Package Details: gromacs 2023.2-1

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/
Keywords: chemistry science simulations
Licenses: LGPL
Submitter: xyproto
Maintainer: hseara (vedranmiletic)
Last Packager: vedranmiletic
Votes: 24
Popularity: 0.000335
First Submitted: 2011-12-14 17:03 (UTC)
Last Updated: 2023-08-04 19:09 (UTC)

Dependencies (11)

Required by (1)

Sources (1)

Latest Comments

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<deleted-account> commented on 2015-06-16 22:54 (UTC)

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).

<deleted-account> commented on 2015-06-16 20:08 (UTC)

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)

<deleted-account> commented on 2015-06-15 13:44 (UTC)

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

hseara commented on 2015-06-02 20:24 (UTC)

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 (UTC)

@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.

<deleted-account> commented on 2015-05-24 02:03 (UTC)

5.0.5 has been released

hseara commented on 2015-01-13 12:15 (UTC)

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 (UTC)

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 (UTC)

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 (UTC)

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

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