[gmx-users] Profiling mdrun with GProf

[Dave Michael]

My question was/still is "how can I set up the build options so that GProf
can count the exact times a function is called" and "gprof can probably do
that job" is not an answer.
Here are my cmake build options:
-DGMX_SIMD=None -DGMX_GPU=OFF -DGMX_OPENMP=OFF -DCMAKE_BUILD_TYPE=Profile
-DGMX_MPI=OFF -DGMX_USE_RDTSCP=OFF

The problem I'm seeing is that "do_force" is still missing from the output
log, along with all the other "do_force_*" functions as well as all other
electrostatic function calls.
And the -fno-inline flag won't override any always_inline attributes. Is
there a smart way to remove all inlining attributes from the source code or
should I use search & replace?

Dave

On Tue, Nov 17, 2015 at 2:36 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> I answered the one actual question you asked ;-) I'm sorry I had to spend
> my time guessing what your unstated intentions were, and what you thought
> was "missing." :-) gprof can probably do that job, assuming that -O0 and a
> no-inlining flag actually override source-code annotations for inlining.
>
> Mark
>
> On Tue, Nov 17, 2015 at 1:05 PM Dave Michael <dm.cid.lab at gmail.com> wrote:
>
> > I'm not interested in any performance and/or any time-domain profiling.
> > Please just answer my questions without any additional comments.
> > I just want to get the exact name of the functions called in a mdrun on a
> > particular simulation and the exact number of times it gets called.
> >
> > On Tue, Nov 17, 2015 at 1:27 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > On Tue, Nov 17, 2015 at 11:55 AM Dave Michael <dm.cid.lab at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > I need some help with using gprof and mdrun.
> > > >
> > >
> > > To what end? Note that the end of the .log file provides a very rough
> > > profile already.
> > >
> > >
> > > > Here's a short story of what I've tried so far:
> > > > - a bunch of other tools (perf, zoom, valgrind) - not quite what I
> was
> > > > looking for
> > > > - settled on GProf (and I want to count ALL function calls)
> > > > - compiled the code with the "Profile" option
> > > > - reduced -O3 to -O0 and had some success here (but some things are
> > still
> > > > missing)
> > > >
> > >
> > > A profile not at -O3 is of zero value.
> > >
> > >
> > > > Can someone help me out?
> > > >
> > > > Also, where are the compiler flags store (i.e. where can I specify a
> > > > no-inline option)?
> > > >
> > >
> > > CMake has various compiler-flag options you can play with (e.g. try the
> > > advanced mode of ccmake). But all that you will observe is that the
> > > functions that are no longer inlined should have been, because we make
> > > extensive use of inlined functions in performance-critical kernels.
> > >
> > > Mark
> > >
> > >
> > > > Dave
> > > > --
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