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

CGI is too slow

First thing to try: Add the "measureTiming=1" parameter to the CGI call.

If you still have no idea, you can ctrl-C and look for where it's stuck. Or run gprof, to show how much CPU time each function takes, or valgrind, which includes most of the I/O time.

Profiling with gprof

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

Profiling with valgrind

Gprof shows you only CPU time. If you're stuck in I/O somewhere, gprof won't show it. You need to do ctrl-c a few times (best) or you can use valgrind again

 valgrind --tool=callgrind --dump-instr=yes --simulate-cache=yes --collect-jumps=yes hgTracks
 callgrind_annotate callgrind.out.<yourPID> | less

The tool kCacheGrind allows better inspection of the results than callgrind_annotate, but is a GUI program. It's on the big dev VM.