Package Details: gromacs 5.1.2-1

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: 13
Popularity: 0.753845
First Submitted: 2011-12-14 17:03
Last Updated: 2016-02-16 16:04

Latest Comments

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.

jbarnett commented on 2015-07-14 20:15

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

jbarnett commented 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.

jbarnett commented 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.

jbarnett commented 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".

jbarnett commented 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.

jbarnett commented 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]].

jbarnett commented 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).

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