Fedora Core 4 problems (?) ...

From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Sat Oct 01 2005 - 08:08:55 CDT

Dear All,

I'm having trouble getting the NAMD prebuild executables to run on a FC4
box (both versions 2.5 and 2.6b1). The program starts normally, can run
for hours and then segfaults (with no trace in the log file). I've updated
kernel and glibc, but the problem persists.

Here is the gdb run on a core file produced by NAMD 2.5 :

_______________________________________________________________________________

GNU gdb Red Hat Linux (6.3.0.0-1.21rh)
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you
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Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "i386-redhat-linux-gnu".
(gdb) file /usr/local/NAMD_2.5/namd2
Reading symbols from /usr/local/NAMD_2.5/namd2...done.
Using host libthread_db library "/lib/libthread_db.so.1".
(gdb) core core.6053
Reading symbols from shared object read from target memory...done.
Loaded system supplied DSO at 0x40000000
Core was generated by `/usr/local/NAMD_2.5/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 /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/libnss_files.so.2...done.
Loaded symbols for /lib/libnss_files.so.2
#0 0x08129e2b in destr_detour216.0.209 ()
(gdb) where
#0 0x08129e2b in destr_detour216.0.209 ()
#1 0x0812a8f8 in ComputeHomeTuples<BondElem, bond, BondValue>::doWork ()
#2 0x0812a79a in ComputeSelfTuples<BondElem, bond, BondValue>::doWork ()
#3 0x0824b74d in WorkDistrib::enqueueBonds ()
#4 0x0824b72d in CkIndex_WorkDistrib::_call_enqueueBonds_LocalWorkMsg ()
#5 0x0827c1f9 in CkDeliverMessageFree ()
#6 0x0827d5e3 in _processHandler ()
#7 0x082b5e25 in CmiHandleMessage ()
#8 0x0a518340 in ?? ()
#9 0x0a3cf530 in ?? ()
#10 0x082b5ed2 in CsdScheduleForever ()
#11 0x0a3aa6c8 in ?? ()
#12 0x00000000 in ?? ()
(gdb) q
____________________________________________________________________________

Any ideas ?

Thanks,
Nicholas

-- 
            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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