[Biodevelopers] Blastall core dump on Alpha running Redhat 7.2

[Chris Dwan]

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:

------------------------------------------------------------------------ 
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[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  
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Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for  
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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
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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:

------------------------------------------------------------------------ 
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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)
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-Chris Dwan