[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Mark Abraham]

Hi,

On Thu, Oct 22, 2015 at 6:58 PM 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.
>

It can't be if you've done it properly. Use a new, empty build directory.


> 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?
>

Yes, but needlessly complex. You can run grompp anywhere, copy the file to
the Cray, and use the resulting .tpr on the compute nodes, like I said a
while ago.


> 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.
>

Perhaps Cray supplied a cmake, but it doesn't run on the compute nodes, and
has nothing at all to do with the back end compilers, and your system
admins can and should be willing to download and install a more recent
cmake for you and everybody else :-)

Mark


> 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
>>>>>
>>>>>
>>>>
>>>
>>
>