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| Name: gromacs-devel | Distribution: openSUSE:Factory:zSystems |
| Version: 2022.4 | Vendor: openSUSE |
| Release: 1.1 | Build date: Sat Jan 7 17:13:56 2023 |
| Group: Development/Libraries/C and C++ | Build host: s390zp28 |
| Size: 1140599 | 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. This package contains development libraries and header for GROMACS
Apache-2.0 AND LGPL-2.1-or-later AND BSD-3-Clause
* 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
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/usr/include/gromacs/math/units.h /usr/include/gromacs/math/utilities.h /usr/include/gromacs/math/vec.h /usr/include/gromacs/math/vectypes.h /usr/include/gromacs/mdrun /usr/include/gromacs/mdrun/simulationinputhandle.h /usr/include/gromacs/mdtypes /usr/include/gromacs/mdtypes/inputrec.h /usr/include/gromacs/mdtypes/md_enums.h /usr/include/gromacs/options /usr/include/gromacs/options.h /usr/include/gromacs/options/abstractoption.h /usr/include/gromacs/options/basicoptions.h /usr/include/gromacs/options/filenameoption.h /usr/include/gromacs/options/filenameoptionmanager.h /usr/include/gromacs/options/ioptionsbehavior.h /usr/include/gromacs/options/ioptionscontainer.h /usr/include/gromacs/options/ioptionscontainerwithsections.h /usr/include/gromacs/options/ivaluestore.h /usr/include/gromacs/options/optionfiletype.h /usr/include/gromacs/options/optionflags.h /usr/include/gromacs/options/options.h /usr/include/gromacs/options/timeunitmanager.h /usr/include/gromacs/pbcutil /usr/include/gromacs/pbcutil/pbc.h /usr/include/gromacs/restraint /usr/include/gromacs/restraint/restraintpotential.h /usr/include/gromacs/selection /usr/include/gromacs/selection.h /usr/include/gromacs/selection/indexutil.h /usr/include/gromacs/selection/nbsearch.h /usr/include/gromacs/selection/position.h /usr/include/gromacs/selection/selection.h /usr/include/gromacs/selection/selectioncollection.h /usr/include/gromacs/selection/selectionenums.h /usr/include/gromacs/selection/selectionoption.h /usr/include/gromacs/selection/selectionoptionbehavior.h /usr/include/gromacs/selection/selectionoptionmanager.h /usr/include/gromacs/topology /usr/include/gromacs/topology/atomprop.h /usr/include/gromacs/topology/atoms.h /usr/include/gromacs/topology/block.h /usr/include/gromacs/topology/forcefieldparameters.h /usr/include/gromacs/topology/idef.h /usr/include/gromacs/topology/ifunc.h /usr/include/gromacs/topology/index.h /usr/include/gromacs/topology/symtab.h /usr/include/gromacs/topology/topology.h /usr/include/gromacs/trajectory /usr/include/gromacs/trajectory/trajectoryframe.h /usr/include/gromacs/trajectoryanalysis /usr/include/gromacs/trajectoryanalysis.h /usr/include/gromacs/trajectoryanalysis/analysismodule.h /usr/include/gromacs/trajectoryanalysis/analysissettings.h /usr/include/gromacs/trajectoryanalysis/cmdlinerunner.h /usr/include/gromacs/trajectoryanalysis/topologyinformation.h /usr/include/gromacs/utility /usr/include/gromacs/utility/arrayref.h /usr/include/gromacs/utility/basedefinitions.h /usr/include/gromacs/utility/baseversion.h /usr/include/gromacs/utility/classhelpers.h /usr/include/gromacs/utility/current_function.h /usr/include/gromacs/utility/enumerationhelpers.h /usr/include/gromacs/utility/exceptions.h /usr/include/gromacs/utility/fileptr.h /usr/include/gromacs/utility/flags.h /usr/include/gromacs/utility/futil.h /usr/include/gromacs/utility/gmxassert.h /usr/include/gromacs/utility/listoflists.h /usr/include/gromacs/utility/pleasecite.h /usr/include/gromacs/utility/programcontext.h /usr/include/gromacs/utility/range.h /usr/include/gromacs/utility/real.h /usr/include/gromacs/utility/smalloc.h /usr/include/gromacs/utility/stringutil.h /usr/include/gromacs/utility/unique_cptr.h /usr/include/gromacs/version.h /usr/include/nblib /usr/include/nblib/basicdefinitions.h /usr/include/nblib/box.h /usr/include/nblib/exception.h /usr/include/nblib/gmxcalculatorcpu.h /usr/include/nblib/integrator.h /usr/include/nblib/interactions.h /usr/include/nblib/kerneloptions.h /usr/include/nblib/listed_forces /usr/include/nblib/listed_forces/bondtypes.h /usr/include/nblib/listed_forces/calculator.h /usr/include/nblib/listed_forces/definitions.h /usr/include/nblib/molecules.h /usr/include/nblib/nblib.h /usr/include/nblib/nbnxmsetuphelpers.h /usr/include/nblib/particlesequencer.h /usr/include/nblib/particletype.h /usr/include/nblib/simulationstate.h /usr/include/nblib/topology.h /usr/include/nblib/tpr.h /usr/include/nblib/util /usr/include/nblib/util/setup.h /usr/include/nblib/util/traits.hpp /usr/include/nblib/util/util.hpp /usr/include/nblib/vector.h /usr/lib64/libgmxapi.so /usr/lib64/libgromacs.so /usr/lib64/libnblib_gmx.so /usr/lib64/pkgconfig/libgromacs.pc /usr/share/cmake /usr/share/cmake/gmxapi /usr/share/cmake/gmxapi/gmxapi-config-version.cmake /usr/share/cmake/gmxapi/gmxapi-config.cmake /usr/share/cmake/gmxapi/gmxapi-release.cmake /usr/share/cmake/gmxapi/gmxapi.cmake /usr/share/cmake/gromacs /usr/share/cmake/gromacs/gromacs-config-version.cmake /usr/share/cmake/gromacs/gromacs-config.cmake /usr/share/cmake/gromacs/gromacs-hints.cmake /usr/share/cmake/gromacs/libgromacs-release.cmake /usr/share/cmake/gromacs/libgromacs.cmake /usr/share/gromacs/template /usr/share/gromacs/template/CMakeLists.txt /usr/share/gromacs/template/Makefile.pkg /usr/share/gromacs/template/README /usr/share/gromacs/template/cmake /usr/share/gromacs/template/cmake/FindGROMACS.cmake /usr/share/gromacs/template/template.cpp
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