[gmx-users] g_cluster segmentation fault

[Craig Kitchen]

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.

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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