[gmx-developers] What is the best choice to profile

Mark Abraham mark.j.abraham at gmail.com
Thu Aug 7 16:56:18 CEST 2014


First, what are you hoping to learn? Many questions have a known answer, or
are known not to have a clear answer ;-)

It's a compound problem. Profilers that just need to compile with standard
profiling flags are fine - just configure with -DCMAKE_BUILD_TYPE=Profile
and go for it. Those that need to influence the compilation or linker line
are more problematic. Just passing the (full path to) the wrapper compiler
should work fine. If you need to pass things to the wrapper compiler, make
yourself a script to wrap the wrapper compiler and give that to CMake.
Whether the things the tool's wrapper compiler does clashes with things
GROMACS is doing varies a lot, and you will need to get involved in the
details to see what the origin of any problems are. That's not anybody's
fault, per se, but the writer of a wrapper compiler typically hopes the end
user is not managing details themselves, but to get high performance you
often have to manage details, and some of those details show up on the
compiler command lines generated by the GROMACS build system. And naturally
you'll be interested in MPI+OpenMP+CUDA, each of which compounds the
problem with further wrapper compilers or command-line stuff.

Once it's working, you have the problem of whether you can get useful data.
Instrumenting every function call, or compromising function inlining is
guaranteed to be useless because that overhead kills things. The main
interesting case to profile is where the MD step iteration time is a few
milliseconds, and you can't introduce thousands of increments of tens of
nanoseconds and get sensible profiles. So either you have to restrict the
instrumentation to high-level functions (which is painful; the output at
the end of the GROMACS log file is a coarse version of this averaged over
many steps and execution contexts), or use a sampling-based approach.

Then you need to start collecting data after the run-time performance
tuning that mdrun does has already stabilized - at least a few hundred MD
steps. Longer if the MD load is imbalanced, which is also the main
interesting case to consider for code modifications.


On Wed, Aug 6, 2014 at 10:58 AM, Theodore Si <sjyzhxw at gmail.com> wrote:

> what kind of tools work best with gromacs 5.0?
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