This is for binary files or python files on unix machines, examples are given in bash. 

I haven't profiled Mac files though I think Charles has. Only profile files in fast mode - no point in profiling debug builds!

Profiling python IMP files:

1) Use the CPU_PROFILE flag to specify an output .prof file (on some systems you might also need to add LD_PRELOAD=/usr/lib64/libprofiler.so - probably not):

$ CPUPROFILE=./barak.prof /home/barak/imp_git/fast/setup_environment.sh python expensive_test_statistics_from_simulation_data.py &> LOG

2) Use "pprof --pdf <path-to-python-binary> <path-to-.prof-file>" to print to PDF format - perhaps the process id will be appended to the output profile file. Use "--gv", "--txt" or some of the other pprof options if you like.

pprof --pdf /usr/bin/python barak.prof_31784  > 31784.pdf

Profiling binary IMP files:

1) Run your binary IMP program as you usually would, but with the --cpu_profile flag.
   (this is a generic IMP flag, which will create a .prof file with profiling information. The default .prof file will be created in the current folder, or edit CPU_PROFILE to change the path of the output .prof file).

2) Use "pprof --pdf <path-to-binary-IMP-file> <path-to-.prof-file>" to print to PDF format. Use "--gv", "--txt" or some of the other pprof options if you like.

Comments:

1) Documentation of gperftools https://github.com/gperftools/gperftools

2) See also possibly partially updated IMP page on profiling https://github.com/salilab/imp/blob/4941f4e11403bac687a64b273f80f1ccc70b3522/doc/manual/profiling.md

3) Try "pprof --help" for some interesting options