[gmx-users] grompp error(Segmentation fault)

[Mark Abraham]

On 25/04/2010 6:28 AM, Arik Cohen wrote:
> Thank a lot for your very fast response !. Here are the requested details:
>
> 1. Version 4.07 is being used.
>
> 2. Upgrading from version 4.04 to 4.07 doesn't help.
>
> 3. The grompp command given is:
>
> grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
> 1bgq_Complex_b4ion..tpr

Last time you gave this command line, your final filename had only one 
period in it. Now it has two. This can be one reason why people giving 
help want to see copy-pasted inputs and outputs, not things filtered 
through people's heads :-)

Since the segfault is arising during the handling of files early in 
grompp, perhaps this double period is the cause of the problem (even 
though it should not be a problem in principle!). Try a normal filename 
with one period.

Mark

> 4. em.mdp:
>
> integrator = l-bfgs
> nsteps = 50000
> nstlist = 1
> rlist = 1.0
> coulombtype = PME
> rcoulomb = 1.0
> vdw-type = cut-off
> rvdw = 1.0
> nstenergy = 10
> emtol = 5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0
> define = -DFLEXIBLE ; using flexible water model
>
>
> 5. The grompp command is issued in this case, before genion. However,
> even when running it alone the same problem arises.
>
> 6. The program is being run on Fedora 12 inside
> VMware(2.6.32.11-99.fc12.i686, 32-bit).
>
> 7. Running the same command on another OS and type of
> machine(fc10.x86_64) does not solve the problem
>
> 7. The output:
>
> :-) G R O M A C S (-:
>
> Gnomes, ROck Monsters And Chili Sauce
>
> :-) VERSION 4.0.7 (-:
>
>
> Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
> Copyright (c) 1991-2000, University of Groningen, The Netherlands.
> Copyright (c) 2001-2008, The GROMACS development team,
> check out http://www.gromacs.org for more information.
>
> This program is free software; you can redistribute it and/or
> modify it under the terms of the GNU General Public License
> as published by the Free Software Foundation; either version 2
> of the License, or (at your option) any later version.
>
> :-) grompp_d (double precision) (-:
>
> Option Filename Type Description
> ------------------------------------------------------------
> -f MDP/em.mdp Input, Opt! grompp input file with MD parameters
> -po mdout.mdp Output grompp input file with MD parameters
> -c 1bgq_Complex_b4ion.pdb Input Structure file: gro g96 pdb tpr tpb
> tpa
> -r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
> -n index.ndx Input, Opt. Index file
> -p 1bgq_Complex.top Input Topology file
> -pp processed.top Output, Opt. Topology file
> -o 1bgq_Complex_b4ion..tpr Output Run input file: tpr tpb tpa
> -t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
> -e ener.edr Input, Opt. Energy file: edr ene
>
> Option Type Value Description
> ------------------------------------------------------
> -[no]h bool no Print help info and quit
> -nice int 0 Set the nicelevel
> -[no]v bool yes Be loud and noisy
> -time real -1 Take frame at or first after this time.
> -[no]rmvsbds bool yes Remove constant bonded interactions with virtual
> sites
> -maxwarn int 0 Number of allowed warnings during input processing
> -[no]zero bool no Set parameters for bonded interactions without
> defaults to zero instead of generating an error
> -[no]renum bool yes Renumber atomtypes and minimize number of
> atomtypes
>
> Ignoring obsolete mdp entry 'title'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
> checking input for internal consistency...
>
> WARNING 1 [file MDP/em.mdp, line unknown]:
> For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
>
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top//ffamber99sb.itp
> Opening library file
> /usr/local/gromacs/share/gromacs/top//ffamber99sbnb.itp
> Opening library file
> /usr/local/gromacs/share/gromacs/top//ffamber99sbbon.itp
> Segmentation fault (core dumped)
>
>
> Thanks a lot in advance for all your help
>
> Arik
>
>
> On 4/23/2010 4:45 PM, Mark Abraham wrote:
>> On 24/04/2010 7:28 AM, Arik Cohen wrote:
>>> I'll be most thankful if any one would be able to help me with the
>>> following problem.
>>
>> Giving more complete information will give you a much better chance.
>> It's not our job to be the family doctor and ask questions :-)
>>
>> What GROMACS version is it? Does upgrading to 4.0.7 help?
>>
>>> While running the grompp (in both single and double precision) command I
>>> get a Segmentation fault (core dumped) error.
>>
>> When? What was the output to date?
>>
>>> The error persist even
>>> after recompiling the GROMACS with gcc-4.4.3(previously I was running
>>> 4.04 compiled with the buggy gcc-4.1 compiler).
>>
>> Does it happen on another machine?
>>
>>> The command I'm using is:
>>>
>>> grompp_d -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top -o
>>> 1bgq.tpr
>>
>> What's in the .mdp file?
>>
>> Mark