From: Paul Bauer Date: Mon, 31 Aug 2020 15:15:45 +0000 (+0200) Subject: Merge branch 'release-2020' into master X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=788b8ae3b46fc13f39fb81fd8e8cf64498c4d5c9;p=alexxy%2Fgromacs.git Merge branch 'release-2020' into master Resolved Conflicts: CMakeLists.txt admin/ci-scripts/build-and-test-py-gmxapi-0.1.sh admin/ci-scripts/build-and-test-sample_restraint-2020.sh admin/clang-tidy.sh admin/gitlab-ci/global.gitlab-ci.yml admin/gitlab-ci/gromacs.gitlab-ci.yml admin/gitlab-ci/python-gmxapi.gitlab-ci.yml cmake/gmxManageGPU.cmake cmake/gmxManageNvccConfig.cmake cmake/gmxVersionInfo.cmake share/CMakeLists.txt src/config.h.cmakein src/gromacs/CMakeLists.txt src/gromacs/analysisdata/CMakeLists.txt src/gromacs/ewald/pme.cpp src/gromacs/fileio/tpxio.cpp src/gromacs/fileio/writeps.cpp src/gromacs/gmxana/gmx_hbond.cpp src/gromacs/gmxana/gmx_lie.cpp src/gromacs/gmxana/gmx_xpm2ps.cpp src/gromacs/gmxpreprocess/genrestr.cpp src/gromacs/gmxpreprocess/tests/CMakeLists.txt src/gromacs/gpu_utils/gpu_utils.cu src/gromacs/gpu_utils/tests/pinnedmemorychecker.cpp src/gromacs/math/CMakeLists.txt src/gromacs/options/CMakeLists.txt src/gromacs/pbcutil/CMakeLists.txt src/gromacs/topology/mtop_util.cpp src/gromacs/trajectoryanalysis/CMakeLists.txt src/gromacs/utility/CMakeLists.txt Change-Id: I9c364fc3a8e1d9ba9821e06155136ffc6f46b8cd --- 788b8ae3b46fc13f39fb81fd8e8cf64498c4d5c9 diff --cc src/gromacs/ewald/pme.cpp index 403ea96095,a30d67b3a2..912216964c --- a/src/gromacs/ewald/pme.cpp +++ b/src/gromacs/ewald/pme.cpp @@@ -550,21 -561,20 +550,21 @@@ static int div_round_up(int enumerator return (enumerator + denominator - 1) / denominator; } -gmx_pme_t* gmx_pme_init(const t_commrec* cr, - const NumPmeDomains& numPmeDomains, - const t_inputrec* ir, - gmx_bool bFreeEnergy_q, - gmx_bool bFreeEnergy_lj, - gmx_bool bReproducible, - real ewaldcoeff_q, - real ewaldcoeff_lj, - int nthread, - PmeRunMode runMode, - PmeGpu* pmeGpu, - const gmx_device_info_t* gpuInfo, - PmeGpuProgramHandle pmeGpuProgram, - const gmx::MDLogger& mdlog) +gmx_pme_t* gmx_pme_init(const t_commrec* cr, + const NumPmeDomains& numPmeDomains, + const t_inputrec* ir, + gmx_bool bFreeEnergy_q, + gmx_bool bFreeEnergy_lj, + gmx_bool bReproducible, + real ewaldcoeff_q, + real ewaldcoeff_lj, + int nthread, + PmeRunMode runMode, + PmeGpu* pmeGpu, + const DeviceContext* deviceContext, + const DeviceStream* deviceStream, + const PmeGpuProgram* pmeGpuProgram, - const gmx::MDLogger& /*mdlog*/) ++ const gmx::MDLogger& mdlog) { int use_threads, sum_use_threads, i; ivec ndata; diff --cc src/gromacs/gmxpreprocess/tests/CMakeLists.txt index 979cdb166f,3be1db5528..5398c140a3 --- a/src/gromacs/gmxpreprocess/tests/CMakeLists.txt +++ b/src/gromacs/gmxpreprocess/tests/CMakeLists.txt @@@ -32,19 -32,18 +32,20 @@@ # To help us fund GROMACS development, we humbly ask that you cite # the research papers on the package. Check out http://www.gromacs.org. -gmx_add_unit_test(GmxPreprocessTests gmxpreprocess-test - editconf.cpp - genconf.cpp - genion.cpp - genrestr.cpp - gpp_atomtype.cpp - gpp_bond_atomtype.cpp - insert_molecules.cpp - readir.cpp - solvate.cpp - topdirs.cpp - ) +gmx_add_gtest_executable(gmxpreprocess-test + CPP_SOURCE_FILES + editconf.cpp + genconf.cpp + genion.cpp ++ genrestr.cpp + gpp_atomtype.cpp + gpp_bond_atomtype.cpp + insert_molecules.cpp + readir.cpp + solvate.cpp + topdirs.cpp + ) +gmx_register_gtest_test(GmxPreprocessTests gmxpreprocess-test SLOW_TEST) # Currently these can be slow to run in Jenkins, so they are in # several test binaries. diff --cc src/gromacs/gromacs-config.cmake.cmakein index cb7879d510,7ea1facd85..df67591a02 --- a/src/gromacs/gromacs-config.cmake.cmakein +++ b/src/gromacs/gromacs-config.cmake.cmakein @@@ -57,15 -57,15 +57,19 @@@ endif( include(${_gmx_import_file}) unset(_gmx_import_file) -get_target_property(_libs libgromacs INTERFACE_LINK_LIBRARIES) +get_target_property(_libs Gromacs::libgromacs INTERFACE_LINK_LIBRARIES) if (_libs MATCHES "tng_io::tng_io") include(CMakeFindDependencyMacro) - find_dependency(TNG_IO) + find_dependency(TNG_IO REQUIRED) +endif() +if (_libs MATCHES "OpenMP::OpenMP_CXX") + include(CMakeFindDependencyMacro) + find_dependency(OpenMP REQUIRED) endif() + if (_libs MATCHES "OpenMP::OpenMP_CXX") + include(CMakeFindDependencyMacro) + find_dependency(OpenMP REQUIRED) + endif() unset(_libs) set(GROMACS_INCLUDE_DIRS) diff --cc src/gromacs/math/CMakeLists.txt index e0c2fadac8,b36ef2f7d3..16d6ccd740 --- a/src/gromacs/math/CMakeLists.txt +++ b/src/gromacs/math/CMakeLists.txt @@@ -36,8 -35,13 +36,13 @@@ file(GLOB MATH_SOURCES *.cpp) set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MATH_SOURCES} PARENT_SCOPE) -# TODO: (https://redmine.gromacs.org/issues/988) Find a new convention for defining public API. +# TODO: (https://gitlab.com/gromacs/gromacs/-/issues/988) Find a new convention for defining public API. install(FILES + do_fit.h + functions.h + units.h + utilities.h + vec.h vectypes.h DESTINATION include/gromacs/math) diff --cc src/gromacs/taskassignment/decidegpuusage.cpp index f2ae54cc08,e9f98298b8..38d61a6720 --- a/src/gromacs/taskassignment/decidegpuusage.cpp +++ b/src/gromacs/taskassignment/decidegpuusage.cpp @@@ -667,12 -669,12 +667,12 @@@ bool decideWhetherToUseGpuForUpdate(con // does not support it, the actual CUDA LINCS code does support it if (gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0) { - errorMessage += "Non-connecting constraints are not supported"; + errorMessage += "Non-connecting constraints are not supported\n"; } - if (!UpdateConstrainCuda::isNumCoupledConstraintsSupported(mtop)) + if (!UpdateConstrainGpu::isNumCoupledConstraintsSupported(mtop)) { errorMessage += - "The number of coupled constraints is higher than supported in the CUDA LINCS " + "The number of coupled constraints is higher than supported in the GPU LINCS " "code.\n"; } diff --cc src/gromacs/utility/CMakeLists.txt index 7e3f5cfc2b,739dfaed66..93e82808cd --- a/src/gromacs/utility/CMakeLists.txt +++ b/src/gromacs/utility/CMakeLists.txt @@@ -51,10 -50,13 +51,14 @@@ if(GMX_INSTALL_LEGACY_API install(FILES arrayref.h baseversion.h - classhelpers.h + classhelpers.h enumerationhelpers.h - exceptions.h + exceptions.h + listoflists.h + fileptr.h + futil.h + flags.h + pleasecite.h programcontext.h range.h smalloc.h