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2019

Due in about 2 months (01/01/2019)

Annual major release

50%

97 issues   (46 closed — 51 open)

Issues by
Bug

21/40
Feature

9/13
Task

16/44
Related issues
Bug #2141: Each new invocation of mdrun needs it's own setting to use MPI on 28 cores
Bug #2192: grompp should read floats (e.g charge) from data files to double, to avoid accumulating round-off error
Bug #2244: Test rerun with FEP
Bug #2293: libraries target naming in cmake
Bug #2404: Enabling floating point exceptions makes some tests fail
Bug #2416: TPI producing invalid results with nsteps too small
Bug #2417: Physical validation tests fail with default installation
Bug #2420: OpenCL implementation not doing device sanity checks
Bug #2430: gmx trjconv gets invalid pointer if tpr is not provided
Bug #2450: OpenCL runtime version check missing
Bug #2479: gmx_mtop c++ change exposing bugs in gmx trjconv
Bug #2480: pdb2gmx does not protonate correctly for united-atom Gromos
Bug #2493: Command line file passing no longer works for gmxana tools
Bug #2494: mdrun -noappend detects incorrect part
Bug #2507: MSAN error in TNG
Bug #2533: GROMACS fails to build with lmfit-7.0
Bug #2536: clFFT execution not timed in PME
Bug #2553: Incorrect COM velocity correction with frozen atoms
Bug #2571: clang-tidy cmake needs improvement
Bug #2577: pdb2gmx chainsep is broken
Bug #2599: do_dssp works incorrectly with unknown residues
Bug #2604: gmx msd appears broken in master
Bug #2612: HostAllocationPolicy shares pointers and pinning setting through shared_ptr
Bug #2625: Movement of pull group COM atom of a large pull group can cause crashes
Bug #2635: Failing to detect GPUs should not write to terminals
Bug #2636: DD code writes to terminals too much
Bug #2642: mdrun with SIMD triggers floating point exceptions
Bug #2646: gmxapi uses major() and minor() which clashes with deprecated glibc macros
Bug #2647: Removing CGLO_TEMPERATURE flag in MD Setup leads to fatal error because of missing bonded interactions
Bug #2649: Virial calculation necessary for correct energy calculation on GPU
Bug #2664: gmxapi tests using gmx to make a .tpr needs to be quieter
Bug #2666: anaeig is not calculating entropy using the quasiharmonic formula anymore
Bug #2668: gmx anaeig entropy output are not consistent between runs
Bug #2681: clang-6 native CUDA undefined template warnings
Bug #2688: ccache detection is static
Bug #2689: gpu timer state not cleaned up
Bug #2692: docs should not have unused files
Bug #2693: Several memory leaks in mdrun
Bug #2704: investigate change to log file
Feature #1054: implicit solvent parallelization
Feature #2054: PME on GPU
Feature #2072: target hardware description is silent about the result
Feature #2305: Switch to dynamic number of groups in .tpr file
Feature #2307: Implememnt the QM/MM functionality in GROMACS
Feature #2308: Implement QM/MM updates in GROMACS preprocessor
Feature #2309: Implement MiMiC QM/MM workflow in the GROMACS core
Feature #2510: Implement update groups
Feature #2597: gmx cluster improuvement
Feature #2626: Enable outputting average pull forces (and positions)
Feature #2651: clean up mdrun log file handling
Feature #2667: Suggested steps for calculating entropy in solution and binding
Feature #2691: MiMiC needs reference documentation
Task #1043: Contrib policy
Task #1868: implement mdrun -rerun better, simplifying do_md
Task #1943: make sure releases are submitted early for Debian Experimental
Task #2122: Stop using where()
Task #2146: salvage documentation from old webpage
Task #2161: update the way testing matrices are specified
Task #2183: GPU-accessed memory page-locking and page sizes
Task #2336: improve on relative tolerance tests for tabulated interaction
Task #2344: Agree on standards for different types of output and log files
Task #2353: improve on relative tolerance for constructing tables
Task #2355: update bundled googletest
Task #2408: device busy error with CC 2.0 and 6.1 in the same run
Task #2425: testing multisim with multiple ranks per simulation
Task #2438: bump OpenCL requirement to 1.2
Task #2453: PME OpenCL porting effort
Task #2454: OpenCL infrastructure improvements
Task #2475: make OpenCL 1st class-citizen in the build system
Task #2498: OpenCL memory pinning/mapping
Task #2500: detect and allow linking external clFFT
Task #2515: clFFT RocM compatibility problem
Task #2518: redesign task-assignment code for OpenCL
Task #2522: OpenCL context duplication
Task #2524: struct alignment/packing for OpenCL host & device code
Task #2527: Rename GpuEventSynchronizer to something more fitting (after mergin PME OpenCL)
Task #2528: PME GPU tuning
Task #2529: Improve test timeouts handling
Task #2537: Simplify PME solve reduction
Task #2539: Support hwloc 2.x.x
Task #2569: announce deprecations in GROMACS 2019
Task #2650: revise OpenCL stack recommendations
Task #2655: Remove NVML support
Task #2656: Revise docs/user-guide/mdrun-performance.rst for the 2019 release
Task #2660: rework OpenCL nbnxn kernel constants
Task #2665: remove fermi support
Task #2672: check & document execution width requirements in OpenCL
Task #2673: assess / eliminate c_oclPruneKernelJ4Concurrency constant duplication
Task #2675: bonded CUDA offload task
Task #2684: make sure ARM perf libs for FFTs / BLAS works
Task #2685: tweak jenkins post-submit test to use ARMPL for FFTs
Task #2690: relax new dependency cycle
Task #2695: bonded GPU module timing
Task #2696: ensure PME queue is flushed
Task #2697: improve FFT library flavor/version reporting
Task #2699: Test POWER9