Performance And Debugging Tools: GPC

Memory Profiling

PurifyPlus

This is IBM/Rational's set of tools for memory profiling and code testing. Specifically, the tools are: purify, purecov and quantify.

In order to gain access to these tools, you need to source the script that defines them to your shell:

  source /scinet/gpc/Rational/purifyplus_setup.sh

The documentation for getting started with these tools is in the directory:

 /scinet/gpc/Rational/releases/PurifyPlus.7.0.1/docs/pdf

or here: PurifyPlus Getting Started.

Valgrind

Valgrind http://valgrind.org/ is a suite of tools for debugging and profiling programs especially useful for finding memory problems, such as memory leaks and segfaults. To use it on the GPC you must first load the module valgrind.

 module load valgrind

In serial valgrind can simply by run as follows, with no need to recompile your binary

valgrind --tool=memcheck ./a.out

there are many useful flags such as --leak-check=yes and --show-reachable=yes that can be found by running valgrind --help on consulting the man pages.

Valgrind can also be used in parallel with MPI as well, http://valgrind.org/docs/manual/mc-manual.html#mc-manual.mpiwrap in a similar fashion, however a library needs to preloaded first.

 LD_PRELOAD=${SCINET_VALGRIND_LIB}/valgrind/libmpiwrap-amd64-linux.so mpirun -np 2 valgrind --tool=memcheck ./a.out

Besides being a extremely good at finding memory problems, valgrind comes with a tool called cachegrind which can find cache use problems in your code; its use is described in our Intro To Performance.

Debugging

gdb

GDB is solid source-language level serial debugger. This SNUG TechTalk from Nov 2010 introduces debugging with gdb. Use module load gdb to ensure you are using the most recent version of gdb.

Performance Profiling

gprof

gprof is a very useful tool for finding out where a program is spending its time; its use is described in our Intro To Performance.

Open|SpeedShop

OpenSpeedshop is a tool for performing sampling and MPI tracing of a program on the GPC. It's use is outlined in our Intro to Performance. It is right now compiled for use only with openmpi and gcc-4.4; to use it,

module load gcc openmpi openspeedshop

To run a sampling experiment with the program, run the program through openspeedshop then use the same program to view the results:

$ openss -f "./a.out" pcsamp
[program runs as usual, outputs extra performance data at the end]
$ openss -f [experimentname].openss

It can also trace MPI calls and give detailed statistics about the time spent in MPI routines by process number; to test this on a run done on one of the devel nodes,

$ module load gcc openmpi/1.3.2-gcc-v4.4.0-ofed openspeedshop
$ openss -f "mpirun -np 6 ./a.out" mpit
[program runs as usual, outputs extra performance data at the end]
$ openss -f [experimentname].openss

this can also be used to perform tracing on batch jobs by ensuring module load gcc openmpi/1.3.2-gcc-v4.4.0-ofed openspeedshop is in your .bashrc and mpirun-ing the program as shown above.

Scalasca

Scalasca is a sophisticated tool for analyzing performance and finding common performance problems. We describe it in our Intro to Performance.