Re: glibc detected : corrupted double-linked list: 0xa4657ad8

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Aug 18 2009 - 05:44:58 CDT

Could this have something to do with the static linkage of namd to tcl ? ..
It looks as if in the linking stage, the namd compilation showed these
warnings:

/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixCompat.o):
In function `TclpGetGrGid':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixCompat.c:(.text+0x6c):
warning: Using 'getgrgid' in statically linked applications requires at
runtime the shared librar
ies from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixCompat.o):
In function `TclpGetGrNam':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixCompat.c:(.text+0x4c):
warning: Using 'getgrnam' in statically linked applications requires at
runtime the shared librar
ies from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixFCmd.o):
In function `GetGroupAttribute':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixFCmd.c:(.text+0x78):
warning: Using 'endgrent' in statically linked applications requires at
runtime the shared librarie
s from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixFile.o):
In function `TclpGetUserHome':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixFile.c:(.text+0xad0):
warning: Using 'getpwnam' in statically linked applications requires at
runtime the shared librari
es from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixCompat.o):
In function `TclpGetPwUid':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixCompat.c:(.text+0x2c):
warning: Using 'getpwuid' in statically linked applications requires at
runtime the shared librar
ies from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixFCmd.o):
In function `GetOwnerAttribute':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixFCmd.c:(.text+0x2d8):
warning: Using 'endpwent' in statically linked applications requires at
runtime the shared librari
es from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixCompat.o):
In function `TclpGetHostByAddr':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixCompat.c:(.text+0xac):
warning: Using 'gethostbyaddr' in statically linked applications
requires at runtime the shared l
ibraries from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclUnixCompat.o):
In function `TclpGetHostByName':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/tclUnixCompat.c:(.text+0x8c):
warning: Using 'gethostbyname' in statically linked applications
requires at runtime the shared l
ibraries from the glibc version used for linking
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/lib/libtcl8.4.a(tclIOSock.o):
In function `TclSockGetPort':
/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/unix/../generic/tclIOSock.c:(.text+0x50):
warning: Using 'getservbyname' in statically linked applications
requires at runtime the s
hared libraries from the glibc version used for linking
cp
/workgpfs/deisa/lrz00021/lrz101ao/apps/charm++/6.1.2/mpi-bluegenep-xlc/bin/charmrun
charmrun
mpixlc -Isrc -I/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/include
-DNAMD_TCL -O3 -qhot -DNAMD_VERSION=\"CVS\"
-DNAMD_PLATFORM=\"BlueGeneP-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRAC
OPY -o flipdcd src/flipdcd.c || \
echo "#!/bin/sh\necho unavailable on this platform" > flipdcd; \
chmod +x flipdcd
C command: mpixlc -Isrc
-I/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/include -DNAMD_TCL
-O3 -qhot -DNAMD_VERSION="CVS" -DNAMD_PLATFORM="BlueGeneP-MPI"
-DREMOVE_PROXYRESULTMSG_
EXTRACOPY -o flipdcd src/flipdcd.c
mpixlc -Isrc -I/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/include
-DNAMD_TCL -O3 -qhot -DNAMD_VERSION=\"CVS\"
-DNAMD_PLATFORM=\"BlueGeneP-MPI\" -DREMOVE_PROXYRESULTMSG_EXTRAC
OPY -o flipbinpdb src/flipbinpdb.c || \
echo "#!/bin/sh\necho unavailable on this platform" > flipbinpdb; \
chmod +x flipbinpdb
C command: mpixlc -Isrc
-I/workgpfs/deisa/lrz00021/lrz101ao/apps/tcl/8.4.14/include -DNAMD_TCL
-O3 -qhot -DNAMD_VERSION="CVS" -DNAMD_PLATFORM="BlueGeneP-MPI"
-DREMOVE_PROXYRESULTMSG_
EXTRACOPY -o flipbinpdb src/flipbinpdb.c

Vlad Cojocaru wrote:
> Dear NAMD users,
>
> I am trying to run NAMD on a Blue Gene P . The CVS code from 16th
> August was compiled by the people responsible at the supercomputer site.
> However when i tried to run it I get an error "glibc detected ...:
> corrupted double-linked list: 0xa4657ad8" ....
>
> Now the code was compiled against tcl 8.5 but the details of the
> compilation I don't know as I didn't do it myself ...
>
> in my configuration file I have a foreach loop that loks like this one
> below..
>
> foreach factor {100 10 1 0.1 0} {
> constraintScaling $factor
> if { $factor != 0 } {
> run 1000
> } elseif { $factor == 0 } {
> run 5000
> }
> }
>
> The error comes up after the first call to tcl in the logfile . My
> guess is that the error comes from the linking to the tcl libraries
> but I am not sure ...
>
> The person at the supercomputer site says its a bug in NAMD ...
>
> Does any of you have an idea what might go wrong here ?
>
> Thanks
> Vlad
>

-- 
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Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533202
Fax: ++49-6221-533298
e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/
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