Re: Re: segmentation fault when running ABF

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Wed Aug 06 2008 - 04:13:05 CDT

Hi Alex,

Well .. I tried to compile using my own compilation of tcl8.5 because
when trying with the precompiled libs (for linux-amd64) from the namd
webpage (with the -static option added to the icc compiler) I get the
error1 (see below). Second, when I tried to compile tcl 8.3.5 I get a
configure error (error2 below). When I looked for the configure error on
the tcl webpage I found the answer "tcl8.3.5" is an old verison .. if
you upgrade, tcl should configure correctly". Then I thought OK .. I use
the latest tcl and I should be fine .... So, that's the background of it ..

I also tried to add -DUSE_NON_CONST to my tcl8.5 compilation but still
in vain ....

Now, I guess I should try tcl 8.4 ..... as it seems that nobody has
tried to build namd with tcl8.5 ...

For the record, I am trying on two different machines, both amd64
architectures, on both intel 10.1.015 compilers. the namd code was
downloaded from the cvs a week ago ...

Best wishes
vlad

--------------error 1--------------------------------------------
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclLoadDl.o):
In function `TclpLoadFile':
tclLoadDl.c:(.text+0x5d): warning: Using 'dlopen' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclUnixPipe.o):
In function `TclpCreateTempFile':
tclUnixPipe.c:(.text+0xe0): warning: the use of `tmpnam' is dangerous,
better use `mkstemp'
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclUnixFCmd.o):
In function `GetGroupAttribute':
tclUnixFCmd.c:(.text+0xcc1): warning: Using 'getgrgid' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclUnixFCmd.o):
In function `SetGroupAttribute':
tclUnixFCmd.c:(.text+0xf41): warning: Using 'getgrnam' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclUnixFCmd.o):
In function `GetGroupAttribute':
tclUnixFCmd.c:(.text+0xd0b): warning: Using 'endgrent' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclUnixFCmd.o):
In function `SetOwnerAttribute':
tclUnixFCmd.c:(.text+0x10ab): warning: Using 'getpwnam' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
obj/dcdlib.o: In function `write_dcdheader(int, char*, int, int, int,
int, int, double, int)':
src/dcdlib.C:(.text+0xcbf): warning: Using 'getpwuid' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclUnixFCmd.o):
In function `GetOwnerAttribute':
tclUnixFCmd.c:(.text+0xdee): warning: Using 'endpwent' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclUnixChan.o):
In function `TcpGetOptionProc':
tclUnixChan.c:(.text+0xf88): warning: Using 'gethostbyaddr' in
statically linked applications requires at runtime the shared libraries
from the glibc version used for linking
obj/vmdsock.o: In function `vmdsock_connect(void*, char const*, int)':
vmdsock.C:(.text+0x29f): warning: Using 'gethostbyname' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib/libtcl8.3.a(tclIOSock.o):
In function `TclSockGetPort':
tclIOSock.c:(.text+0x59): warning: Using 'getservbyname' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):(.data+0x20):
multiple definition of `__libc_malloc_initialized'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:(.data+0x20):
first defined here
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_new_arena':
(.text+0x730): multiple definition of `_int_new_arena'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x1976):
first defined here
ld: Warning: size of symbol `_int_new_arena' changed from 904 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 219 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `__malloc_check_init':
(.text+0xc50): multiple definition of `__malloc_check_init'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x6a4c):
first defined here
ld: Warning: size of symbol `__malloc_check_init' changed from 144 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 166 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_free':
(.text+0xfd0): multiple definition of `_int_free'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x224a):
first defined here
ld: Warning: size of symbol `_int_free' changed from 1450 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 1748 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_malloc':
(.text+0x19d0): multiple definition of `_int_malloc'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x6b0):
first defined here
ld: Warning: size of symbol `_int_malloc' changed from 4806 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 3449 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_memalign':
(.text+0x2b80): multiple definition of `_int_memalign'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x2b2c):
first defined here
ld: Warning: size of symbol `_int_memalign' changed from 468 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 578 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_valloc':
(.text+0x2dd0): multiple definition of `_int_valloc'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x3158):
first defined here
ld: Warning: size of symbol `_int_valloc' changed from 470 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 62 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `_int_realloc':
(.text+0x2e10): multiple definition of `_int_realloc'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x1cfe):
first defined here
ld: Warning: size of symbol `_int_realloc' changed from 1356 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 1276 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `free':
(.text+0x16b0): multiple definition of `free'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x2d34):
first defined here
ld: Warning: size of symbol `free' changed from 30 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 190 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `malloc':
(.text+0x3650): multiple definition of `malloc'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x2d5a):
first defined here
ld: Warning: size of symbol `malloc' changed from 56 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 466 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o):
In function `realloc':
(.text+0x3a90): multiple definition of `realloc'
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o:memory.c:(.text+0x3372):
first defined here
ld: Warning: size of symbol `realloc' changed from 46 in
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
to 738 in
/usr/lib/gcc/x86_64-linux-gnu/4.1.2/../../../../lib64/libc.a(malloc.o)
Fatal Error by charmc in directory
/scratch/node-06-01/cojocavd/Software/namd/namd2-test-tcl/Linux-amd64-icc
   Command icpc -shared-intel -xO -rdynamic
-L/scratch/node-06-01/cojocavd/Software/tcl-test/linux-amd64/lib
-L/scratch/node-06-01/cojocavd/Software/fftw-namd/lib
-I/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/include
-DCMK_OPTIMIZE=1 -Iinc -Isrc -O3 -static -ip -fno-rtti -o namd2
-L/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib
-I/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../include
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libldb-rand.o
obj/buildinfo.o obj/common.o obj/dcdlib.o obj/erf.o obj/fitrms.o
obj/main.o obj/mainfunc.o obj/memusage.o obj/strlib.o obj/AlgSeven.o
obj/AlgRecBisection.o obj/AlgNbor.o obj/AtomMap.o obj/BackEnd.o
obj/BroadcastMgr.o obj/BroadcastClient.o obj/CollectionMaster.o
obj/CollectionMgr.o obj/Communicate.o obj/Compute.o obj/ComputeAngles.o
obj/ComputeBonds.o obj/ComputeConsForce.o obj/ComputeConsForceMsgs.o
obj/ComputeCrossterms.o obj/ComputeCylindricalBC.o
obj/ComputeDihedrals.o obj/ComputeDPME.o obj/ComputeDPMEMsgs.o
obj/ComputeDPMTA.o obj/ComputeEField.o obj/ComputeEwald.o
obj/ComputeExt.o obj/ComputeFullDirect.o obj/ComputeHomePatch.o
obj/ComputeHomePatches.o obj/ComputeImpropers.o obj/ComputeGlobal.o
obj/ComputeGlobalMsgs.o obj/ComputeGridForce.o obj/ComputeMap.o
obj/ComputeMgr.o obj/ComputeNonbondedSelf.o obj/ComputeNonbondedPair.o
obj/ComputeNonbondedUtil.o obj/ComputeNonbondedStd.o
obj/ComputeNonbondedFEP.o obj/ComputeNonbondedLES.o
obj/ComputeNonbondedPProf.o obj/ComputePatch.o obj/ComputePatchPair.o
obj/ComputePme.o obj/ComputeRestraints.o obj/ComputeSphericalBC.o
obj/ComputeStir.o obj/ComputeTclBC.o obj/ConfigList.o obj/Controller.o
obj/ccsinterface.o obj/DataStream.o obj/DumpBench.o
obj/FreeEnergyAssert.o obj/FreeEnergyGroup.o obj/FreeEnergyLambda.o
obj/FreeEnergyLambdMgr.o obj/FreeEnergyParse.o obj/FreeEnergyRestrain.o
obj/FreeEnergyRMgr.o obj/FreeEnergyVector.o obj/GlobalMaster.o
obj/GlobalMasterServer.o obj/GlobalMasterTest.o obj/GlobalMasterIMD.o
obj/GlobalMasterTcl.o obj/GlobalMasterSMD.o obj/GlobalMasterTMD.o
obj/GlobalMasterFreeEnergy.o obj/GlobalMasterEasy.o
obj/GlobalMasterMisc.o obj/GridForceGrid.o obj/GromacsTopFile.o
obj/heap.o obj/HomePatch.o obj/IMDOutput.o obj/InfoStream.o
obj/LdbCoordinator.o obj/LJTable.o obj/Measure.o obj/MStream.o
obj/MigrateAtomsMsg.o obj/Molecule.o obj/NamdCentLB.o obj/NamdNborLB.o
obj/NamdState.o obj/NamdOneTools.o obj/Node.o obj/Output.o
obj/Parameters.o obj/ParseOptions.o obj/Patch.o obj/PatchMgr.o
obj/PatchMap.o obj/PDB.o obj/PDBData.o obj/PmeBase.o obj/PmeKSpace.o
obj/PmeRealSpace.o obj/ProcessorPrivate.o obj/ProxyMgr.o
obj/ProxyPatch.o obj/Rebalancer.o obj/RecBisection.o obj/ReductionMgr.o
obj/RefineOnly.o obj/RefineTorusLB.o obj/ScriptTcl.o obj/Sequencer.o
obj/Set.o obj/Settle.o obj/SimParameters.o obj/Sync.o obj/TclCommands.o
obj/TorusLB.o obj/WorkDistrib.o obj/pub3dfft.o obj/vmdsock.o obj/parm.o
obj/imd.o obj/CompressPsf.o obj/AtomsDisInfo.o obj/FileIO.o
obj/dcdplugin.o moduleinit7303.o -lmoduleNeighborLB -lmodulecommlib
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libmemory-default.o
/scratch/node-06-01/cojocavd/Software/charm-6.0/net-linux-amd64-tcp-icc10amd/bin/../lib/libthreads-default.o
-lck -lconv-cplus-y -lconv-core -lconv-util -lckqt -ldl -ltcl8.3 -ldl
-lsrfftw -lsfftw -lm -lmoduleNeighborLB -lmodulecommlib -lm returned
error code 1
charmc exiting...
rm -f moduleinit7303.C moduleinit7303.o
make: *** [namd2] Error 1

---------------------------------------error2----------------------------------------------------------------------------------------------
checking system version (for dynamic loading)... ./configure: line 6208:
syntax error near unexpected token `)'
./configure: line 6208: ` OSF*)'

Axel Kohlmeyer wrote:
> On Tue, 5 Aug 2008, Vlad Cojocaru wrote:
>
> VC> Dear all,
> VC>
> VC> Just to add that the same errors I get when running the tcl forces tutorial.
> VC> So, the problem does not appear to be with the abf module but rather with
> VC> the entire tcl interface ..
>
>
> vlad,
>
> i don't know about tcl-8.5, but several things changed between
> tcl-8.3 and tcl-8.4, particularly related to adding "const" to
> the tcl declarations. the default setup of NAMD still assumes
> tcl-8.3, IIRC.
>
> did you set -DUSE_NON_CONST in your tcl flags?
> AFAIK, this is required for tcl-8.4 to be backward compatible.
>
> if you compile tcl by yourself (why? and why tcl-8.5 if it has
> not been tested and you obviously don't want to port NAMD to tcl-8.5),
> you're probably be better off compiling tcl-8.3 or tcl-8.4 for the
> time being...
>
> VC>
> VC> Best wishes
> VC> vlad
> VC>
> VC> Vlad Cojocaru wrote:
> VC> > Dear namd community,
> VC> >
> VC> > I have successfully compiled the cvs code of namd on AMD opteron with the
> VC> > intel 10.1 compilers. I started testing it and on a standard MD simulation
>
> what patch level of the intel 10.1?
> early patch levels were _very_ problematic with high
> optimization levels.
>
> cheers,
> axel.
>
> VC> > (NVE, NVT, and NPT) everything works fine. However when I try to use the
> VC> > abf method (using the abf method present in the lib subdirectory), I get a
> VC> > segmentation fault (see output below). The script shown below runs
> VC> > absolutely fine when using the distributed binaries (for amd64-tcp). Now
> VC> > this looks to me as tcl issue. As you might notice from the output, namd
> VC> > executable is dynamically linked to tcl8.5 which I compiled just before
> VC> > compiling NAMD.
> VC> >
> VC> > It looks as if namd reads the abf_script.tcl, and the distance-com.tcl
> VC> > scripts.
> VC> > Has anybody seen something like this before and/or does anybody have any
> VC> > idea what might happen here? Are there maybe incompatibilities between the
> VC> > 1.6 version of ABF script and tcl8.5 ?
> VC> >
> VC> > Best wishes
> VC> > vlad
> VC> >
> VC> >
> VC> > -----------------------output when segmentation fault
> VC> > Info: TCL GLOBAL FORCES ACTIVE
> VC> > Info: TCL GLOBAL FORCES SCRIPT
> VC> > /scratch/node-06-01/cojocavd/Software/namd/namd2/Linux-amd64-icc/lib/abf/abf_script.tcl
> VC> >
> VC> > -------------
> VC> > TCL: ABF> ---------------------------------------------
> VC> > TCL: ABF> Adaptive Biasing Force protocol version 1.6
> VC> > TCL: ABF> ---------------------------------------------
> VC> > TCL: ABF>
> VC> > TCL: ABF> Using coordinate type : distance-com
> VC> > TCL: ABF> Distance between COM of two atom groups
> VC> > TCL: ABF> dxi : 0.2
> VC> > TCL: ABF> dSmooth : 0.3
> VC> > TCL: ABF> temp : 300.0 [default]
> VC> > TCL: ABF> outFile : abf.out
> VC> > TCL: ABF> fullSamples : 200
> VC> > TCL: ABF> writeFxiFreq : 0 [default]
> VC> > TCL: ABF> writeXiFreq : 100
> VC> > TCL: ABF> abf2 : 7606 7607 7612 7613 7618 7619 7620 7625 7626
> VC> > TCL: ABF> fMax : 60
> VC> > TCL: ABF> outputFreq : 100
> VC> > TCL: ABF> inFiles : [default]
> VC> > TCL: ABF> historyFile : abf-history.dat
> VC> > TCL: ABF> df : 1.0 [default]
> VC> > TCL: ABF> moveBoundary : 0
> VC> > TCL: ABF> distFile : abf-dist.dat
> VC> > TCL: ABF> forceConst : 100
> VC> > TCL: ABF> xiMin : 0
> VC> > TCL: ABF> xiMax : 15
> VC> > TCL: ABF> abf1 : 1193 3101
> VC> > TCL: ABF>Accumulating force data in 75 bins
> VC> > Info: Interactive MD listening on port 3000.
> VC> > Info: Entering startup phase 8 with 40577 kB of memory in use.
> VC> > Info: Finished startup with 44582 kB of memory in use.
> VC> > Stack Traceback:
> VC> > [0] /lib/libc.so.6 [0x2af2e29af110]
> VC> > [1] Tcl_GetString+0x13 [0x2af2e1d14b5b]
> VC> > [2] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1d3fe72]
> VC> > [3] Tcl_CreateHashEntry+0xe1 [0x2af2e1ce58b3]
> VC> > [4] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1d4308d]
> VC> > [5] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1d43e55]
> VC> > [6] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1cd7199]
> VC> > [7] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1cd10bc]
> VC> > [8] TclEvalObjEx+0x18f [0x2af2e1c7c285]
> VC> > [9] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1d0f554]
> VC> > [10] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1c7b150]
> VC> > [11] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1cd7623]
> VC> > [12] TclObjInterpProcCore+0x2ae [0x2af2e1d24e12]
> VC> > [13] TclObjInterpProc+0x3e [0x2af2e1d25692]
> VC> > [14] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1c7b150]
> VC> > [15] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1cd7623]
> VC> > [16] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1cd10bc]
> VC> > [17] TclEvalObjEx+0x18f [0x2af2e1c7c285]
> VC> > [18] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1d0f554]
> VC> > [19] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1c7b150]
> VC> > [20] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1cd7623]
> VC> > [21] TclObjInterpProcCore+0x2ae [0x2af2e1d24e12]
> VC> > [22] TclObjInterpProc+0x3e [0x2af2e1d25692]
> VC> > [23] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> VC> > [0x2af2e1c7b150]
> VC> > [24] Tcl_EvalEx+0x970 [0x2af2e1c7e0ba]
> VC> > [25] Tcl_Eval+0x15 [0x2af2e1c7b8ab]
> VC> > [26] _ZN15GlobalMasterTcl9calculateEv+0x22b [0x729f1f]
> VC> > [27]
> VC> > _ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x85
> VC> > [0x71bbb7]
> VC> > [28] _ZN18GlobalMasterServer11callClientsEv+0x3e3 [0x720311]
> VC> > [29] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x627
> VC> > [0x71fa13]
> VC> > [30]
> VC> > _ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0x18
> VC> > [0x521fe2]
> VC> > [31] CkDeliverMessageFree+0x8f [0x8b2da3]
> VC> > [32]
> VC> > /scratch/node-06-01/cojocavd/Software/namd/namd2/Linux-amd64-icc/namd2
> VC> > [0x8b3692]
> VC> > [33] _Z15_processHandlerPvP11CkCoreState+0x3e3 [0x8b1f53]
> VC> > [34] CmiHandleMessage+0x5a [0x926e8e]
> VC> > [35] CsdScheduleForever+0x4f [0x926fb5]
> VC> > [36] CsdScheduler+0x1c [0x926c02]
> VC> > [37] _ZN7BackEnd7suspendEv+0xb [0x4bf96f]
> VC> > [38] _ZN9ScriptTcl3runEPc+0x1a3 [0x7f3f91]
> VC> > [39] main+0x240 [0x4b79fc]
> VC> > [40] __libc_start_main+0xda [0x2af2e299c4ca]
> VC> > [41] _ZNSt8ios_base4InitD1Ev+0x4a [0x4b260a]
> VC> >
> VC> > Charmrun> node programs all connected
> VC> > ------------- Processor 0 Exiting: Caught Signal ------------
> VC> > Signal: segmentation violation
> VC> > Suggestion: Try running with '++debug', or linking with '-memory
> VC> > paranoid'.
> VC> > Fatal error on PE 0> segmentation violation
> VC> >
> VC> >
> VC> >
> VC> > ------------abf part of the script--------------
> VC> >
> VC> > #****Adaptive Force Biasing
> VC> > Simulation*******************************************
> VC> > source $NAMDHOME/lib/abf/abf.tcl
> VC> > abf coordinate distance-com
> VC> > abf abf1 {1193 3101}
> VC> > abf abf2 {7606 7607 7612 7613 7618 7619 7620 7625 7626}
> VC> > abf xiMin 0
> VC> > abf xiMax 15
> VC> > abf dxi 0.2
> VC> > abf forceConst 100
> VC> > abf dSmooth 0.3
> VC> > abf fullSamples 200
> VC> > abf outFile abf.out
> VC> > abf historyFile abf-history.dat
> VC> > abf outputFreq 100
> VC> > abf writeXiFreq 100
> VC> > abf distfile abf-dist.dat
> VC> > abf fMax 60
> VC> > abf moveBoundary 0
> VC> > #abf restraintList
> VC> > abf applyBias yes
> VC> > abf usMode no
> VC> >
> VC> >
> VC> >
> VC>
> VC>
>
>

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru
EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg
Tel: ++49-6221-533266
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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