[AMBER] ptraj: SegFault during SOM clustering

From: Anselm Horn <Anselm.Horn.biochem.uni-erlangen.de>
Date: Fri, 30 Mar 2012 18:47:34 +0200

Dear all,

I ran a SOM clustering analysis using ptraj from AT1.5 (patch level 27)
on a NetCDF trajectory of a medium sized system (ca. 60 residues) and
obtained a non-reproducible segmentation fault:

When I rerun the ptraj analysis (same machine), the calculation finishes
sometimes successfully, sometimes it crashes again; rerunning for
several times finally yields a result.

Did anyone experience a similar behaviour?

A collegue from the IT did a first analysis and came up with an error
backtrace (see below); that was, however, not the location where the
putative array out of bounds error occured, he told me. Although he'll
try to figure out the exact error location, I wanted to write to the
Amber list, because he's very busy at the moment with other things.

My second question is thus simply, whether I can trust the results from
my clustering analysis or not - and use a different clustering scheme.

Thanks in advance.

Anselm Horn

Bioinformatik
Institut für Biochemie
Friedrich-Alexander-Universität Erlangen-Nürnberg
Fahrstr. 17
91054 Erlangen
Germany


----------------------------------------
#0 0x00000000004f98c6 in PtrajClusteringConvertSOMNodesToClusters
(This=0x1af3be0, SOMNodes=0x1aeb3d0, ClusterCount=28261344) at
cluster.c:6782
6782 SOMNodes[ClusterIndex]->Stddevs[i] =
SOMNodes[ClusterIndex]->Stddevs[i] / PointCount -
(SOMNodes[ClusterIndex]->Means[i]) * (SOMNodes[ClusterIndex]->Means[i]);

(gdb) backtrace
#0 0x00000000004f98c6 in PtrajClusteringConvertSOMNodesToClusters
(This=0x1af3be0, SOMNodes=0x1aeb3d0, ClusterCount=28261344) at
cluster.c:6782
#1 0x00000000004f7a89 in PtrajClusteringClusterSOM (This=0x1af3be0,
ClusterCount=28226512, map=28261344) at cluster.c:6896
#2 0x0000000000470669 in PtrajPerformClustering (trajInfo=0x1af3be0,
action=0x1aeb3d0) at actions.c:2969
#3 0x000000000046ea06 in transformCluster (action=0x1af3be0,
x=0x1aeb3d0, y=0x1af3be0, z=0x0, box=0x1af3e70, mode=28226512) at
actions.c:3821
#4 0x00000000004640e6 in ptraj (filenamep=0x1af3be0
"\255\032\346.R\310\224@\376\337 @") at ptraj.c:7418
#5 0x0000000000441ad5 in interface (mode=28261344, filename=0x1aeb3d0
"\300F\257\001") at interface.c:92
#6 0x0000000000406c21 in main (argCount=28261344, argPointer=0x1aeb3d0)
at main.c:220




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Received on Fri Mar 30 2012 - 10:00:03 PDT
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