[Biodevelopers] Blastall core dump on Alpha running Redhat 7.2

[cdwan]

The bug I reported before turns out to have a pretty simple resolution: 
  gcc needs the "-mieee" flag on this platform to correctly perform this 
bit of math on my particular platform.  I added the flag to 
"platform/linux.ncbi.mk" and have created a set of binaries which can 
successfully align my sequences.

Here's the rest of the story, for the interested:  I took Joe and 
Iddo's advice, and made a little test program with my lethal values, 
which generate the underflow.

[cdwan at alpha alpha]$ more test.c
#include <math.h>
#include <stdio.h>

int main () {
   double Lambda, searchsp, score, logK;

   Lambda   = 1.374063;
   score    = 518;
   searchsp = 351649;
   logK     = -0.341642;

   printf ("Hello world\n");

   printf ("(-Lambda * score):        %e\n", -Lambda * score);
   printf ("(-Lambda * score) + logK: %e\n", (-Lambda * score) + logK);
   printf ("exp(that):                %e\n", exp((-Lambda * score) + 
logK));
   printf ("searchsp * exp(that):     %e\n", searchsp * exp((-Lambda * 
score) + logK
));

   printf("Goodbye world\n");
}

Then I built it in a very minimal way:

[cdwan at alpha alpha]$ /usr/local/bin/gcc -o test test.c -lm
[cdwan at alpha alpha]$ ./test
Hello world
(-Lambda * score):        -7.117646e+02
(-Lambda * score) + logK: -7.121063e+02
exp(that):                5.447206e-310
Floating exception (core dumped)

It's interesting to me that the underflow happens on a multiplication 
step which should make the number in question *larger*.  My guess is 
that somewhere in the guts of the multiplication routine for floating 
point numbers, they do something clever and fast which can result in a 
smaller number as an intermediate value.

I'll skip all the incorrect compiler flags I tried, and go right to 
this:

[cdwan at alpha alpha]$ /usr/local/bin/gcc -o test test.c -mieee -lm
[cdwan at alpha alpha]$ ./test
Hello world
(-Lambda * score):        -7.117646e+02
(-Lambda * score) + logK: -7.121063e+02
exp(that):                5.447206e-310
searchsp * exp(that):     1.915505e-304
Goodbye world

I suggest that NCBI add the "-mieee" flag to their DEC makefiles.

I also suggest that (as usual), everybody should check all their 
results, look for core files, and never ever trust a computer.  
Sometimes, "no hits" doesn't really mean "no hits."

-Chris Dwan