[gmx-users] Re: g_cluster segmentation fault

[Craig Kitchen]

Hi Mark, 

Works perfectly...

Thanks,

Craig

Craig Kitchen
Department of Chemistry
University of Cambridge
Lensfield Road
Cambridge
CB2 1EW
UK


On 26/03/11, Craig Kitchen <ck363 at cam.ac.uk> wrote:
Dear All,

When running g_cluster on a file generated with g_mdmat I receive a 
segmentation fault. I have tried different versions of Gromacs (4.0.5 and 
4.5.3) on different workstations with both large and small matrices - all 
without success.

Good trouble-shooting and report. You'd likely have been asked to check a 
recent version and with a small matrix :-)

This was a two-part bug - a clean-up function was called when the 
corresponding initialization hadn't been called, and that clean-up function 
assumed that initialization had happened. I fixed both in git.

You can work around this by hacking in src/tools/gmx_cluster.c. Around line 
1260 there will be code like

if (bPBC) {
  gmx_rmpbc_done(gpbc);
}

which you should move one line up (inside a set of braces that mean the 
clean-up is called only after initialization occurs). Don't worry about the 
indenting.

Mark

I am calling g_cluster with:

g_cluster -dm dmat_1.xpm -cutoff 3.4 -g cluster_1.log

Whereupon I receive the error:

Using linkage method for clustering
Reading rms distance matrix 100%
Segmentation fault

The distance matrix (dmat_1.xpm) was generated with:

g_mdmat -f onlyba.gro -s onlyba.gro -t 4.0 -mean dmat_1.xpm

The configuration (onlyba.gro) and matrix file (dmat_1.xpm) are attached 
(and since they are short also pasted below).

Any help on this would be greatly appreciated!

Regards,

Craig

Craig Kitchen
Department of Chemistry
University of Cambridge
Lensfield Road
Cambridge
CB2 1EW
UK




Generated by trjconv : Coarse-Grained Model of EAS Barrels and Loop 
Residues (including bonds) t= 0.00000
 10
  1BA      BA    1  44.780  21.592  37.304  0.0067  0.0035  0.0073
 29BA      BA    2  12.191  38.323   0.704 -0.0084  0.0108 -0.0014
 57BA      BA    3   2.092   9.298  47.957  0.0053 -0.0144  0.0053
 85BA      BA    4  15.664  33.182  25.406  0.0291 -0.0067 -0.0069
113BA      BA    5  47.194  32.613  24.031 -0.0146 -0.0132  0.0184
141BA      BA    6  11.731  25.247  11.921 -0.0100 -0.0049  0.0025
169BA      BA    7  33.751  20.349  25.599 -0.0103 -0.0131  0.0078
197BA      BA    8   2.467  11.277  47.988 -0.0063  0.0188 -0.0001
225BA      BA    9  25.948  26.283  35.007  0.0191  0.0058  0.0047
253BA      BA   10  26.103  27.621  36.697 -0.0057  0.0281 -0.0110
48.00000  48.00000  48.00000


/* XPM */
/* Generated by g_mdmat */
/* This file can be converted to EPS by the GROMACS program xpm2ps */
/* title:   "Mean smallest distance" */
/* legend:  "Distance (nm)" */
/* x-label: "Residue Index" */
/* y-label: "Residue Index" */
/* type:    "Continuous" */
static char *gromacs_xpm[] = {
"10 10   40 1",
"A  c #FFFFFF " /* "0" */,
"B  c #F8F8F8 " /* "0.103" */,
"C  c #F2F2F2 " /* "0.205" */,
"D  c #EBEBEB " /* "0.308" */,
"E  c #E5E5E5 " /* "0.41" */,
"F  c #DEDEDE " /* "0.513" */,
"G  c #D8D8D8 " /* "0.615" */,
"H  c #D1D1D1 " /* "0.718" */,
"I  c #CBCBCB " /* "0.821" */,
"J  c #C4C4C4 " /* "0.923" */,
"K  c #BEBEBE " /* "1.03" */,
"L  c #B7B7B7 " /* "1.13" */,
"M  c #B1B1B1 " /* "1.23" */,
"N  c #AAAAAA " /* "1.33" */,
"O  c #A3A3A3 " /* "1.44" */,
"P  c #9D9D9D " /* "1.54" */,
"Q  c #969696 " /* "1.64" */,
"R  c #909090 " /* "1.74" */,
"S  c #898989 " /* "1.85" */,
"T  c #838383 " /* "1.95" */,
"U  c #7C7C7C " /* "2.05" */,
"V  c #767676 " /* "2.15" */,
"W  c #6F6F6F " /* "2.26" */,
"X  c #696969 " /* "2.36" */,
"Y  c #626262 " /* "2.46" */,
"Z  c #5C5C5C " /* "2.56" */,
"a  c #555555 " /* "2.67" */,
"b  c #4E4E4E " /* "2.77" */,
"c  c #484848 " /* "2.87" */,
"d  c #414141 " /* "2.97" */,
"e  c #3B3B3B " /* "3.08" */,
"f  c #343434 " /* "3.18" */,
"g  c #2E2E2E " /* "3.28" */,
"h  c #272727 " /* "3.38" */,
"i  c #212121 " /* "3.49" */,
"j  c #1A1A1A " /* "3.59" */,
"k  c #141414 " /* "3.69" */,
"l  c #0D0D0D " /* "3.79" */,
"m  c #070707 " /* "3.9" */,
"n  c #000000 " /* "4" */,
/* x-axis:  1 2 3 4 5 6 7 8 9 10 */
/* y-axis:  1 2 3 4 5 6 7 8 9 10 */
"nnnnnnnnVA",
"nnnnnnnnAV",
"nnUnnnnAnn",
"nnnnnnAnnn",
"nnnnnAnnnn",
"nnnnAnnnnn",
"nnnAnnnnnn",
"nnAnnnnUnn",
"nAnnnnnnnn",
"Annnnnnnnn"


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