On 26/03/11, Craig Kitchen <ck...@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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