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| Name: gromacs-openmpi | Distribution: openSUSE Tumbleweed |
| Version: 2024 | Vendor: openSUSE |
| Release: 2.1 | Build date: Thu Feb 8 19:43:15 2024 |
| Group: Productivity/Scientific/Chemistry | Build host: i01-armsrv1 |
| Size: 135072 | Source RPM: gromacs-openmpi-2024-2.1.src.rpm |
| Packager: http://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.
Apache-2.0 AND LGPL-2.1-or-later AND BSD-3-Clause
* Fri Feb 02 2024 Christoph Junghans <junghans@votca.org>
- Aarch64: fix tests and enable neon support
- Tests have race condition, run them serially
* Thu Feb 01 2024 Christoph Junghans <junghans@votca.org>
- Update to 2024
* Highlights:
- The Colvars library can now be used natively from GROMACS. This
simplifies the use of advanced enhanced sampling simulations.
- Reduced artifacts from Lennard-Jones pair interactions on the
pressure by a configurable increase of the Verlet buffer. Can
lead to a slight performance loss, especially for coarse-grained
systems.
- Corrected several aspects of the deform option. Now simulations with
box deformation behave correctly under high shear or when a solid or
membrane fractures. This also means that the deform option is now
suitable for computing viscosities.
- New option for hydrogen mass repartitioning in grompp enables easy
access to performance improvements.
- Improvements to AWH, such as better control of the histogram growth
factor as well as enabling automatic scaling of the target distribution
based on the AWH friction metric.
- Configurable HeFFTe multi-GPU FFT options lets users fine-tune the
settings for specific use-cases.
* See https://manual.gromacs.org/2024.0/release-notes/index.html
* Sun Apr 02 2023 andy great <andythe_great@pm.me>
- Update to 2023
* Highlights:
- The SYCL GPU implementation, which is the GPU portability
layer that supports all major GPU platforms, has received
major extensions in support for both platforms and features.
To ensure portability in practice, the GROMACS GPU portability
layer is actively developed with multiple SYCL implementations
(hipSYCL, oneAPI DPC++, IntelLLVM) and regularly tested on
multiple GPU backends.
- SYCL supports more GPU offload features: bonded forces and
direct GPU-GPU communication with GPU-aware MPI.
- SYCL hardware support includes AMD (including RDNA support
added here) and Intel for production as well as NVIDIA GPUs
(not for production).
- SYCL optimizations targeting important HPC platforms.
- PME decomposition has been optimized and extended to support
offloading the entire PME calculation to multiple GPUs,
including the FFT computation; when combined with cuFFTmp or
heFFTe this enables much improved strong scaling
(experimental feature).
- CUDA Graph support has been added to execute GPU-resident
single-/multi-GPU simulations using thread-MPI entirely on the
GPU to improve performance (experimental feature).
- New ensemble temperature mdp options allow setting the
temperature of the ensemble for simulations without
temperature coupling or with different reference temperatures.
- With gmx dssp, GROMACS now has a native implementation of the
DSSP algorithm, which replaces gmx do_dssp.
* See https://manual.gromacs.org/2023/release-notes/index.html
- Update to 2022.6
* Bugfix release, see
https://manual.gromacs.org/2023/release-notes/2022/2022.6.html
- Update to 2022.5
* Bugfix release, see
https://manual.gromacs.org/2023/release-notes/2022/2022.5.html
* 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.
/usr/bin/gmx_mpi
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Fabrice Bellet, Sat Apr 27 01:37:30 2024