[gmx-users] Segmentation Fault using g_cluster

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 28 09:48:03 CEST 2012

On 28/03/2012 2:14 PM, Davide Mercadante wrote:
> Thank you for the prompt reply.! Indeed, I am using Gromacs version 
> 4.5.5 compiled in double-precision and I am running the analysis on a 
> MacBook PRO.
> I tried to open an issue at http://redmine/gromacs.org but it asks me 
> for login name and passwd which I don't think I have as I never 
> subscribed as developer. I may be wrong though..do I need to register?

Yes, just sign up. We need to be able to contact you to let you know the 
solution or get more information, so anonymous bug submission is not 
very useful.

> I suppose that if this is not an explainable issue at the moment there 
> is no solution to it?

The problem with plain segfaulting is that there's no way to tell what 
caused the problem. GROMACS tries hard not to do this, but clearly it's 
not perfect. There may be a code bug. There may be a way for you to use 
the code better. We just don't know yet. There's certainly room to 
improve the code.


> Thank you again for the reply. It has been much appreciated.
> Davide
> From: Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>>
> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> Date: Wed, 28 Mar 2012 13:29:40 +1100
> To: Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
> Subject: Re: [gmx-users] Segmentation Fault using g_cluster
> On 28/03/2012 1:00 PM, Davide Mercadante wrote:
>> Dear Gromacs Users,
>> I am trying to run g_cluster to find an average structure for my 
>> system and after giving the following command line:
>> g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb 
>> -n --g
>> g_cluster started without problems and continued calculating the 
>> matrix etc...until I got this:
>> Last frame       5000 time 50000.004
>> Allocated 645448320 bytes for frames
>> Read 5001 frames from trajectory allnj10_XM10.xtc
>> Computing 5001x5001 RMS deviation matrix
>> # RMSD calculations left: 0
>> The RMSD ranges from 0.0816802 to 0.301369 nm
>> Average RMSD is 0.208468
>> Number of structures for matrix 5001
>> Energy of the matrix is 364.532 nm
>> WARNING: rmsd minimum 0 is below lowest rmsd value 0.0816802
>> Linking structures **************
>> Sorting and renumbering clusters
>> Found 1425 clusters
>> Writing middle structure for each cluster to pdb_ligplot_XM.pdb
>> Segmentation fault: 11
>> Can you please help me to understand where the problem comes from and 
>> how I can solve it?
>> Any help is greatly appreciated.
> I don't think this should happen. You haven't stated your GROMACS 
> version. If you can reproduce this with 4.5.5., please open an issue 
> here http://redmine.gromacs.org/ and upload your files and 
> instructions on how to reproduce the problem.
> Mark
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