Re: segmentation fault when running ABF

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Aug 05 2008 - 10:34:48 CDT

Dear all,

Just to add that the same errors I get when running the tcl forces
tutorial. So, the problem does not appear to be with the abf module but
rather with the entire tcl interface ..

Best wishes
vlad

Vlad Cojocaru wrote:
> Dear namd community,
>
> I have successfully compiled the cvs code of namd on AMD opteron with
> the intel 10.1 compilers. I started testing it and on a standard MD
> simulation (NVE, NVT, and NPT) everything works fine. However when I
> try to use the abf method (using the abf method present in the lib
> subdirectory), I get a segmentation fault (see output below). The
> script shown below runs absolutely fine when using the distributed
> binaries (for amd64-tcp). Now this looks to me as tcl issue. As you
> might notice from the output, namd executable is dynamically linked to
> tcl8.5 which I compiled just before compiling NAMD.
>
> It looks as if namd reads the abf_script.tcl, and the distance-com.tcl
> scripts.
> Has anybody seen something like this before and/or does anybody have
> any idea what might happen here? Are there maybe incompatibilities
> between the 1.6 version of ABF script and tcl8.5 ?
>
> Best wishes
> vlad
>
>
> -----------------------output when segmentation fault
> Info: TCL GLOBAL FORCES ACTIVE
> Info: TCL GLOBAL FORCES SCRIPT
> /scratch/node-06-01/cojocavd/Software/namd/namd2/Linux-amd64-icc/lib/abf/abf_script.tcl
>
> -------------
> TCL: ABF> ---------------------------------------------
> TCL: ABF> Adaptive Biasing Force protocol version 1.6
> TCL: ABF> ---------------------------------------------
> TCL: ABF>
> TCL: ABF> Using coordinate type : distance-com
> TCL: ABF> Distance between COM of two atom groups
> TCL: ABF> dxi : 0.2
> TCL: ABF> dSmooth : 0.3
> TCL: ABF> temp : 300.0 [default]
> TCL: ABF> outFile : abf.out
> TCL: ABF> fullSamples : 200
> TCL: ABF> writeFxiFreq : 0 [default]
> TCL: ABF> writeXiFreq : 100
> TCL: ABF> abf2 : 7606 7607 7612 7613 7618 7619 7620 7625 7626
> TCL: ABF> fMax : 60
> TCL: ABF> outputFreq : 100
> TCL: ABF> inFiles : [default]
> TCL: ABF> historyFile : abf-history.dat
> TCL: ABF> df : 1.0 [default]
> TCL: ABF> moveBoundary : 0
> TCL: ABF> distFile : abf-dist.dat
> TCL: ABF> forceConst : 100
> TCL: ABF> xiMin : 0
> TCL: ABF> xiMax : 15
> TCL: ABF> abf1 : 1193 3101
> TCL: ABF> Accumulating force data in 75 bins
> Info: Interactive MD listening on port 3000.
> Info: Entering startup phase 8 with 40577 kB of memory in use.
> Info: Finished startup with 44582 kB of memory in use.
> Stack Traceback:
> [0] /lib/libc.so.6 [0x2af2e29af110]
> [1] Tcl_GetString+0x13 [0x2af2e1d14b5b]
> [2] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1d3fe72]
> [3] Tcl_CreateHashEntry+0xe1 [0x2af2e1ce58b3]
> [4] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1d4308d]
> [5] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1d43e55]
> [6] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1cd7199]
> [7] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1cd10bc]
> [8] TclEvalObjEx+0x18f [0x2af2e1c7c285]
> [9] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1d0f554]
> [10] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1c7b150]
> [11] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1cd7623]
> [12] TclObjInterpProcCore+0x2ae [0x2af2e1d24e12]
> [13] TclObjInterpProc+0x3e [0x2af2e1d25692]
> [14] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1c7b150]
> [15] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1cd7623]
> [16] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1cd10bc]
> [17] TclEvalObjEx+0x18f [0x2af2e1c7c285]
> [18] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1d0f554]
> [19] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1c7b150]
> [20] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1cd7623]
> [21] TclObjInterpProcCore+0x2ae [0x2af2e1d24e12]
> [22] TclObjInterpProc+0x3e [0x2af2e1d25692]
> [23] /scratch/node-06-01/cojocavd/Software/tcl/lib/libtcl8.5.so
> [0x2af2e1c7b150]
> [24] Tcl_EvalEx+0x970 [0x2af2e1c7e0ba]
> [25] Tcl_Eval+0x15 [0x2af2e1c7b8ab]
> [26] _ZN15GlobalMasterTcl9calculateEv+0x22b [0x729f1f]
> [27]
> _ZN12GlobalMaster11processDataEPiS0_P6VectorS2_S2_S0_S0_S2_S0_S0_S2_+0x85
> [0x71bbb7]
> [28] _ZN18GlobalMasterServer11callClientsEv+0x3e3 [0x720311]
> [29] _ZN18GlobalMasterServer8recvDataEP20ComputeGlobalDataMsg+0x627
> [0x71fa13]
> [30]
> _ZN18CkIndex_ComputeMgr48_call_recvComputeGlobalData_ComputeGlobalDataMsgEPvP10ComputeMgr+0x18
> [0x521fe2]
> [31] CkDeliverMessageFree+0x8f [0x8b2da3]
> [32]
> /scratch/node-06-01/cojocavd/Software/namd/namd2/Linux-amd64-icc/namd2
> [0x8b3692]
> [33] _Z15_processHandlerPvP11CkCoreState+0x3e3 [0x8b1f53]
> [34] CmiHandleMessage+0x5a [0x926e8e]
> [35] CsdScheduleForever+0x4f [0x926fb5]
> [36] CsdScheduler+0x1c [0x926c02]
> [37] _ZN7BackEnd7suspendEv+0xb [0x4bf96f]
> [38] _ZN9ScriptTcl3runEPc+0x1a3 [0x7f3f91]
> [39] main+0x240 [0x4b79fc]
> [40] __libc_start_main+0xda [0x2af2e299c4ca]
> [41] _ZNSt8ios_base4InitD1Ev+0x4a [0x4b260a]
>
> Charmrun> node programs all connected
> ------------- Processor 0 Exiting: Caught Signal ------------
> Signal: segmentation violation
> Suggestion: Try running with '++debug', or linking with '-memory
> paranoid'.
> Fatal error on PE 0> segmentation violation
>
>
>
> ------------abf part of the script--------------
>
> #****Adaptive Force Biasing
> Simulation*******************************************
> source $NAMDHOME/lib/abf/abf.tcl
> abf coordinate distance-com
> abf abf1 {1193 3101}
> abf abf2 {7606 7607 7612 7613 7618 7619 7620 7625 7626}
> abf xiMin 0
> abf xiMax 15
> abf dxi 0.2
> abf forceConst 100
> abf dSmooth 0.3
> abf fullSamples 200
> abf outFile abf.out
> abf historyFile abf-history.dat
> abf outputFreq 100
> abf writeXiFreq 100
> abf distfile abf-dist.dat
> abf fMax 60
> abf moveBoundary 0
> #abf restraintList
> abf applyBias yes
> abf usMode no
>
>
>

-- 
----------------------------------------------------------------------------
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/
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