[Biodevelopers] Blastall core dump on Alpha running Redhat 7.2

[Joe Landman]

On Thu, 2004-05-06 at 17:53, Chris Dwan wrote:
> I took Iddo's advice and rebuilt with no optimization (no -O flags of 
> any sort).  '-g' is still in there.  Sadly, I get my same core dump.  
> It seems to be a bit slower though... ;)
> 
> On to Joe's questions:  The compiler is gcc 2.96.  Here's a debugger

Egads... gcc 2.96?  Try using 3.4  2.96 had/caused all manner of
exciting (and hard to diagnose) problems.  Compile with -g so we can
catch the symbols.  

Iterate ... :)

>  
> session:
> 
> [cdwan at alpha platform]$ gdb /tmp/ncbi/ncbi/build/blastall /tmp/core
> GNU gdb Red Hat Linux (5.1-4)
> Copyright 2001 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General Public License, and 
> you are
> welcome to change it and/or distribute copies of it under certain 
> conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB.  Type "show warranty" for 
> details.
> This GDB was configured as "alpha-redhat-linux"...
> Core was generated by `/tmp/ncbi/ncbi/build/blastall -d 
> /home/cdwan/pig_seq -i /home/cdwan/seq_2.fsa -'.
> Program terminated with signal 8, Arithmetic exception.
> Reading symbols from /lib/libm.so.6.1...done.
> Loaded symbols for /lib/libm.so.6.1
> Reading symbols from /lib/libpthread.so.0...done.
> 
> warning: Unable to set global thread event mask: generic error
> [New Thread 1024 (LWP 12287)]
> Error while reading shared library symbols:
> Cannot enable thread event reporting for Thread 1024 (LWP 12287): 
> generic error
> Reading symbols from /lib/libc.so.6.1...done.
> Loaded symbols for /lib/libc.so.6.1
> Reading symbols from /lib/ld-linux.so.2...done.
> Loaded symbols for /lib/ld-linux.so.2
> Reading symbols from /lib/libnss_compat.so.2...done.
> Loaded symbols for /lib/libnss_compat.so.2
> Reading symbols from /lib/libnsl.so.1.1...done.
> Loaded symbols for /lib/libnsl.so.1.1
> reading register pc (#64): No such process.
> reading register pc (#64): No such process.
> (gdb) where
> reading register pc (#64): No such process.
> 
> -Chris 

Was there a core file?  Usually this tells you where it dies.  Take a
look at your limit/ulimit stuff to make sure you dump a real core.

Joe

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-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615