[gmx-users] grompp error(Segmentation fault)
Arik Cohen
acohen at biochem.duke.edu
Sun Apr 25 02:23:11 CEST 2010
Thanks again for the ultrafast response.
1. The extra '.' is a typo. (I apologize for that). In the command the
file name appears as 1bgq_Complex_b4ion.tpr
in addition, Both the single precision and double
precision(grompp_d) gives this error.
The compilation was done with gcc-4.4.3 with and without the option
of --disable-float for the double and single precision version
respectively.
2a. This is the first call to grompp
b. The following programs such as pdb2gmx_d, editconf_d and genbox are
working properly.
c.grompp/_d -h is working , giving a description on the program with
the different options available.
3. With regards of running grompp with different forcefield
*Apparently the problem is with the l-bfgs option in the em.mdp file.
This is due to the fact that when changing the integrator option to
steep, the program runs fine *
I'm sorry but I just saw this now.
The l-bfgs integrator was chosen since I need to do normal mode analysis
Thanks a lot
Arik
On 4/24/2010 2:26 PM, Justin A. Lemkul wrote:
> I suppose the next set of questions to ask would be:
>
> 1. How was Gromacs compiled? What options were specified?
> 2. Does every instance of grompp fail? Do other inputs work? What
> does "grompp -h" do?
> 3. Does grompp seg fault with totally different systems (different
> force fields)?
>
> -Justin
>
> 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
>>
>> 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
>
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