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gromacs-2022.4-1.1 RPM for s390x

From OpenSuSE Ports Tumbleweed for s390x

Name: gromacs Distribution: openSUSE:Factory:zSystems
Version: 2022.4 Vendor: openSUSE
Release: 1.1 Build date: Sat Jan 7 17:13:56 2023
Group: Productivity/Scientific/Chemistry Build host: s390zp28
Size: 110630 Source RPM: gromacs-2022.4-1.1.src.rpm
Packager: https://bugs.opensuse.org
Url: https://www.gromacs.org
Summary: Molecular Dynamics Package
GROMACS is a package to perform molecular dynamics computer
simulations and subsequent trajectory analysis. It is developed for
biomolecules like proteins, but it can be used in several other field
like polymer chemistry and solid state physics.

Provides

Requires

License

Apache-2.0 AND LGPL-2.1-or-later AND BSD-3-Clause

Changelog

* Wed Dec 28 2022 Stefan Brüns <stefan.bruens@rwth-aachen.de>
  - Update to 2022.4
    * Bugfix release, see
      https://manual.gromacs.org/current/release-notes/2022/2022.4.html
  - Drop ustream relax_test_tolerance.patch
* Sun Dec 25 2022 Stefan Brüns <stefan.bruens@rwth-aachen.de>
  - Exclude MPI flavor on 32 bit architectures, as MPI communication
    does not work correctly.
* Mon Nov 07 2022 Stefan Brüns <stefan.bruens@rwth-aachen.de>
  - Fix aarch64 build on 15.x, add relax_test_tolerance.patch
  - Relax memory and disk constraints
* Wed Nov 02 2022 Stefan Brüns <stefan.bruens@rwth-aachen.de>
  - Use system muparser package, drop libmuparser2 subpackage
  - Use system zlib
  - Remove bogus/broken library package obsoletes and provides
  - Build openmpi version in separate _multibuild
* Fri Oct 14 2022 Klaus Kämpf <kkaempf@suse.com>
  - Update to 2022.3
    * Bugfix release, see
      https://manual.gromacs.org/current/release-notes/2022/2022.3.html
  - Update to 2022.2
    * Bugfix release, see
      https://manual.gromacs.org/current/release-notes/2022/2022.2.html
  - Update to 2022.1
    * Highlights:
    - Free-energy kernels are accelerated using SIMD, which make
      free-energy calculations up to three times as fast when using GPUs
    - A new formulation of the soft-cored non-bonded interactions for
      free-energy calculations allows for a finer control of the alchemical
      transformation pathways
    - New transformation pull coordinate allows arbitrary mathematical
      transformations of one of more other pull coordinates
    - New interface for multi-scale Quantum Mechanics / Molecular
      Mechanics (QM/MM) simulations with the CP2K quantum chemistry package,
      supporting periodic boundary conditions.
    - grompp performance improvements
    - Cool quotes music playlist
    - Additional features were ported to modular simulator
    - Added AMD GPU support with SYCL via hipSYCL
    - More GPU offload features supported with SYCL (PME, GPU update).
    - Improved parallelization with GPU-accelerated runs using CUDA and
      extended GPU direct communication to support multi-node simulation
      using CUDA-aware MPI.
    * See https://manual.gromacs.org/current/release-notes/2022/2022.1.html
  - split off libmuparser2 into separate package
* Wed May 04 2022 Christoph Junghans <junghans@votca.org>
  - devel package requires binaries as well
* Wed Apr 27 2022 Jan Engelhardt <jengelh@inai.de>
  - Trim boasting from package descriptions.
  - Trim descriptions in less important subpackages for length.
  - Resolve rpmlint reports:
    * "libgromacs4.x86_64: E: shlib-policy-name-error SONAME:
      libgmxapi.so.0, expected package suffix: 0"
    * "libgromacs4.x86_64: E: shlib-policy-name-error SONAME:
      libgromacs.so.6, expected package suffix: 6"
* Sun Dec 05 2021 Max Lin <mlin@suse.com>
  - Update license to "LGPL-2.1-or-later AND Apache-2.0 AND BSD-3-Clause"
* Wed Nov 10 2021 Christoph Junghans <junghans@votca.org>
  - Tag build with "openSUSE" for easier debugging by upstream
* Thu Sep 30 2021 Nicolas Morey-Chaisemartin <nmoreychaisemartin@suse.com>
  - Use openmpi macros to always build with the default openmpi version.
* Mon Jul 12 2021 Christoph Junghans <junghans@votca.org>
  - Enabled legacy api needed for votca-csg
* Mon Jun 28 2021 Atri Bhattacharya <badshah400@gmail.com>
  - Update to version 2021.2:
    * Fixes where mdrun could behave incorrectly.
    * Removed a potential race condition with GPU update (issue
      4024).
    * Avoided issues with global reduction observed with md-vv
      (issue 4031).
    * Prohibited SETTLE interactions for atoms with perturbed masses
      (issue 3959).
    * Rerun now writes pull output correctly (issue 4043).
    * Fixes for ``gmx`` tools.
    * Fix incorrect behaviour with single residue chains in pdb2gmx
      (issue 4029).
    * Fix grompp check for position restraints with absolute
      reference (issue 3996).
    * Fix error when using VMD plugin (issue 3055).
    * Fix file permissions with ``gmx solvate`` and ``gmx genion``
      (issue 4040).
    * Fixes that affect portability.
    * Support for Intel oneAPI compiler 2021.2.
    * Fixed compiler infinity math and MKL flags.
    * Fix Apple OpenCL build (issue 4008).
    * Fixed compilation issue with GCC 11 (issue 4039).
    * Fix bond type in GROMOS force fields (issue 3995).
    * Allow PME on CPU in runs with domain decomposition and GPU
      update (issue 4035).
  - Turn SKIP_RPATH=OFF and SKIP_INSTALL_RPATH=ON instead; skipping
    rpath use entirely causes linking issues with tests, but we
    still want to disable rpaths for the installed libs of course.
  - Rename %{name}-bash to %{name}-bash-completion in keeping with
    naming convention followed by other packages.
  - Add lapack-devel to BuildRequires to use system versions of blas
    and lapack.
  - CMake 3.13 or higher is required; adapt BuildRequires
    accordingly.
  - Disable testing for i586: doesn't work with gmock.
  - Adapt to updated cmake options and drop no longer applicable
    ones.
* Mon Jul 27 2020 Michel Normand <normand@linux.vnet.ibm.com>
  - Increase default disk size from 3 to 6GB in _constraints file
* Fri Feb 28 2020 Christoph Junghans <junghans@votca.org>
  - - version bump to 2019.6 details here:
    http://manual.gromacs.org/documentation/2019.6/release-notes/2019/2019.6.html
    Hightlights:
    - Actually fix PME forces with FE without perturbed q/LJ
    - Avoid overzealous program abort with orientation restraints
    - Calculate Coulomb and LJ reciprocal terms in rerun
    - Added check for inconsistent input of distance restraint labels in gmx disre.
    - Fix compiler errors with Intel compiler
    - Avoid cryptic GPU detection errors when devices are unavailable or out of memory
* Mon Dec 23 2019 Christoph Junghans <junghans@votca.org>
  - version bump to 2019.5 details here:
    http://manual.gromacs.org/documentation/2019.5/release-notes/2019/2019.5.html
    Hightlights:
    - Fix use of uninitialized data on PME only ranks
    - Fix out of range memory access with free-energy calculations
    - Fix error with intermolecular interactions and domain decomposition
    - Fix issues with AWH with pull-geometry ‘direction’ to be periodic
    - Remove assertion failure with AWH when not using the initial stage
    - Fix dihedral angle calculation near 180 degree boundary
    - Remove problematic output of gmx angle tool
    - Check that libhwloc headers and runtime match
    - Fix .gro file formatting with large boxes
    - Fix duplicate PDB CONECT record output
* Fri Nov 15 2019 Christoph Junghans <junghans@votca.org>
  - version bump to 2019.4 details here:
    http://manual.gromacs.org/documentation/2019.4/release-notes/2019/2019.4.html
    Hightlights:
    - Fix incorrect pressure when atoms in CMAP cross a box boundary
    - Fix incorrect LJ cut-off on GPU when rvdw < rcoulomb
    - Fix (unlikely) missing bonded forces with CUDA GPUs and domain decomposition
    - Fix incorrect reporting of final kinetic energy and temperature
    - Fix segmentation fault in grompp and mdrun with cosine COM pulling
    - Fix grompp not adding angle constraints between constraints
    - Fix gmx wham with angle and dihedral geometries
    - Fix bug in gmx xpm2ps
    - Fix bug in gmx anaeig
    - Fix issue with demux.pl script
    - Fixed writing of gro files with index groups
    - Made gmx make_ndx keep chain IDs
    - Fixes that affect portability
* Wed May 08 2019 Christoph Junghans <junghans@votca.org>
  - version bump to 2019.2 details here:
    http://manual.gromacs.org/documentation/2019.2/release-notes/2019/2019.2.html
    Hightlights:
    - Fix L-BGFS minimizer
    - Disallow pull geometry direction-periodic with AWH
    - Fixed mdrun -nsteps option
    - gmx cluster -clndx indices now correct
    - gmx editconf -f in.pdb -o out.pdb again preserves chain IDs
    - Tools again accept .tpr files as input
    - Fix segmentation fault when preparing simulated annealing inputs
    - Fix error in AVX 512 detection code
    - Added warning with the use of GROMOS force fields
    - Prevented internal build of FFTW with clang and AVX-512 SIMD
    - Updated performance guide for recent Intel processors with AVX512 instruction support
* Tue Feb 26 2019 Klaus Kämpf <kkaempf@suse.com>
  - add fdupes
* Mon Feb 25 2019 Christoph Junghans <junghans@votca.org>
  - version bump to 2019.1 details here:
    http://manual.gromacs.org/documentation/2019.1/release-notes/2019/2019.1.html
    Hightlights:
    - Fix error with 2D/3D dynamic load balancing
    - Fix incorrect LJ repulsion force switching on GPUs
    - Fix segmentation fault in mdrun with domain decomposition
    - Fix segmentation fault with energy minimization with the group scheme
    - Correct free-energy Delta H output with mass lambda’s
    - Prevent mdrun -rerun from writing incorrect free-energy output
    - Fix possible division by zero in enforced-rotation code
    - Fix trjconv -ndec
    - Fix using index file groups when .tpr file not supplied
    - Fix tune_pme
    - Fixes that affect portability
    - Explicitly require 64-bit platforms for OpenCL

Files

/usr/bin/demux.pl
/usr/bin/gmx
/usr/bin/xplor2gmx.pl


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