From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Aug 19 2009 - 02:17:55 CDT
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/ ---------------------------------------------------------------------------- EML Research gGmbH Amtgericht Mannheim / HRB 337446 Managing Partner: Dr. h.c. Klaus Tschira Scientific and Managing Director: Prof. Dr.-Ing. Andreas Reuter http://www.eml-r.org ----------------------------------------------------------------------------
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