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2016

GROMACS 2016 release

100%

70 issues   (70 closed — 0 open)

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Bug

46/46
Feature

12/12
Task

12/12
Related issues
Bug #692: Frequency of checking for inter-simulation signalling is too high for large-scale parallel REMD
Bug #860: Checkpoint not created upon reaching time given in maxh
Bug #1135: various detection and -multi don't work well enough together
Bug #1248: nvcc host compiler sanity checks break with cmake >=2.8.10
Bug #1291: GPU/CPU force evaluation time ratio seems wrong
Bug #1338: incorrect automatic selection of MPI threads/DD with GPU
Bug #1636: mdrun -multidir does not write checkpoint files after restart
Bug #1705: trjcat append feature is broken
Bug #1773: "Lambda" (value of fep-lambdas) is output to log at evey step for every simulation
Bug #1777: Teach mdrun about explicit -append
Bug #1787: g_wham uses wrong constant to convert kJ to kcal
Bug #1795: limit test binaries to only one MPI rank where necessary/appropriate
Bug #1799: cmake chooses Python 3 instead of Python 2
Bug #1808: error: 'asm' operand has impossible constraints when compiling gromacs 5.1 on PPC64 and PPC64LE with VSX SIMD
Bug #1857: -multidir for runs with different number of steps only runs for the shortest number of steps
Bug #1882: issue with DD missing impossible exclusions
Bug #1886: master(72a776a27f10c7d0f19cbbae10dd2da78df7c959) fails clang-3.4.0
Bug #1887: gmx insert-molecules cannot write PDB files with PDB input for -f
Bug #1909: SIMD module compilation broken on Power8
Bug #1910: error: 'Simd4Real' was not declared in this scope while building with -DGMX_SIMD=SSE2 -DGMX_DOUBLE=ON
Bug #1911: some internal unit tests fail with segmentation fault in gmock
Bug #1926: gmx analysis tools require big-endian TRR trajectories
Bug #1933: some internal unit tests fail with illegal instruction (mrrc) on armv7hfp in wallcycle_have_counter()
Bug #1935: hbond wrong literature reference
Bug #1942: maxh option and checkpoint writting do not work with REMD simulations
Bug #1945: Lakcing checks in mdp option parsing
Bug #1946: hwloc slow
Bug #1951: mdrun segfaults with -ntmpi 1
Bug #1955: Segmentation fault when minimizing box of water
Bug #1958: Segfault with non-interacting atoms with Verlet scheme
Bug #1960: Constraints violate freeze groups where not all coordinates are frozen
Bug #1968: V-rescale thermostat and replica exchange broken
Bug #1976: make_ndx "AND" keyword seems broken
Bug #1978: IMD include files not always sufficient
Bug #1979: ../../lib/libgromacs.so.3.0.0: undefined reference to `vmddlclose'
Bug #1980: warning: "_POSIX_THREAD_CPUTIME" is not defined
Bug #1981: dd121 regressiontest fails with >=4 MPI ranks + OpenMP
Bug #1986: Test failures on i386 in NormalDistributionTest
Bug #1987: Test suite failures on several less-common architectures
Bug #1988: Double-precision SIMD test failure on powerpc
Bug #1993: calc_verlet_buffer_size can't handle nstlist==1
Bug #1997: big-endian power7 testbits is broken
Bug #1998: membed is apparently broken
Bug #2000: cmake 3.5.1 + ninja not quite happy with dev-guide build system
Bug #2008: -msse2 not passed to compiler flags with -DGMX_SIMD=SSE2
Bug #2023: Segfault again with non-interacting atoms and verlet cutoff
Feature #879: Normal modes with vsites and/or shells does not work
Feature #1346: COM pulling increased flexibility and clarification
Feature #1394: 16-wide MIC SIMD bonded interaction kernels
Feature #1612: generating SIMD code
Feature #1790: Semi-automatic select correct STL version for C++11
Feature #1833: provide means to inspect/change nvcc flags
Feature #1861: Add support for trajectories of part of the system to new analysis framework
Feature #1863: write tng files with velocities from mdrun
Feature #1932: More citations for membrane protein embedding algorithms
Feature #1956: Add support for building against external tinyxml2
Feature #1957: Add support for building against external lmfit
Feature #1962: smarter box-size checking with the pull code
Task #1072: REMD continuation
Task #1390: manage C+11 support and CUDA better
Task #1396: add install step to continuous-integration testing
Task #1415: Get rid of legacyheaders/
Task #1444: break up the nbnxn_cuda module into multiple compilation units
Task #1643: improve CPU/GPU hardware reporting
Task #1804: investigate OpenCL + MPI
Task #1831: remove CUDA polling wait
Task #1921: work around issues with AMD APPSDK 3.0
Task #1938: work around broken NVIDIA JIT caching
Task #1982: work around compilation error with nvcc + glibc 2.23
Task #1992: mdrun should not advise users of things that don't matter