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

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Aug 19 2009 - 02:46:08 CDT

Ok, sorry I managed to compile tcl 8.4.19 ..
There was a mistake in the Makefile that was not obvious to find ....

I'll let you know if NAMD compiles/runs successfully now ...

Best wishes
Vlad

Vlad Cojocaru wrote:
> George, other namd users,
>
> Do you have a step-by-step recipe for compiling NAMD on Blue Gene P ?
> I am not even able to build tcl 8.4.19 .... I get "sythax errors" in
> tclUnixInit.c file ....
>
> Is there a specific tcl version for Blue Gene P ?
> Also .. what about fftw, which one do you use on Blue Gene P ?
>
> I decided to give it a trial myself and compile it as I dont seem to
> have an explanation for the glic errors I reported earlier ..
>
> Best wishes
> Vlad
>
> George Madalin Giambasu wrote:
>> Vlad,
>>
>> First - this error shows that namd has been linked against tcl8.4,
>> not tcl8.5.
>> Second - I get the same warnings on BGP when compiling namd, but
>> namd works, even with tcl loops. I use/compile tcl8.4.19 l library.
>>
>>
>> george
>>
>> Vlad Cojocaru wrote:
>>> 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
>>>>
>>>
>>
>

-- 
----------------------------------------------------------------------------
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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