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gprof --line taking _forever_

From: David Mathog
Subject: gprof --line taking _forever_
Date: Wed, 14 Apr 2004 08:55:34 -0700

I'm trying to profile the "blastall" program from the NCBI toolbox.
(ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/CURRENT/ncbi.tar.gz).  The
programs were all compiled with "gcc -g -pg -O3" on a RH 7.3 system
with gcc 3.3.3. One of the programs was run:

time /usr/common/ncbi_new/ncbi/build/blastall -p blastp -d nr_lcl -i
a1hu.pfa  -b 10 -v 10 >testout.txt

to produce a gmon.out file. The default gprof command works:

 gprof  /usr/common/ncbi_new/ncbi/build/blastall 

However, when I try this:

 grpof --line /usr/common/ncbi_new/ncbi/build/blastall

the CPU pegs at 99% and stays there for at least 45 minutes
(it's still running as I write this.)

This seems like an excessive amount of time for a line profile.
The same method works fine on other (smaller) programs.  The
toolbox though, contains a humongous number of files (694 *.c files
containing 1.2M lines of code - not all of which are included in
blastall). It also creates some static libraries which are linked
into the executable.

Is this a bug in gprof or does it just take a hideously long time
on this sort of source code?

Is there some trick that is required to make gprof --line work
more quickly  with a program like this?

I already know which routines the program spends most of its time
in (from the first gprof).  Is there a way to run gprof so
that it only reports line usage from those routines?

Any other suggestions?


David Mathog
Manager, Sequence Analysis Facility, Biology Division, Caltech

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