From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Sat Oct 01 2005 - 08:42:21 CDT
Continuing with my previous message, it seems that I was wrong to assume
that version 2.6b1 would segfault for the same reason as 2.5. Here is the
gdb output for the 2.6b1 executable (and apologies for the mail traffic) :
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This GDB was configured as "i386-redhat-linux-gnu".
(gdb) file /usr/local/NAMD_2.6b1/namd2
Reading symbols from /usr/local/NAMD_2.6b1/namd2...done.
Using host libthread_db library "/lib/libthread_db.so.1".
(gdb) core core.7261
Reading symbols from shared object read from target memory...done.
Loaded system supplied DSO at 0x40000000
Core was generated by `/usr/local/NAMD_2.6b1/namd2 equi.namd'.
Program terminated with signal 11, Segmentation fault.
warning: svr4_current_sos: Can't read pathname for load map: Input/output error
Reading symbols from /lib/libm.so.6...done.
Loaded symbols for /lib/libm.so.6
Reading symbols from /lib/libdl.so.2...done.
Loaded symbols for /lib/libdl.so.2
Reading symbols from /usr/lib/libz.so.1...done.
Loaded symbols for /usr/lib/libz.so.1
Reading symbols from /usr/lib/libstdc++.so.5...done.
Loaded symbols for /usr/lib/libstdc++.so.5
Reading symbols from /lib/libc.so.6...done.
Loaded symbols for /lib/libc.so.6
Reading symbols from /lib/ld-linux.so.2...done.
Loaded symbols for /lib/ld-linux.so.2
Reading symbols from /lib/libgcc_s.so.1...done.
Loaded symbols for /lib/libgcc_s.so.1
Reading symbols from /lib/libnss_files.so.2...done.
Loaded symbols for /lib/libnss_files.so.2
#0 0x0812c6a4 in ComputeNonbondedUtil::calc_pair ()
(gdb) backtrace
#0 0x0812c6a4 in ComputeNonbondedUtil::calc_pair ()
#1 0x08127d3e in ComputeNonbondedPair::doForce ()
#2 0x081b2364 in ComputePatchPair::doWork ()
#3 0x08288e55 in WorkDistrib::enqueueWorkA ()
#4 0x08288e35 in CkIndex_WorkDistrib::_call_enqueueWorkA_LocalWorkMsg ()
#5 0x082cd629 in CkDeliverMessageFree ()
#6 0x082cfb1f in _processHandler ()
#7 0x08327859 in CmiHandleMessage ()
#8 0x08c4b450 in ?? ()
#9 0x08b0bd50 in ?? ()
#10 0x08327994 in CsdScheduleForever ()
#11 0x08b05198 in ?? ()
#12 0x085389b0 in Cpv_CmiHandlerMax_ ()
#13 0x004c70c0 in ?? ()
#14 0x08b37128 in ?? ()
#15 0x08b2add8 in ?? ()
#16 0x08b2adc8 in ?? ()
#17 0x08328def in CsdScheduler ()
#18 0x080da0a6 in BackEnd::suspend ()
#19 0x08264c63 in ScriptTcl::Tcl_run ()
#20 0x0834229c in TclInvokeStringCommand ()
#21 0x08376d05 in EvalObjv ()
#22 0x08377392 in Tcl_EvalEx ()
#23 0x0836f03e in Tcl_EvalFile ()
#24 0x08264406 in ScriptTcl::run ()
#25 0x080d63b4 in main ()
(gdb) q
________________________________________________________________________________
--
Dr Nicholas M. Glykos, Department of Molecular
Biology and Genetics, Democritus University of Thrace,
Dimitras 19, 68100 Alexandroupolis, GREECE, Fax ++302551030613
Tel ++302551030620 (77620), http://www.mbg.duth.gr/~glykos/
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