[Biodevelopers] Blastall core dump on Alpha running Redhat 7.2

[Joe Landman]

Chris:

  This is an underflow.  I used to argue (some years ago) with the 
DEC/Compaq guys about it (throwing an exception when they should have 
done a round-to-zero).  This is in the FP status word, and I am not sure 
if I remember where to look exactly for the changes.  Take a look in GLIBC 
docs about setting the FP status words so that denorm round to zero is set 
(sets underflows to 0 rather than tossing an exception).

Joe

On Fri, 7 May 2004, Chris Dwan wrote:

> 
> Further work on the problem has me stumped again and looking for more  
> clues:
> 
> Per Joe and Iddo's suggestion, I installed gcc 3.4 and am now using it.  
>   I have rebuilt the NCBI toolkit with optimization OFF and using the -g  
> flag, so as to retain symbols for debugging.  This gave the following:
> 
> ------------------------------------------------------------------------ 
> ------
> [cdwan at alpha ~]$ gdb /tmp/ncbi/ncbi/build/bl2seq ./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/bl2seq -i  
> /home/cdwan/seq_1.fsa -j /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/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
> #0  0x12004bd1c in BlastKarlinStoE_simple ()
> 
> (gdb) where
> #0  0x12004bd1c in BlastKarlinStoE_simple ()
> #1  0x12001926c in BlastNtGappedScoreInternal ()
> #2  0x12001df04 in BlastNTGetGappedScore ()
> #3  0x1200d1a04 in BLASTPerformFinalSearch ()
> #4  0x1200d0f70 in BLASTPerformSearch ()
> #5  0x1200076e4 in BlastTwoSequencesCoreEx ()
> #6  0x120007fa8 in BlastTwoSequencesCore ()
> #7  0x12000b358 in BlastTwoSequencesByLocWithCallback ()
> #8  0x12000b744 in BlastTwoSequencesWithCallback ()
> #9  0x120004bf0 in Nlm_Main ()
> #10 0x12034bda4 in main ()
> #11 0x200000fd10c in __libc_start_main (main=0x12034bd48 <main>, argc=7,
>      ubp_av=0x11ffff8b8, init=0x1200034f8 <_init>,
>      fini=0x2000002d778 <_dl_debug_mask>, rtld_fini=0,  
> stack_end=0x11ffff8a0)
>      at ../sysdeps/generic/libc-start.c:129
> ------------------------------------------------------------------------ 
> ------
> 
> I inserted some idiot-prints in the function BlastKarlinStoE_simple and  
> determined that the fault occurs on the following line:
> 
>    return searchsp * exp((Nlm_FloatHi)(-Lambda * S) + kbp->logK);
> 
> My printouts of the values in the function look like this:
> 
> ------------------------------------------------------------------------ 
> ------
> Entering BlastKarlinStoE_simple
> ^^  searchsp: 351649.000000 Lambda: 1.374063 S: 489 logK: -0.341642
> ^^  -Lambda * S:                    -671.916867
> ^^  exp((-Lambda * S) + kbp->logK): 1.101132e-292
> ^^  searchsp * the above:           3.872119e-287
> Leaving BlastKarlinStoE_simple
> Entering BlastKarlinStoE_simple
> ^^  searchsp: 351649.000000 Lambda: 1.374063 S: 518 logK: -0.341642
> ^^  -Lambda * S:                    -711.764697
> ^^  exp((-Lambda * S) + kbp->logK): 5.446862e-310
> Floating exception (core dumped)
> ------------------------------------------------------------------------ 
> ------
> 
> -Chris Dwan
> 
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