[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Ana Marija]

Thanks everybody for all your help!

On Thu, Oct 22, 2015 at 12:20 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

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