Debugging cgi-scripts

See also:

• README.debug in the source tree
• Debug the cgi-scripts with GDB

Debugging with GDB

Complete instructions:

make sure you have compiled with -ggdb by adding

 export COPT=-ggdb

to your .bashrc (if using bash). You might need to make clean; make cgi afterwards. Also make sure that the CGIs use the right hg.conf. Run

 export HGDB_CONF=<PATHTOCGIS>/hg.conf

Then:

 cd cgi-bin
 gdb --args hgc 'hgsid=4777921&c=chr21&o=27542938&t=27543085&g=pubsDevBlat&i=1000235064'

To not forget the quotes, do not include the question mark from your internet browser.

To get a stacktrace of the place where it's aborting:

 break errAbort
 where

Finding memory problems with valgrind

Sometimes the program crashes at random places, because the stack or other datastructures have been destroyed by rogue code. You need valgrind to find the buggy code.

Run the program like this:

 valgrind --tool=memcheck --leak-check=yes pslMap ~max/pslMapProblem.psl ~max/pslMap-dm3-refseq.psl out.temp

Profiling with gprof

When the program is too slow, you can ctrl-C and look for where it's stuck. Or run gprof, to show how much time each function takes.

First, recompile with another gcc option added or add it to your .bashrc

  export COPT=-ggdb -pg

Then run hgTracks, go to the cgi-bin directory and run gprof on the newly created gprof file:

 gprof hgTracks gmon.out | less

hgTracks with the default tracks gave me this today:

 Each sample counts as 0.01 seconds.
   %   cumulative   self              self     total           
  time   seconds   seconds    calls  ms/call  ms/call  name     
  17.65      0.06     0.06  1145954     0.00     0.00  hashLookup
   8.82      0.09     0.03   281068     0.00     0.00  cloneString
   5.88      0.11     0.02   113781     0.00     0.00  hashAdd
   5.88      0.13     0.02   113781     0.00     0.00  hashAddN
   5.88      0.15     0.02    67666     0.00     0.00  lmCloneString
   4.41      0.17     0.02                             lmCloneMem
   2.94      0.18     0.01  1055248     0.00     0.00  hashFindVal