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| Name: gromacs-devel | Distribution: SUSE Linux Enterprise 15 SP3 |
| Version: 2019.6 | Vendor: openSUSE |
| Release: bp153.1.1 | Build date: Tue Apr 20 10:48:29 2021 |
| Group: Development/Libraries/C and C++ | Build host: obs-arm-8 |
| Size: 1298110 | Source RPM: gromacs-2019.6-bp153.1.1.src.rpm |
| Packager: https://bugs.opensuse.org | |
| Url: http://www.gromacs.org | |
| Summary: Molecular dynamics package | |
GROMACS is a versatile and extremely well optimized package to perform molecular dynamics computer simulations and subsequent trajectory analysis. It is developed for biomolecules like proteins, but the extremely high performance means it is used also in several other field like polymer chemistry and solid state physics. This package contains development libraries and header for GROMACS
GPL-2.0-or-later AND Apache-2.0
* 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
* Tue Nov 13 2018 Christoph Junghans <junghans@votca.org>
- version bump to 2018.4 details here:
http://manual.gromacs.org/documentation/2018.4/release-notes/2018/2018.4.html
Highlights:
- Correct PME forces with free energy without perturbed charges/LJ
- Add constraint contribution to foreign Hamiltonian differences
- Add mass contribution to foreign Hamiltonian differences
- Work around bugs with expanded ensemble runs
- Checkpoint continuations require suitable .tpr files
- Fix mindist output file checks
- Fix gmx helix segmentation faults
- Fix bug in entropy calculation in gmx anaeig
- Fixed an issue where the log file could sometimes report an incorrect initial dynamic load balancing state
- Fix Bromine parameters in amber forcefield files
- Made normal-mode analysis work for more than one molecule
- Disallow rerun using same filename as output file
- Fix issue when building GROMACS without TNG
* Wed Nov 07 2018 Christoph Junghans <junghans@votca.org>
- version bump to 2018.3 details here:
http://manual.gromacs.org/documentation/2018.3/release-notes/2018/2018.3.html
Highlights:
- Multi-domain GPU runs can no longer miss pair interactions
- Fix Conjugate Gradient assertion failure at end of minimization
- Multi-domain Conjugate Gradient minimimization no longer segfaults.
- Fix pairlist buffer with Brownian Dynamics
- Avoid “atom moved to far” errors
- grompp now checks that pull groups are not close to half the box size
- Fixed segmentation fault in mdrun with QM/MM ONIOM scheme
- Fixed syntax error in make_gromos_rtp.py
- Fix gmx solvate topology updating
- Fix bfactor output error caused by fix for Issue 2511
- Made sure that gmx rms can skip values
- Fix trjconv when not providing structure file
- Fix enforced rotation energy output
- Fix nvcc host compiler check triggering
- Report up to date hwloc version information
- Disable single compilation unit with CUDA 9.0
- Avoid aborting mdrun when GPU sanity check detects errors
- Improve OpenCL kernel performance on AMD Vega GPUs
* Sat Jul 21 2018 junghans@votca.org
- version bump to 2018.2 details here:
http://manual.gromacs.org/documentation/2018.2/release-notes/2018/2018.2.html
Highlights:
- Prevented OpenCL timing memory leak
- Fixed MPI error after constraint failure during energy minimization
- Fixed moving frozen atoms with constraints
- Fixed COM removal moving frozen atoms
* Wed Apr 04 2018 junghans@votca.org
- version bump to 2018.1 details here:
http://manual.gromacs.org/documentation/2018.1/release-notes/2018/2018.1.html
Highlights:
- Fixed leap-frog integrator with Nose-Hoover T coupling and Parrinello-Rahman P coupling
- Used SIMD bondeds without perturbed interactions
- Fixed bonds whose displacement was zero
- Fixed centre-of-mass motion removal on part of the system
- Fixed multi-simulations with multiple ranks per simulation
- Improved inter-simulation signalling implementation
- Fixed FEP calculations with SHAKE
- Fixed handling of mdp define statement assigning preprocessor values
- Prevented log file energy average printing dividing by zero
* Fri Mar 23 2018 guillaume.gardet@opensuse.org
- Add _constraints file to avoid build failure and timeout on tests
for slow CPU workers
* Fri Jan 19 2018 junghans@votca.org
- version bump to 2018 details here:
http://manual.gromacs.org/documentation/2018/ReleaseNotes/index.html
Highlights:
- A new dual-list dynamic-pruning algorithm for the short-ranged interactions
- PME long-ranged interactions can now run on a single GPU
- AWH (Accelerated Weight Histogram) method is now supported
- A physical validation suite is added, which runs a series of short simulations
- Conserved quantities are computed and reported for more integration schemes
- disable GPU on ppc64le, build error
- use internal tinyxml2 as tinxml-6 is broken with gromacs, only testing is build it anyhow
* Sat Nov 04 2017 junghans@votca.org
- enable GPU support via OpenCL
* Wed Oct 25 2017 kkaempf@suse.com
- adapt to new openlmi package - source mpivars.h during build
* Fri Sep 15 2017 junghans@votca.org
- version bump to 2016.4 details here:
http://manual.gromacs.org/documentation/2016.4/ReleaseNotes/index.html
Highlighs:
- Disabled PME tuning with the group scheme
- Fixed value of Ewald shift
- Fixed orientation restraint reference
- Fixed bugs with setup for orientation restraints
- Worked around missing OpenMP implementation in orientation restraints
- Enable group-scheme SIMD kernels on recent AVX extensions
- Fix FEP state with rerun
- Fixed COM pull force with SD
- Fix PBC bugs in the swap code
- Fixed flat-bottomed position restraints with multiple ranks
- Fixed null pointer print in DD
- Improved the “files not present” error message
- Fixed LJ-PME + switch grompp error
- Fixed unused SIMD PME table kernel
- Fixed bugs in most double-precision Simd4 implementations
- Avoid inf in SIMD double sqrt()
- Fix NVML error messages
- Fixed IMD interface malfunctions
- Fixed initial temperature reporting
- Fix exception in SIMD LJ PME solve
* Tue Aug 08 2017 junghans@votca.org
- Fix build on Factory
* Mon May 08 2017 junghans@votca.org
- __builddir is not overwritable on SLE-12, so use subdirs
- disable test on s390x (too slow)
* Tue Mar 14 2017 junghans@votca.org
- version bump to 2016.3 details here:
http://manual.gromacs.org/documentation/2016.1/ReleaseNotes/index.html
- Highlights:
- Made distance restraints work with threads and DD
- Fixed Ewald surface+3DC corrections
- Fixed opening of wall table files
- Fixed bug in gmx insert-molecules.
- Made virial reproducible
- Updated to support FFTW 3.3.5
- Permitted automatic load balancing to disable itself when it makes the run slower
- Improved the accuracy of timing for dynamic load balancing with GPUs
- Corrected kernel launch bounds for Tesla P100 GPUs
- Improved logic handling if/when the run is terminated for SETTLE warnings
- Fixed bug in gmx wham for reading pullx files.
- Fixed ouput bug in gmx wham
- Fixed deadlock with thread-MPI
- Made error reporting in grompp more user friendly
- Fixed SIMD suggestion for VMX
- Fixed script xplor2gmx.pl to work with GMXDATA
- Fixed default nice level in mdrun-only build
- Fixed math-test false positive
- Improved documentation
- OpenCL error string are now written, instead of cryptic error codes
- Fixed build with GMX_USE_TNG=off
- Removed variable-precision .gro writing
- Fixed BG/Q platform files and install guide
- Reduced the memory required for free-energy simulations
* Sat Nov 05 2016 junghans@votca.org
- version bump to 2016.1 details here:
http://manual.gromacs.org/documentation/2016/ReleaseNotes/index.html
- Highlights:
- Made distance restraints work with threads and DD
- Fixed Ewald surface+3DC corrections
- Fixed opening of wall table files
- Fixed bug in gmx insert-molecules.
- Made virial reproducible
- Permitted automatic load balancing to disable itself when it makes the run slower
- Improved the accuracy of timing for dynamic load balancing with GPUs
- Corrected kernel launch bounds for Tesla P100 GPUs
- Improved logic handling if/when the run is terminated for SETTLE warnings
- Fixed bug in gmx wham for reading pullx files.
- Fixed ouput bug in gmx wham
- Fixed deadlock with thread-MPI
- Made error reporting in grompp more user friendly
- Fixed SIMD suggestion for VMX
- Fixed script xplor2gmx.pl to work with GMXDATA
- Fixed default nice level in mdrun-only build
- Fixed math-test false positive
- Improved documentation
- Fixed build with GMX_USE_TNG=off
- Removed variable-precision .gro writing
- Reduced the memory required for free-energy simulations
* Wed Aug 24 2016 junghans@votca.org
- version bump to 2016 details here:
http://manual.gromacs.org/documentation/2016/ReleaseNotes/index.html
- Highlights:
- As always, we’ve got several useful performance improvements, with or without GPUs. CPU-side SIMD and threading enhancements will make GPU-accelerated simulations faster even if we’d left the GPU code alone! Thanks to these and additional GPU kernel improvements, in GPU-accelerated runs expect around 15% improvement in throughput. (And not just for plain vanilla MD, either... the pull code now supports OpenMP threading throughout, and multi-simulations have less coupling between simulations.)
- We have a new C++11 portability layer permitting us to accelerate in SIMD on the CPU lots of minor routines. These will also often improve runs that use accelerators or many nodes through better load balancing. POWER8, ARM64, AVX512 (KNL), and more are fully SIMD accelerated now because they are supported in the new portability layer!
- We made further SIMD acceleration of bonded interactions which reduces their calculation time by about a factor of 2. This improves load balance at high parallelization by a factor of 2, and shows significantly better scaling.
- Similarly, SIMD acceleration of SETTLE reduces the time for constraints by a factor of 3 to 5 - which has a strong effect for GPU runs.
- OpenCL GPU support is now available with all combinations of MPI, thread-MPI and GPU sharing (ie. the same as CUDA). Kernel performance has improved by up to 60%. AMD GPUs benefit the most, OpenCL on NVIDIA is generally still slow.
- Tools in the new analysis framework can handle trajectories that are subsets of the simulation system.
- New pull coordinate geometries angle-axis, dihedral, and normal angle.
- Checkpoint restarts work only in the cases where the implementation can always do what the user wants.
- The version numbering has changed to be the year of the release, plus (in future) a patch number. GROMACS 2016 will be the initial release from this branch, then GROMACS 2016.1 will have the set of bugs that have been fixed in GROMACS 2016, etc.
* Wed Oct 14 2015 junghans@votca.org
- version bump to 5.1 details here:
http://manual.gromacs.org/documentation/5.1/ReleaseNotes/index.html
- html documentation is gone
- devel package now includes cmake macros and config files
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