Package Details: gromacs 2019.1-1

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: 18
Popularity: 0.557972
First Submitted: 2011-12-14 17:03
Last Updated: 2019-02-18 14:04

Latest Comments

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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.

Anonymous comment on 2015-05-24 02:03

5.0.5 has been released

hseara commented on 2015-01-13 12:15

IMPORTANT NOTE:
- if you have a rather new INTEL CPU you might encounter that gromacs does not compile spiting errors related to AVX2_256. They look like this:

#####
/tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/vector_operations.h:157:1: note: The ABI for passing parameters with 32-byte alignment has changed in GCC 4.6
gmx_simd_iprod_d(gmx_simd_double_t ax, gmx_simd_double_t ay, gmx_simd_double_t az,
^
In file included from /usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/immintrin.h:41:0,
from /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h:40,
from /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/simd.h:118,
from /tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/gmxlib/bondfree.c:62:
/tmp/yaourt-tmp-hector/aur-gromacs/src/gromacs-5.0.4/src/gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256.h: In function ‘gmx_simd_cvt_dib2db_avx2_256’:
/usr/lib/gcc/x86_64-unknown-linux-gnu/4.9.2/include/avxintrin.h:1441:1: error: inlining failed in call to always_inline ‘_mm256_castpd128_pd256’: target specific option mismatch
_mm256_castpd128_pd256 (__m128d __A)
...
####

If this is your case just edit both cmake commands, one for sigle another for double precision, in the build function with:
-DGMX_SIMD=AVX_256



dotsdl commented on 2014-12-28 16:15

Thanks duca for establishing and maintaining this pkgbuild! It's been a real help. Thanks to hseara for taking it up!

duca commented on 2014-12-26 16:27

Guys, I am transfering this package to hseara. He's been doing most of the work keeping a functional pkgbuild already.

I was the first post of a pkgbuild for gromacs back in the 4.0.x days and i'm confident that it'll be on good hands.

hseara commented on 2014-12-09 10:45

Please, update the package with the fix below. Right now does not build.

poluyan commented on 2014-11-28 15:53

Thank you, eomarjee. Now it builds successfully!
Hope that the original PKGBUILD file will be modified.

Anonymous comment on 2014-11-28 10:00

47c47
< install -D -m755 ${srcdir}/${pkgname}-${pkgver}/scripts/completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"
---
> install -D -m755 ${srcdir}/${pkgname}-${pkgver}/src/programs/completion/gmx-completion.bash "${pkgdir}/usr/share/bash-completion/completions/gromacs"

Methylzero commented on 2014-11-07 10:59

This package has failed to build on my system. I am not sure why.

-- Installing: Creating symbolic link /tmp/yaourt-tmp-manjarouser/aur-gromacs/pkg/gromacs/usr/bin/g_wheel_d
install: cannot stat ‘/tmp/yaourt-tmp-manjarouser/aur-gromacs/src/gromacs-5.0.2/scripts/completion.bash’: No such file or directory
==> ERROR: A failure occurred in package().