Package Details: gromacs 2020.4-1

Git Clone URL: https://aur.archlinux.org/gromacs.git (read-only, click to copy)
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: 20
Popularity: 0.000873
First Submitted: 2011-12-14 17:03
Last Updated: 2020-10-14 19:35

Dependencies (12)

Required by (1)

Sources (1)

Latest Comments

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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]].

Anonymous comment on 2015-06-16 22:54

One other thing - you shouldn't have to set SIMD instructions unless you get an error, so that probably should be removed. By default GROMACS chooses the best (http://www.gromacs.org/Documentation/Installation_Instructions_5.0#simd-support).

Anonymous comment on 2015-06-16 20:08

One suggestion - the current PKGBUILD has both single and double precision enabled by default. I think a more "sane" default would just be single precision since according to the GROMACS site double precision is "slower, and not normally useful." (http://www.gromacs.org/Documentation/Installation_Instructions_5.0#typical-gromacs-installation)

Anonymous comment on 2015-06-15 13:44

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

hseara commented on 2015-06-02 20:24

Thanks for the tip. I was always wondering how come none of the gromacs developers where unaware of this problem. Now, I see. The problem was in my side.
I will add this tip in the next release.

necomancer commented on 2015-05-30 03:56

@hseara

If you are using a haswell CPU, modify march=native in the /etc/makepkg.conf:

https://wiki.archlinux.org/index.php/Makepkg#Architecture.2C_compile_flags

would sovle the problem, anyway, the gromacs recommends AVX2_256 enabled if a haswell CPU was used.