segmentation fault when running ABF

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Tue Aug 05 2008 - 10:20:32 CDT

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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