{"push_id":1176132631,"size":51,"distinct_size":1,"ref":"refs/heads/master","head":"a9df95b63f566c0e13e34c46f61db09084d469b8","before":"2a44d783290fc03570d2416766bd692c1cb4ed83","commits":[{"sha":"08ccff066da231b7cb7ff5b3a7db257eecb1f549","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"New quote\n\nChange-Id: I1f36460618cd9fd919e5f3117934bfd3d939e76f","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/08ccff066da231b7cb7ff5b3a7db257eecb1f549"},{"sha":"1e8dec802b86078cd3710d06fc09309b1a5f7f28","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"Fix reading of bonded tables\n\nThe old approach specified only a filename prefix, and init_forcerec\nwould expect to be able to append _b0 to generate the filename for the\nzeroth bonded table, etc. This failed a check in early command-line\nparsing when no file that matched just the prefix could be found.\nPairs are unaffected because there's only one table. Short-ranged\nenergy-group tables are not affected because they require that the\nfile with default name exists.\n\nCommand-line parsing now requires -tableb to name all tabulated bonded\ninteraction table files explicitly, and does the normal check that\nthey exist. init_forcerec will find any name in that list that matches\nthe required pattern. The concept of a default filename prefix for\ntabulated bonded interactions no longer applies, but the old\n'table_b0.xvg' naming still works. Added some comments and Doxygen to\nexplain what the old code was doing. Amended the user documentation\nsuitably.\n\nOne could add further checks e.g. that there are no table filenames\nprovided that are unused by the topology, but it is likely the need\nfor such checks will go away when the topology will name the files\ndirectly.\n\nAdd some integration tests to show the functionality no longer\nproduces an error. Infrastructure to actually verify energies and\nforces is waiting for review in Gerrit.\n\nExpanded some string- and filename-handling infrastructure to meet\nthe new needs.\n\nImproved the robustness of the check that the derivative column is\napproximately the negative of the numerical derivative of the value\ncolumn.\n\nFixes #1913\n\nChange-Id: If0a7cd69a40eb95fbda20eaaf4c3002782772f0e","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/1e8dec802b86078cd3710d06fc09309b1a5f7f28"},{"sha":"57b5e5a4dba93c5720986c52a77549182776ae1a","author":{"name":"Erik Lindahl","email":"0318bc6a0b7bafa12db0e2bb793bb0e44b35ac46@kth.se"},"message":"Detect the usage of hwtop XML caching\n\nThe environment variable HWLOC_XMLFILE can be used\nto speed up hwloc detection e.g. on Xeon Phi. Documented\nin the user guide, and made sure we detect when such\ncaching was used to avoid strange future bug reports.\n\nFixes #1946.\n\nChange-Id: Id99385fb7cc1e2692fb9b06fa187424058aaa213","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/57b5e5a4dba93c5720986c52a77549182776ae1a"},{"sha":"d1e823507cc92247b57d060347a6106ca5505a06","author":{"name":"Roland Schulz","email":"b55b33f3c6bf06c3c4849f022ac53c534a832f7d@intel.com"},"message":"Fix build with clang 3.1+3.2\n\nChange-Id: I8bffaa081d4cf52662e46fcd6c58667b4528fa04","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/d1e823507cc92247b57d060347a6106ca5505a06"},{"sha":"b08ab12cb418d553d46d46fd67970215ee2d3d21","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"Simplified and updated OpenCL compilation\n\nMoved into gmx and new ocl namespace, updated variable naming, updated\nstring handling, treated many more error conditions, also with\nexceptions, used more RAII, used more of the standard GROMACS\nutility infrastructure.\n\nRemoved some string databases functions that existed merely to be\nlooked up once.\n\nChanged to write OpenCL build log to file pointer provided by the\ncaller, if needed, rather than a separate file. This currently uses\nstderr, so can't yet work well with multiple ranks, but neither did\nthe old approach. We need a proper MPI-aware logging module, first.\n\nSeparated the caching functionality into its own source file. Changed\nthe naming of binary cache to reflect the name of the kernel source\nfile whose binary is being cached. Noted further requirements if we\nwould re-activate caching at some point, but since it is still\nde-activated, this is not worth further effort now.\n\nRemoved the requirement that we must be able to read source code, if\ninstead a binary cache is available.\n\nRequired that compileProgram compile kernels for the vendor of the\ntarget device. This was always the behaviour, but there is no reason\nto be able to select alternative things there.\n\nSimplified the passing of preprocessor defines required by the caller\nof compileProgram to the JIT compilation.\n\nRemoved use of GMX_OCL_FORCE_CPU in log file coordination, as CPU\nOpenCL devices are not supported.\n\nRefs #1720\n\nChange-Id: I25e78526f55715c779819e96d6bf6b52ad9394c6","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/b08ab12cb418d553d46d46fd67970215ee2d3d21"},{"sha":"3c6ba9c734d8b883eca6bc7919cdd97307798985","author":{"name":"Berk Hess","email":"9868e2c993787891bc4f0c6964d312429763db85@kth.se"},"message":"Add grompp check for unbound atoms\n\ngrompp now print a note for atoms that are not connected by\na potential or constraint to any other atom in the same moleculetype,\nsince this often means the user made a mistake.\n\nRefs #1958.\n\nChange-Id: Iabb00563c76a9f7954f84d89d1c67d438f2c31ff","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/3c6ba9c734d8b883eca6bc7919cdd97307798985"},{"sha":"41833007e76944090665dae0bc0b4963741bec18","author":{"name":"Berk Hess","email":"9868e2c993787891bc4f0c6964d312429763db85@kth.se"},"message":"Add check for finite energies\n\nAdded a check for finite total potential energy. This check is nearly\nfree and can catch issues with incorrectly set up systems before users\nget a confusing constraint or PME error. Note that this check is only\nperformed at steps where energies are calculated, so it will often\nnot catch an exploding system.\n\nChange-Id: If33245a96cecae78c9077a825cb22335c853a810","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/41833007e76944090665dae0bc0b4963741bec18"},{"sha":"fcc7c4c4c3891aa2db8cd45904797b5f152e1e6f","author":{"name":"Berk Hess","email":"9868e2c993787891bc4f0c6964d312429763db85@kth.se"},"message":"Avoid numerical overflow with overlapping atoms\n\nThe verlet kernels did not allow overlapping atoms, even if they were\nnot interacting (in contrast to the group kernels). Fixed by clamping\nthe interaction distance so it can not become smaller than ~6e-4\nin single and ~1e-18 in double, and when this number is later\nmultiplied by zero parameters it will not influence forces. The\nclamping should never affect normal interactions; we would previously\ncrash for distances that were this small.\nOn Haswell, RF and PME kernels get 3% and 1% slower, respectively.\nOn CUDA, RF and PME kernels get 1% and 2% faster, respectively.\n\nFixes #1958.\n\nChange-Id: I83b88f0e9ca34dc151a8b907f334a95a1a4301cc","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/fcc7c4c4c3891aa2db8cd45904797b5f152e1e6f"},{"sha":"aa2ed12093029904889b5a4437cd506ff9f9aad2","author":{"name":"Berk Hess","email":"9868e2c993787891bc4f0c6964d312429763db85@kth.se"},"message":"Reposition nbnxn filler particles\n\nAs particles are now allowed to overlap in the nbnxn kernels,\nthe ugly, complicated scheme to create different coordinates for\nthe filler particles in nbnxn cells can be removed.\n\nChange-Id: Ic25c3b4bc82065b2b6b25f721d34eda3e6c23c0e","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/aa2ed12093029904889b5a4437cd506ff9f9aad2"},{"sha":"e83f08034f601a3599de751394c18802f1cf7d03","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"Second 2016 beta release\n\nChange-Id: I6350da03d04580da4b1bd11dc66fa79dbef9a47e","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/e83f08034f601a3599de751394c18802f1cf7d03"},{"sha":"21421822dc6f6eb90fcdbb21179c9c005e5ee0d8","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"Fix reference to vmdio.c to be vmdio.cpp\n\nFixes #1979\n\nChange-Id: I441ad6ace31325a6804f6031f32a1ca4600766e5","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/21421822dc6f6eb90fcdbb21179c9c005e5ee0d8"},{"sha":"13e0dc7121d4b16eac44e1029a5dc28ef577fcc1","author":{"name":"Teemu Murtola","email":"de3a435e249bbaaa54ef489d0f815475210f5192@gmail.com"},"message":"Improve make_ndx help text\n\nClarify the use of boolean operators.  The old help text could\nincorrectly hint that AND, OR, and NOT would work as keywords.\nAdd a reference to gmx select that in most cases can serve as a\nreplacement.\n\nFixes #1976.\n\nChange-Id: I0284c849c398e5b09569453d7d0f19b9639a6d0c","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/13e0dc7121d4b16eac44e1029a5dc28ef577fcc1"},{"sha":"a8ddf04fae334502a4d9e248ac5aff0f346b3122","author":{"name":"Patrick Welche","email":"3b795e9af0e2830f0b783a8d3bf8d425ed50bc78@cam.ac.uk"},"message":"Ensure IMD include dependencies work\n\nMakes sure select() and the necessary struct types are declared.\n\nFixes #1978\n\nChange-Id: I3f7e545c95f26b5cf0398ed14e6206c08ba9735d","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/a8ddf04fae334502a4d9e248ac5aff0f346b3122"},{"sha":"966381a3ca704a9683b99d4f1bef9b2b51123dcf","author":{"name":"Roland Schulz","email":"b55b33f3c6bf06c3c4849f022ac53c534a832f7d@intel.com"},"message":"Fix ICC 16u3 build\n\nThe C++11 check was triggering a bug in a corner case (empty\ndefaulted move constructor), which wasn't present in the actual\ncode.\n\nChange-Id: I650580497fe2ad9b67777d2f8a216cdb2c14bf12","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/966381a3ca704a9683b99d4f1bef9b2b51123dcf"},{"sha":"208c65ce31e655c541c6349c517012026a9a2f08","author":{"name":"Szilárd Páll","email":"9d9f5892eaa6fa4427a3b4c2c4e2a14f8f874caa@gmail.com"},"message":"Fix OpenCL binary cache file name generation\n\nThe binary cache names was generated from the full path prefixed\nwith a constant string which is a not a valid filename.\n\nAlso added assertion on the file pointer passed to fclose.\n\nChange-Id: I838cf9a2e19385afaf26b80a15be2b74973d3a4c","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/208c65ce31e655c541c6349c517012026a9a2f08"},{"sha":"13122790bfe398aa4bcecf5d0f4f4bb2568bd177","author":{"name":"Szilárd Páll","email":"9d9f5892eaa6fa4427a3b4c2c4e2a14f8f874caa@gmail.com"},"message":"Add env. var. to enable OpenCL caching\n\nOpenCL binary caching is disabled by default (due to concurrency and\nversions not being safely handled), but during development, being\nable to avoid the kernel compilation overhead can speed up testing and\nbenchmarking tremendously. This change adds an environment variable\nthat can be used to manually trigger binary caching.\n\nChange-Id: I5879acf040216ad75dbb54e7ecec001aae8af8a5","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/13122790bfe398aa4bcecf5d0f4f4bb2568bd177"},{"sha":"63e5d7899234414204485e49cafa6c608f038718","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"Ignore stderr when detecting SIMD and build info\n\nCray and some other stupid compilers echo extra stuff to stderr when\ncompiling a normal source file. Unfortunately, the standard CMake\ntry_run cannot ignore stderr.\n\nRefactored some try_run calls to try_compile + try_run. This\nincidentally makes build-host detection run faster because the same\nbinary is not compiled multiple times. The results of the detections\nare now set up so that an initial default value is constructed,\nreplaced if the compilation and run both succeed, before finally being\ncached.\n\nNoted some TODOs for future cleanup of the duplication in such code.\n\nFixes #1881.\n\nChange-Id: Icb770872f853cff3ef60426d9980f463341eb1cf","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/63e5d7899234414204485e49cafa6c608f038718"},{"sha":"0bf91807dcae3567dd65ccf29c1d15653f334951","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"Make more CMake variables advanced\n\nThis keeps the ccmake display down to things users are reasonably\nlikely to want to change.\n\nFixes #1764\n\nChange-Id: Ia78387bb32f5d6c7f6b82e453b155fdf657a044a","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/0bf91807dcae3567dd65ccf29c1d15653f334951"},{"sha":"d051c40f6adcb00fc9d3f9c4fbbc0ff4f5f1f615","author":{"name":"Mark Abraham","email":"247eaaad410c71367ccd7b8ffa4afe130f4ba526@gmail.com"},"message":"Fix compatibility with older CMake\n\nLINK_LIBRARIES is introduced in 2.8.11. We don't test anywhere that\nCMake hardware detection works.\n\nChange-Id: Icb5812c3971219085b8e91634e4cd08451041118","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/d051c40f6adcb00fc9d3f9c4fbbc0ff4f5f1f615"},{"sha":"78a3d3f0aaa25bdf0a9ceda4460a92553c3ad355","author":{"name":"Berk Hess","email":"9868e2c993787891bc4f0c6964d312429763db85@kth.se"},"message":"Handle partially frozen and constrained atoms\n\nAtoms frozen along some, but not all dimensions would still be moved\nalong all dimensions by constraints. Now such dimensions are frozen.\nNote that the initial configuration might not obey the constraints,\nwhich leads to conflicting demands of freezing and constraining.\nPartially frozen atoms in the initial configuration will still be\nconstrained along all dimensions (but will be frozen during the run).\n\nFixes #1960.\n\nChange-Id: Ic4d43a2840fabc084aec4237abf6a589eaa72f37","distinct":false,"url":"https://api.github.com/repos/gromacs/gromacs/commits/78a3d3f0aaa25bdf0a9ceda4460a92553c3ad355"}]}
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