[gmx-users] gromacs 4.6.7 plumed -Segmentation fault

[Justin Lemkul]

On 10/22/15 12:34 PM, Ana Marija 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?
>

The error message itself tells you the most likely problem.  Your topology has 
some formatting or sequence that is broken, causing misinterpretation or 
misapplication of a [ settles ] directive.

-Justin

> 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
>>>
>>>
>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================