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

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Aug 19 2009 - 04:43:40 CDT

George, NAMD users,

Just to keep updated on this thread ... I believe its useful if somebody
deals with the same problems ...

The CVS code (18 August) did compile correctly on the Blue Gene P with
tcl 8.4.19. However, the glibc runtime errors did not disappear ...
These errors appear now regardless of the tcl version and regardless on
person doing the compilation ...

NAMD 2.6 runs fine on this Blue Gene P without tcl support ...
In order to test whether the glibc runtime errors depend on the NAMD
version, I tried to compile myself the NAMD 2.6 source (against tcl
8.4.19). However, I am keep on getting this message "An unknown "pragma
ivdep" is specified" ... then the compilation fails with the message below.
Maybe somebody has an idea how to fix this ....

Best wishes
Vlad

"src/ComputeTclBC.C", line 37.38: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
[])".
"src/ComputeTclBC.C", line 37.38: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 39.41: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
[])".
"src/ComputeTclBC.C", line 39.41: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 43.39: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
[])".
"src/ComputeTclBC.C", line 43.39: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 45.39: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
[])".
"src/ComputeTclBC.C", line 45.39: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 47.41: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
[])".
"src/ComputeTclBC.C", line 47.41: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 49.40: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
*)".
"src/ComputeTclBC.C", line 49.40: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 51.41: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
*)".
"src/ComputeTclBC.C", line 51.41: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 53.44: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
*)".
"src/ComputeTclBC.C", line 53.44: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 55.42: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
*)".
"src/ComputeTclBC.C", line 55.42: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 57.45: 1540-0256 (S) A parameter of type
"extern "C" int (*)(void *, Tcl_Interp *, int, const char **)" cannot be
initialized with an expression of type "int (ClientData, Tcl_Interp *,
int, char *
*)".
"src/ComputeTclBC.C", line 57.45: 1540-1205 (I) The error occurred while
converting to parameter 3 of "Tcl_CreateCommand(Tcl_Interp *, const char
*, extern "C" int (*)(void *, Tcl_Interp *, int, const char **), ClientData,
extern "C" void (*)(void *))".
"src/ComputeTclBC.C", line 63.39: 1540-0257 (S) An object or reference
of type "char *" cannot be initialized with an expression of type "const
char *".
"src/ComputeTclBC.C", line 66.35: 1540-0257 (S) An object or reference
of type "char *" cannot be initialized with an expression of type "const
char *".
"src/ComputeTclBC.C", line 122.33: 1540-0257 (S) An object or reference
of type "char *" cannot be initialized with an expression of type "const
char *".
make: *** [obj/ComputeTclBC.o] Error 1
l

Vlad Cojocaru wrote:
> 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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