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2019

Due in 15 days (01/01/2019)

Annual major release

73%

106 issues   (75 closed — 31 open)

Issues by
Bug

39/51
Feature

12/12
Task

24/43
Related issues
Bug #1714: Website: Links to the online manual are broken
Bug #2141: Each new invocation of mdrun needs it's own setting to use MPI on 28 cores
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 #2468: incorrect GPU timing reported with OpenCL and domain decomposition
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 #2503: post-submit has warnings
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 #2562: Clarify how to do float->int rounding
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 #2648: icc 18 post-submit fails to compile not_null tests
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 #2681: clang-6 native CUDA undefined template warnings
Bug #2689: gpu timer state not cleaned up
Bug #2692: docs should not have unused files
Bug #2704: investigate change to log file
Bug #2722: gmxapi may over-manage RPATH
Bug #2726: FP exception in cufft 7.0
Bug #2734: regressiontests/kernel core dumps on ppc64le
Bug #2737: AMD OpenCl failes release build in complex tests
Bug #2753: Segmentation fault in MiMiC parallel runs with Intel MPI
Bug #2765: gmxapi MPI tests don't handle many-core systems
Bug #2768: clang 7.0.0 warns about unused variable in gmxapi
Bug #2769: mdrun freezes when running too many threads
Bug #2775: number of ranks reporting was wrong
Bug #2778: Some pictures appear too small in the web reference manual
Bug #2800: gmx analyze cannot use lmfit
Feature #1054: implicit solvent parallelization
Feature #2072: target hardware description is silent about the result
Feature #2305: Switch to dynamic number of groups in .tpr file
Feature #2307: Implement MiMiC-based 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 #2691: MiMiC needs reference documentation
Feature #2748: Power9 build system support
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 #2193: OpenCL code modernization assuming v1.2 reqd
Task #2336: improve on relative tolerance tests for tabulated interaction
Task #2344: Agree on standards for different types of output and log files
Task #2355: update bundled googletest
Task #2379: check leftover FIXMEs in r2018
Task #2408: device busy error with CC 2.0 and 6.1 in the same run
Task #2438: bump OpenCL requirement to 1.2
Task #2453: PME OpenCL porting effort
Task #2454: OpenCL infrastructure improvements
Task #2500: detect and allow linking external clFFT
Task #2515: clFFT RocM compatibility problem
Task #2528: PME GPU tuning
Task #2529: Improve test timeouts handling
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 #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 #2677: bonded task scheduling
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 #2699: Test POWER9
Task #2723: Update mdrun-performance.rst to clearly express the nature of task
Task #2724: Clean up organization of bonded cuda module
Task #2751: checking for Sphinx executable version needs improvement
Task #2756: gmxapi integration testing
Task #2772: check performance on POWER9
Task #2777: add ARM-related perf recommendations ot the used guide
Task #2784: update parallel lincs reference manual section for update groups
Task #2793: update performance checklist