From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Tue Aug 18 2009 - 12:05:22 CDT
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
>>
>
-- ________________________________________________________________________ George Madalin Giambasu PhD Student University of Minnesota Phone : (612) 625-6317 Department of Chemistry Fax : (612) 626-7541 207 Pleasant St. SE e-mail: Minneapolis, MN USA 55455-0431 GeorgeMGiambasu_at_umn.edu York Research Group giambasu_at_gmail.com http://theory.chem.umn.edu/ ________________________________________________________________________
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