GitHub PushEvent at 2014-09-20 09:02:06
Repository: gromacs
Actor: gromacs-upload
Payload: {"shas":[["0292846bea5e51ba1390cff81c23491f73287a6e","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Version bump after 4.6.6 release\n\nChange-Id: Ifac0db3a07caba28c123d233b54356a1db0d79ba","Mark Abraham",false],["3c78eb7e5287622e704007e89503bb4e5a6145fc","c195b508e6f0c57aeafdb5e96947e2b79e6a4b40@kth.se","Added tests for denormal and underflow for simd exp()\n\nThe SIMD math functions are not expected to handle\nthe denormal range correctly, but it should at least\nbe clamped to zero rather than producing garbage\nvalues. No changes required to the math function,\nso it appears to pass these tests as-is.\n\nChange-Id: I841c2948c81f6b62f42e60ff30ffd5e4f77926fa","Erik Lindahl",false],["27189bbaad21147893b239b2457843f515e69d77","a9dc1f59aa334ab11422a01433159e7248003587@kth.se","Fixed PME bug with high OpenMP thread count\n\nPME energies and forces could be incorrect with combined MPI+OpenMP\nparallelization. This would, only, happen when\npmegrids->nthread_comm[YY] >= 2, which can only occur with high OpenMP\nthread count with multiple large prime factors.\nIt's unlikely that this issue affected production runs.\n\nFixes #1572.\n\nChange-Id: I03b38c279c8f8ab2e111dad0976edad88b3ea93b","Berk Hess",false],["dc75f6fb3258c7c2745270fe934b9a934baee2a1","01183f156a2a6162e583011cd4263f86ff57a409@gmail.com","Verify MD5 sum for FFTW download\n\nSince ExternalProject provides confusing error messages with MD5\nchecking enabled, add a custom download step that works as expected.\nWhen passed a local file as the URL, ExternalProject does the MD5\nverification just fine, so the code now downloads the tarball in a\ncustom step and then passes that local file to ExternalProject.\n\nThis allows removing the lengthy security warning that appeared there if\none was just following the quick-and-dirty installation instructions,\nand likely only confused novice users.  While this change may not\nimprove overall security significantly, it hopefully allows everyone to\nagree to remove that warning and thus improve the end-user experience.\n\nChange-Id: I9ac5a30ae5858b7a6557ccb2d981cc909457d020","Teemu Murtola",false],["9e8061e13f48b1393e251e07eb94165f15ead4af","0d270388f2f92757a5de0f4bd891d3b392c44c4f@utk.edu","Workaround for ICC 14\n\nProblem was only present with BUILD_SHARED_LIBS=no\n\nChange-Id: Ieb4377d819aa5eff3d139cdbe55775989118a738","Roland Schulz",false],["2120df62cb5b6a1a743194c059f5e2ab76e4bae7","a9dc1f59aa334ab11422a01433159e7248003587@kth.se","Fix hang with LJ-PME and empty domains\n\nWith LJ-PME and DD domains with 0 atoms and LJ-PME mdrun could hang.\nFixes #1571.\n\nChange-Id: Ie205954c4f5e1a52df846a69972f735867eea15d","Berk Hess",false],["9635099c5aa3122110e84ba8ea3b999342011ba5","c195b508e6f0c57aeafdb5e96947e2b79e6a4b40@kth.se","Changed names of test files to avoid Fujitsu compiler bug\n\nThe Fujitsu compilers use an older version of the Clang\nparser where certain static class initializers (e.g. strings)\nare put in a static initializer function stub named after\nthe file and class. When the first such class has identical\nnames in two different files where the last part of the\nname is identical, this will result in clashing symbols\nat link time. Working around this would require an extra\n(unused) class definition in each file that would pollute the\ncode, so for now we merely rename the files where it occurs\nand hope that the compilers will be fixed (a bug report has\nbeen submitted).\n\nChange-Id: If552a06950facb0cdbb6e34e0b324aafa6083ae8","Erik Lindahl",false],["61ca37ff7b4b8aa9c436818c1e04f1d63ea5dd0d","c195b508e6f0c57aeafdb5e96947e2b79e6a4b40@kth.se","Fix portability issue with ArrayRef initializer overloading\n\nSome compilers (in particular the Fujitsu compilers that are\nderived from an earlier version of Clang) will not allow\noverloading functions where one version uses a pointer to a\ntype, and the other a vector iterator to the same type - likely\nbecause they have implemented iterators with pointers.\nRegardless of what the C++ standard says, we need this working\non K computer, so this patch replaces the overloaded\ninitializers with non-member functions that create an ArrayRef\nor ConstArrayRef either from pointers, an array,\nor iterators.\n\nChange-Id: I4c4e327c869920cc08e3f955e88cb3a5b28c7e87","Erik Lindahl",false],["c1cdb61c09a96c2b70ce8a0a305ab3167d001ea4","0d270388f2f92757a5de0f4bd891d3b392c44c4f@utk.edu","Merge release-4-6 into release-5-0\n\nConflicts:\n\tCMakeLists.txt (version bump ignored)\n\nChange-Id: I4ba0209b5f69b6470470530662a0b27390a02771","Roland Schulz",false],["9b4154ace94c210cd93320638db883e32a4a6df8","0d270388f2f92757a5de0f4bd891d3b392c44c4f@utk.edu","Check MD5sum for regressiontest\n\nBecause we decided it is important for FFTW we should do it for\nthe tests too. Is only done for non -dev versions.\n\nChange-Id: Id7d1ee027bd302ad7cb10f46d93b0f435872c67e","Roland Schulz",false],["ebfd9140ea5bfd364ba7f586d2316de59df21456","a9dc1f59aa334ab11422a01433159e7248003587@kth.se","Added checks for TPI + Verlet scheme\n\nChange-Id: I040f4cc9dbb8ff25ed97d18cca0b4a2c1e7014b0","Berk Hess",false],["d5958252fb4116cfb6ad2081b7067b89f87c4e59","c195b508e6f0c57aeafdb5e96947e2b79e6a4b40@kth.se","Replace __LP64__ with check for pointer size\n\nThe __LP64__ define is not set e.g. on PGI compilers,\nso instead we use a portable way of checking for\npointer size based on defines from stdint.h.\n\nChange-Id: Ib2dd6e45c2b168add07f5478d59aec487a91ab9e","Erik Lindahl",false],["8b7f2d16750c2c433c4aaebeaf4123a1fccc10f4","c195b508e6f0c57aeafdb5e96947e2b79e6a4b40@kth.se","Improve Gromacs portability\n\nThis patch addresses a few general portability issues\nthat we have experienced at least on Fujitsu compilers\n(K computer) and (partly) for Pathscale x86 compilers.\n- I have added a generic compiler definition fallback\n  for boost, so it will work on unidentified compilers.\n- There is now  a define for gmock-1.7.0 to handle\n  the case where wcscasecmp() is not available. We use\n  this by default since it is not important for us.\n- If we do not find atomics for sparc64 we now warn and\n  fall back on mutexes rather than the compile dying.\n- The compiler flag checks have been updated from\n  cmake-3.0, and more warning checks added.\n- Since some non-GCC compilers set _GNUC_ for\n  compatibilty, we do not assume all such compilers\n  support tr1, but use the internal tr1/tuple definition\n  in Gmock by default.\n- Before using the sched.h affinity functions, we now\n  check that all the functions we need are supported,\n  rather than just one of them.\n\nChange-Id: I31b7f0f46a9d03a627c73a0789b4a9b24fa860ee","Erik Lindahl",false],["3f6b97982fc70ee6baf9a9d159a301b224b68c15","c195b508e6f0c57aeafdb5e96947e2b79e6a4b40@kth.se","Make internal BLAS/LAPACK messages less noisy\n\nBLAS and LAPACK are close to insignificant to Gromacs, so\navoid multi-line noisy warnings about \"fallback\" solutions;\nthose will just worry users and make them spend time investigating\nunder what conditions it might play a role, when we really don't\ncare much for BLAS/LAPACK performance. Message has been\nchanged to short inconspicuous status lines when we are using\nbuilt-in versions.\n\nChange-Id: I9f1b0c769907521d5cb6325c8d67cd61ca8a803a","Erik Lindahl",false],["909f8293c8fbbd416d16b793b61322ab0344664f","908cfcb4a79d5d45e1ec998bc9b6659460c18c76@kth.se","Avoid stack overflow on Windows with CMake > 2.8.10.2\n\nCMake used to add \"/STACK:10000000\" to the default linker flags. That\nwas removed in version 2.8.11-rc1. The default value used by MSVC is\napparently too small because mdrun crashes with a stack overflow when\nbuilt on Windows with MSVC or ICC and CMake newer than 2.8.10.2.\n\nThe issue is already fixed in GROMACS 5.0 and master by I1e9858ae3. This\nis a backport for release-4-6 of that commit.\n\nChange-Id: Ib9238e513da8e86049d9e56c82262055d3c8b349","Stefan Fleischmann",false],["546f7c57431c6c5d0c88017243ad3240fbd65092","a9dc1f59aa334ab11422a01433159e7248003587@kth.se","Corrected SIMD math overflow documentation\n\nAdded more details to the SIMD pmecorr and exp documentation.\nCorrected the source of the PME-LJ kernel overflow.\n\nChange-Id: If3f5a27a3bb49ebb67fc24d43ed849e75175cf3c","Berk Hess",false],["0a27e96b15d7ea4cfffa179512cc858123e91d7b","6bd758daef6350b75dea4e7011cdf6bb2f39c608@gwdg.de","Fixed output of eigenvalues in g_covar. Fixes #1575\n\nCommit 972032bfb8cd38 introduced a bug that would lead to eigenvalues\nonly written to .xvg file if \"-last\" is explicitly stated on the\ncommand line. Otherwise no eigenvalues would appear in the .xvg file.\nThe eigenvalues are written in a loop from '0' to 'end', but since\n'end' is initialized with '-1', the loop would never be executed.\nThis patch moves the code that computes 'end' one block upwards\nbefore the output to file.\n\nChange-Id: I738c9dd77ff9e6e2daae89b6d2063755dfba88af","Carsten Kutzner",false],["e3d1a2232511301142cebe889d5b10dc21d0d653","0d270388f2f92757a5de0f4bd891d3b392c44c4f@utk.edu","Merge release-5-0 into master\n\nConflicts (trivial):\n\tsrc/gromacs/commandline/pargs.cpp\n\tsrc/gromacs/gmxlib/gmx_thread_affinity.c\n\tsrc/gromacs/options/filenameoption.cpp\n\nManual changes required for ConstArrayRef:\n       src/gromacs/commandline/pargs.cpp\n       src/gromacs/options/filenameoption.cpp\n       src/gromacs/selection/selection.cpp\n       src/gromacs/selection/tests/nbsearch.cpp\nManual moved REGRESSIONTEST_MD5SUM from\n       CMakeLists.txt to cmake/gmxVersionInfo.cmake\n\nChange-Id: I1a2038f72c1e1cfed830de5c540ab278dbb39cfe","Roland Schulz",false],["5ab7482e2e51aa3df1bc95f1b934d784a014a1ad","01183f156a2a6162e583011cd4263f86ff57a409@gmail.com","Disable analysisdata generic tests if not compilable\n\nIf Google Test claims that typed tests are not supported, exclude the\nanalysisdata generic tests that use this functionality from compilation\n(since they wouldn't compile).  Instead, add a dummy test that at least\nshows a developer who runs the unit test executable directly that\nsomething is missing (the ctest run still passes without any messages).\n\nChange-Id: Iba9bcc4b993e5213fe48e24d52b09474e5801fa8","Teemu Murtola",false],["d4aef0618508ea19abb0c0ab541c553fa5e92312","c77fa36e024582f895b7890956168d58ecb78926@gmail.com","Fix wallcycle counting with md-vv, sd and sd2\n\nPreviously the coordinate update for the first half of velocity Verlet\nand (where applicable) the second half of the SD integrators was left\nout of the walltime accounting, and showed up in the \"Rest\"\nsection. With this fix, the number of \"update\" steps reported depends\non exactly which flavour of which integrator is in use, because\nthere's also some number of calls to do constraining and/or energy\ncommunication. Those numbers vary with either the flavour of\nintegrator, or the number of iterations MTTK actually needs.\n\nChange-Id: Ib294455b7277caf89018c413d6c1c0ebf93c6ddb","Mark Abraham",false]],"size":142,"ref":"refs/heads/qmmm","head":"ff7df3d3a66025c10a7e0a4f251f87a418a9f359"}