Package Details: gromacs 2019.2-1

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: 19
Popularity: 0.990991
First Submitted: 2011-12-14 17:03
Last Updated: 2019-04-17 13:06

Pinned Comments

hseara commented on 2019-04-15 20:13

Installation notes

With cmake update to v3.14.x, gromacs is no longer capable of identifying correctly the CPU and therefore the appropriated SIMD level for compilation. If you want to compile gromacs with SIMD while the problem is not solved add the following option to PKGBUILD:

-DGMX_SIMD={AVX_128_FMA, AVX_256, AVX2_256, AVX2_128, AVX_512}

The KEYWORD depends on the SIMD support provided by your CPU.

Usage notes
source /etc/profile.d/GMXRC.bash

Latest Comments

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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.

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.