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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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().

duca commented on 2014-07-04 13:59

In the lab i work we dont usually even update unless an important bug is found on the one we use or some important feature is released with a new version.

Our upgrade from 3 to 4 was quite bumpy and even within the first releases of the 4 series.



Anyway thank you for your feedbacks, guys.

hseara commented on 2014-07-02 05:27

Please do not update to gromacs5 until the developers consider it suitable for production runs. Right now this is not the case. Notice for example the note in the download section where clearly states: "Please note that these are not yet regarded as production quality, pending further testing, but the code is now feature-stable."

In my humble opinion and with the experience in the transition from gromacs3 to gromacs4 it will take at least one or more releases to be safe to use for production quality runs. I think we should wait until then a bit for the update and in the mean while keep in the 4.6 branch. Soon there will be an update 4.6.6 will includes all bug fixes in gromacs5.