[gmx-users] Building full GROMACS and mdrun only with MPI and GPU: FFTW and regression tests

[João M. Damas]

On Fri, Jan 10, 2020 at 4:01 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Fri, 10 Jan 2020 at 10:49, João M. Damas <jmdamas at itqb.unl.pt> wrote:
>
> > Hi all,
> >
> > I am trying to build GROMACS in a similar fashion to what is described in
> > section 2.3.5 of the manual (weblink
> > <
> >
> http://manual.gromacs.org/documentation/2019.5/install-guide/index.html#testing-gromacs-for-correctness
> > >),
> > i.e. a full build of GROMACS without any particular flags, and then a
> build
> > of mdrun only, with MPI and GPU enabled.
> >
> > My first issue would be with the compilation of the FFT library, namely
> the
> > recommended FFTW through -DGMX_BUILD_OWN_FFTW=ON. I find that flag very
> > useful, but with a recipe as described in section 2.3.5, it would mean
> > compiling FFTW twice, which is a waste of time. Do you recommend for me
> to
> > compile FFTW separately on my own or is there a way/flag to pass the
> > compiled static library to the mdrun building step?
> >
>
> No, the only way to do that is to have installed FFTW somewhere and have
> both builds pick it up, e.g. through using cmake
> -DCMAKE_PREFIX_PATH=/path/to/your/fftw. It's also not a lot of time, for
> something you do rarely, so I would just ignore the inefficiency.
>
Thanks, that's what I thought. I'll see which of the two options is the
best for my case.

>
>
> > My second issue is with the regression tests. Using the procedure of
> > section 2.3.5, with a mdrun building recipe like this:
> >
> > cmake3 .. \
> >        -DCMAKE_INSTALL_PREFIX=${SOFTWARE_INSTALL_PREFIX} \
> >        -DGMX_BUILD_OWN_FFTW=ON \
> >        -DGMX_DEFAULT_SUFFIX=OFF \
> >        -DGMX_BINARY_SUFFIX=_mpi \
> >        -DGMX_LIBS_SUFFIX=_mpi \
> >
>
> There's no need to do this - you're turning off the suffixing and then
> doing the default behaviour yourself. It should work, but we don't try to
> test it :-)
>
Oh, a bit of over-engineering from my part, I see 😅. I didn't actually
test that the -DGMX_MPI=ON changed the default suffix. Thanks for the
feedback.

>
>        -DGMX_MPI=ON \
> >        -DGMX_GPU=ON \
> >        -DGMX_BUILD_MDRUN_ONLY=ON
> > make -j ${NPROCS}
> > make install
> >
> > there are issues with running `./gmxtest.pl all -np ${NPROCS} -mdrun
> > mdrun_mpi`. Since I am using the same install prefix for both building
> > steps, I am using the suffix flags stated, but then I need to fix
> > gmxtest.pl (namely
> > change the autosuffix variable from 1 to null) to make the tests run
> > (succesfully). Am I doing something wrong with the suffixes? I believe I
> > need them if I want to install on the same prefix.
> >
>
> No. ./gmxtest.pl -nosuffix is useful for testing in the case you are
> doing,
> and even though you're over-managing the suffixes, nothing's wrong.
>
I guess that's the flag I was looking for! I'll try it. Thanks.

>
>
> > Finally, is there a better way of doing this process to achieve the same
> > result (i.e. a full build of GROMACS without any particular flags, and
> then
> > a build of mdrun only, with MPI and GPU enabled)? In the case that
> section
> > is outdated.
> >
>
> This is the current procedure. There's currently no significant difference
> between gmx_mpi mdrun and mdrun_mpi, except that one could reasonably want
> to try harder to build the latter to link in a fully static way (which can
> be worth a percent or two of performance).
>
Thanks for the extra input on this matter, I appreciate it.

>
> Mark
>
> Thank you in advance,
> > João
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-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613