmail.com>
wrote:

> I just tried to install it with:
> 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_GPU=OFF -DGMX_MPI=OFF
> -DCMAKE_INSTALL_PREFIX=/lustre/beagle2/ams/gro/gromacs-4.6.7/build
> -DGMX_X11=OFF
>
> but the error is the same as above.
>
> My goal with this installation (without cross compiler) was to use it to
> generate input files and than use another installation of gromacs compiled
> with cross compilers to complete the run. Where I would use the same
> version of gromacs  in both cases, 4.6.7. Can you please confirm me that
> this is acceptable approach?
>
> The reason why I can't use newer version of gromacs is that I only have
> cmake 2.8.4 on this machine and it is impossible to install newer version
> of cmake because it is tied to gnu version we got from Cray etc.
>
>
>
> On Thu, Oct 22, 2015 at 11:51 AM, Szilárd Páll <sin.pecado at gmail.com>
> wrote:
>
>> On Thu, Oct 22, 2015 at 6:34 PM, Ana Marija <sokovic.anamarija at gmail.com>
>> wrote:
>>
>>> 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?
>>>
>>
>> As Justin said, this isn't an issue with the GROMACS build anymore (but
>> rather with the inputs). So it seems that the original problem is solved -
>> unless you really need to run grompp on the compute nodes.
>>
>> BTW, I hope you know that 4.6.7 is a rather old and outdated version; the
>> 5.0 and 5.1 series has been released since and the former is AFAIK
>> supported by PLUMED!
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>
>>>
>>> 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
>>>>>
>>>>>
>>>>
>>>
>>
>