Package Details: gromacs 2019.2-1

Git Clone URL: https://aur.archlinux.org/gromacs.git (read-only)
Package Base: gromacs
Description: A versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
Upstream URL: http://www.gromacs.org/
Licenses: LGPL
Submitter: xyproto
Maintainer: hseara
Last Packager: hseara
Votes: 19
Popularity: 0.637538
First Submitted: 2011-12-14 17:03
Last Updated: 2019-04-17 13:06

Pinned Comments

hseara commented on 2019-04-15 20:13

Installation notes

With cmake update to v3.14.x, gromacs is no longer capable of identifying correctly the CPU and therefore the appropriated SIMD level for compilation. If you want to compile gromacs with SIMD while the problem is not solved add the following option to PKGBUILD:

-DGMX_SIMD={AVX_128_FMA, AVX_256, AVX2_256, AVX2_128, AVX_512}

The KEYWORD depends on the SIMD support provided by your CPU.

Usage notes
source /etc/profile.d/GMXRC.bash

Latest Comments

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sebstar commented on 2016-07-14 08:55

Thanks for the PKGBUILD!
There's one odd thing though. Am I the only one whose installation prefix specification is totally ignored by Cmake?
In build() cmake is run with -DCMAKE_INSTALL_PREFIX=/usr/. But that is totally ignored, as is revealed during package(): gromacs was still installed into ${pkgdir}/usr/local/gromacs, not ${pkgdir}/usr, so I had to replace all instances of /usr with /usr/local/gromacs.

hseara commented on 2015-07-15 12:21

1) Now tests are run by default. If you do not want them comment out the "make check" lines.
2) License has been corrected to LGPL
3) Specific SIMD is not longer enforced. Gromacs will detect the best for your system. If you have any problem with this modify march=native in the /etc/makepkg.conf
4) I have cleaned the PKGBUILD and some options which are default
5) I will like to keep both double and single compilation together as many times double are also required especially for minimizing. In the future we might consider a separated split package.
6) I want to minimize the usage of AUR-libraries, that's why I won't make default fftw-bettersimd. You can also make another package, Eg. gromacs-fftw-bettersimd, to incorporate your changes if you want to.

hseara commented on 2015-07-15 12:20

1) Now tests are run by default. If you do not want them comment out the "make check" lines.
2) License has been corrected to LGPL
3) Specific SIMD is not longer enforced. Gromacs will detect the best for your system. If you have any problem with this modify march=native in the /etc/makepkg.conf
4) I have cleaned the PKGBUILD and some options which are default
5) I will like to keep both double and single compilation together as many times double are also required especially for minimizing. In the future we might consider a separated split package.

Anonymous comment on 2015-07-14 20:15

FYI any who are trying to enable tests replace "make test" with "make check".

Anonymous comment on 2015-07-14 20:07

Thanks for the response. Concerning the test, don't comment out "make test", because that is not the correct command. Just replace it with "make check".

hseara commented on 2015-07-11 18:27

1) Tests do not work for everybody and If you want to pass them nothing forbids you to pass them. Just edit the PKGBUILD before building
2) I want to minimize the usage of AUR-libraries, that's why I won't make default fftw-bettersimd. Still every user is free to change the dependency if he wants before deleting it. You can also make another package, Eg. gromacs-fftw-bettersimd, to incorporate your changes if you want to.
3) I will like to keep both double and single compilation together as many times double are also required especially for minimizing.
4) I will change the licence to LGPL as you say.

Anonymous comment on 2015-06-25 01:27

Here's my suggested PKGBUILD:
https://gist.github.com/wesbarnett/6d521b66301ebe9eb786

Then people can follow the wiki article if the want double precsion, MPI, GPU, etc.

Anonymous comment on 2015-06-16 23:46

Sorry to keep commenting, the license should be LGPL, not GPL. Also "make check" works for me, not "make test".

Anonymous comment on 2015-06-16 23:10

A GROMACS-enhanced fftw library is now available in AUR as "fftw-bettersimd".

Also a few thoughts: GROMACS should detect the appropriate SIMD instructions for your processor, so that flag probably doesn't need to be set. Also, is -DGMX_OPENMP a real flag? I can't find it in the documentation. I also think that a better default would be better to just have it compile for single precision, since most people don't need double precision. I'm currently working on the GROMACS wiki page.

Anonymous comment on 2015-06-16 23:10

A GROMACS-enhanced fftw library is now available in AUR as "fftw-bettersimd".

Also a few thoughts: GROMACS should detect the appropriate SIMD instructions for your processor, so that flag probably doesn't need to be set. Also, is -DGMX_OPENMP a real flag? I can't find it in the documentation. I also think that a better default would be better to just have it compile for single precision, since most people don't need double precision. I'm currently working on the GROMACS wiki page [[GROMACS|here]].