[gmx-developers] The build process, and profiling

[Joe Jordan]

Even reading the first couple of chapters of Radovan Bast's book, "CMake
Cookbook" could help give a clear understanding of the basics of CMake. If
you can't get access, you can at least look at a few of the examples
https://github.com/dev-cafe/cmake-cookbook.

On Mon, Apr 13, 2020 at 9:11 AM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi Jan,
>
> On Sun, 12 Apr 2020 at 14:59, jan <rtm443x at googlemail.com> wrote:
>
>> Hi all,
>> I've been trying to get profiling working, although I understand
>> that's not what gromacs needs. I'm using bit as a way of getting used
>> to everything. I'm also aware the manual says gprof probably won't be
>> that useful - Pall says there'll be too much overhead to get useful
>> timings. That's ok.
>> Nonetheless, I can't get it working. If I enable gprof using
>>
>>  -DCMAKE_BUILD_TYPE=Profile
>>
>> then gmon.out is about 20K and
>>
>> gprof gmx
>>
>> gets me only a longish output describing labels (such as self, % time
>> etc) but no actual profiling data.
>>
>
> By default, the build makes a wrapper binary gmx, with almost all the
> functionality pushed into libgromacs.so. gprof often does not do a good job
> of profiling shared libraries. Configure with cmake
> -DBUILD_SHARED_LIBRARIES=off and gprof has more chance.
>
> Also, just running gmx only returns the usage, so doesn't take any time.
> So maybe gprof doesn't report anything because there's not enough time
> analyzed for it to say anything? Mostly gmx mdrun is the only thing
> interesting for profiling, although sometimes other tools are of interest,
> like grompp. You will need a rather long mdrun for gprof's sampling
> approach to do a good job - as an uninformed guess, nothing under 10
> minutes.
>
> Looking at the GCC docs it needs to be compiled with -pg, and linked
>> with the same flags. Digging through the makefile stuff it *seems*,
>> AFAICT, that both flags are being passed for compilation and linking.
>> But no gprof output. Could well be I broke the build somehow, but I
>> don't know.
>>
>
> Wildly unlikely
>
>
>> About the build process, I don't understand even how to make sense of
>> it. For example Cmake makes makefiles, ok, but many such generated
>> makefiles seem to themselves call back to Cmake, eg. copied from a
>> makefile produced by Cmake:
>>
>>
>> # The CMake executable.
>> CMAKE_COMMAND = /usr/bin/cmake
>>
>> # Special rule for the target install/strip
>> install/strip: preinstall
>>         @$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan
>> "Installing the project stripped..."
>>         /usr/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
>> .PHONY : install/strip
>>
>>
>> So cmake calls on make which calls on cmake?
>>
>
> The cmake binary bundles multiple functionalities, including for
> supporting functionality that works across platforms, such as one might use
> during file copying during install stages, or pretty-printing to terminals
> during the build. See its man page.
>
> I really need to get a feeling of how the build is structured, so
>> could anyone drop some useful hints or pointers please.
>>
>
> cmake's tutorial material is a useful start if you're just not familiar
> with it at all. It's a build system generator, not a build system. As such,
> there are CMakeLists.txt files in most GROMACS directories that direct the
> process. Some general functionality is found in the top-level cmake
> directory too. By the way, there's lots of useful documentation at
> http://jenkins.gromacs.org/job/Documentation_Nightly_master/javadoc/dev-manual/index.html but
> if you spot something missing, please let us know!
>
> Mark
>
>
>> Pall has given me pointers to other profiling tools (again with the
>> caveat that it's not what gmx needs, but this is part of my learning
>> curve).
>>
>> cheers
>>
>> jan
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