AUR (en) - gromacs

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/
Keywords:	chemistry science simulations
Licenses:	LGPL-2.1-only
Submitter:	xyproto
Maintainer:	hseara (vedranmiletic)
Last Packager:	vedranmiletic
Votes:	23
Popularity:	0.000001
First Submitted:	2011-12-14 17:03 (UTC)
Last Updated:	2024-11-08 05:39 (UTC)

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.

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

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.

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]].

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).

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)

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

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.

@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.

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