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4.6

100%

104 issues   (104 closed — 0 open)

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Estimated time 4.50 hours
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Bug

81/81
Feature

11/11
Task

12/12
Related issues
Bug #571: test/fix/update cmake builds on BlueGene
Bug #573: CMake doesn't detect Altivec support
Bug #620: Total dipole in energy files is incorrect
Bug #740: Problem related to static/shared libraries and conflicts with FFTW
Bug #767: electrostatic forces with PME and DD
Bug #797: bd giving incorrect results, such as a temperature 2x as high as it should be in release-4-5-patches
Bug #798: SigTerm during file I/O causes gmx_error
Bug #810: CHARMM cp=0 dihedrals are not ignored
Bug #811: tutorials
Bug #847: tpbconv with index file can produce incorrect tpr files
Bug #849: C++ Compile with MPI fails
Bug #878: unify GROMACS header printing
Bug #882: trjconv creates infinite trajectory
Bug #884: Don't allow mixed-precision appending
Bug #891: do_dssp no longer complies with dssp input
Bug #893: g_rmsf group index instead of atom number in output
Bug #898: broken link in online manual
Bug #900: crash in OpenMP code.
Bug #910: g_msd entering infinite loop when analyzing systems with xy periodicity.
Bug #923: Get rid of the raw SSE assembly kernels
Bug #927: TPI in 4.6 segfauts
Bug #929: likely free energy bug in gather_f_bspline
Bug #937: OpenMP bug with MSVC 2010
Bug #947: PowerPC invsqrt is never used
Bug #952: Add license file to cpack distribution
Bug #958: MPI on Windows
Bug #970: segfault in tip4pflex test case
Bug #971: Build fails with cmake double fftw
Bug #977: Fix cpack source archive generation: Root folder
Bug #978: Bus error on Mac Os when running g_x2top -quiet -man nroff
Bug #981: CPU acceleration auto-detection fails with (some?) gcc <=v4.4
Bug #982: segfault in genion
Bug #984: valgrind errors in grompp
Bug #993: Shell code in single precision gives non-reproducible forces
Bug #998: MSVC AVX flag check isn't working
Bug #1001: REMD statistics not collected properly any more
Bug #1002: g_dist lists ndx input as optional but fails if no index file provided
Bug #1008: mdrun fails when run with FE code and 4.5-generated tpr
Bug #1015: make install-mdrun broken on release-4.6
Bug #1018: cmake and gpu acceleration
Bug #1019: Timing stats broken
Bug #1020: g_enemat options
Bug #1021: Building release-4-6 difficult on Mac OS X with recent hardware
Bug #1023: -mfma4 flag omitted with GMX_ACCELERATION=AVX_128_FMA
Bug #1024: REMD and Verlet lists
Bug #1034: Gromacs 4.6 segmentation fault with mdrun
Bug #1037: CMake detects SSE4.1 but compilation fails
Bug #1038: CFLAGS are not updated when ACCLERATION is changed
Bug #1041: mdrun-openmm segmentation fault
Bug #1042: mdrun de-rails over classic water/0192 with GPU support compiled in, but not active
Bug #1044: GMXRC alters the contents of the shell's special parameters
Bug #1049: pick_nbnxn_kernel needs reworking
Bug #1051: Cuda host compiler with CMake 2.8.10.1
Bug #1052: g_hbond -dist -ang outputs
Bug #1055: GPU accleration with CPU acceleration None crashes
Bug #1059: mdrun with 2 GPU's: some systems run, others segfault without error message.
Bug #1060: 4.6-beta1 box implodes on GPU
Bug #1062: System crashing with Acceleration=None and GPU
Bug #1066: FMA and icc
Bug #1068: SIMD group kernels don't work on 32bit Windows
Bug #1071: segfault in grompp with pulling and free-energy (if foreign_lambda empty)
Bug #1074: AVX256 Double precision fails to build with gcc 4.7.0
Bug #1075: mdrun doesn't build on non-x86
Bug #1088: CUDA_TOOLKIT_ROOT_DIR warnings in clean build on non-CUDA-system
Bug #1089: PP-PME load balancing discards tested fastest setting
Bug #1090: g_bar isnt compatible with current free energy code in mdrun
Bug #1092: MSVC AVX nbnxn kernels don't compile
Bug #1093: MSVC AVX double precision kernel fail tests
Bug #1094: remove g_dih
Bug #1096: Make sure CPU Generalized Born interactions work
Bug #1097: nbnxn pme kernel fails when building 32-bit AVX_256 version on MSVC 2012
Bug #1098: mdrun randomly hangs for 32-bit builds running on >1 thread on OS X
Bug #1100: segfault with hybrid GPU-CPU acceleration
Bug #1101: fix & improve CPU oversubscription handling
Bug #1103: g_helix refers to nonexistent file
Bug #1113: Expanded ensemble mdp settings need documentation
Bug #1121: slow MD with sd integrator and GPU / verlet
Regression tests suite - Bug #1150: regressiontests tarball contains incorrectly named directory
Feature #632: Implementation of periodic improper dihedrals is incomplete
Feature #912: include list of compiler flags in the binary version information
Feature #913: include basic hardware information in the log file
Feature #914: CMake support for architecture-specific optimizations
Feature #994: Na/NA confusion in g_sas (vdwradii.dat)
Feature #1077: mdrun should have a feature to report available hardware
Feature #1078: Improve stderr output
Feature #1080: Improve CPU pinning of mdrun
Feature #1081: Single precision is really mixed precision
Feature #1086: implement the two frequently used thread-pinning strategies
Task #645: Remove autoconf-related files / port to CMake
Task #815: update CMake modules with latest version
Task #853: Fix FAHCORE because it can no longer use -DMPI in CMakeLists.
Task #861: document hinting of library locations using CMAKE_PREFIX_PATH
Task #922: enable command-line option checking in tools
Task #974: Document use of environment variables
Task #992: Vsite parameters for DNA (AMBER)
Task #1031: Autoinstall FFTW
Task #1058: gcc 4.4.something up to at least 4.6.0 can't compile AVX256 kernels
Task #1076: Gromacs 4.6 needs an updated install guide
Task #1108: for releases, regenerate shell completion files in scripts directory