From: Andrey Alekseenko Date: Tue, 14 Sep 2021 17:16:06 +0000 (+0300) Subject: Merge remote-tracking branch 'origin/release-2021' into master X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=f5975e9ff9d7ecfb83e4943fd45e321c2f036708;p=alexxy%2Fgromacs.git Merge remote-tracking branch 'origin/release-2021' into master Conflicts: cmake/gmxVersionInfo.cmake src/gromacs/ewald/pme_gather.cu src/gromacs/ewald/pme_gpu_calculate_splines.cuh src/gromacs/ewald/pme_gpu_internal.cpp src/gromacs/ewald/tests/pmetestcommon.cpp src/gromacs/gmxana/gmx_cluster.cpp src/gromacs/gmxpreprocess/gen_vsite.cpp src/gromacs/simd/support.cpp src/gromacs/tools/trjconv.cpp --- f5975e9ff9d7ecfb83e4943fd45e321c2f036708 diff --cc cmake/gmxVersionInfo.cmake index c4485a330f,e9ef890f20..34c3a02492 --- a/cmake/gmxVersionInfo.cmake +++ b/cmake/gmxVersionInfo.cmake @@@ -229,6 -228,15 +229,15 @@@ else( endif() set(GMX_VERSION_STRING "${GMX_VERSION}${GMX_VERSION_SUFFIX}") + set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}") -set(REGRESSIONTEST_BRANCH "release-2021") ++set(REGRESSIONTEST_BRANCH "master") + # Run the regressiontests packaging job with the correct pakage + # version string, and the release box checked, in order to have it + # build the regressiontests tarball with all the right naming. The + # naming affects the md5sum that has to go here, and if it isn't right + # release workflow will report a failure. + set(REGRESSIONTEST_MD5SUM "93956ea42c4d16fdd541518c05972989" CACHE INTERNAL "MD5 sum of the regressiontests tarball for this GROMACS version") + # If you are making a custom fork of GROMACS, please describe your # fork, perhaps with its version number, in the value of # GMX_VERSION_STRING_OF_FORK here. This string will appear in the diff --cc src/gromacs/ewald/pme_gpu_calculate_splines.cuh index 6e663175e0,1e3ccefb01..1ff60f7ed1 --- a/src/gromacs/ewald/pme_gpu_calculate_splines.cuh +++ b/src/gromacs/ewald/pme_gpu_calculate_splines.cuh @@@ -173,8 -173,12 +173,12 @@@ __device__ __forceinline__ void pme_gpu * \tparam[in] atomsPerBlock Number of atoms processed by a block - should be accounted for * in the sizes of the shared memory arrays. * \tparam[in] atomsPerWarp Number of atoms processed by a warp - * \tparam[in] writeSmDtheta Bool controlling if the theta derivative should be written to shared memory. Enables calculation of dtheta if set. - * \tparam[in] writeGlobal A boolean which tells if the theta values and gridlines should be written to global memory. Enables calculation of dtheta if set. - * \tparam[in] writeSmDtheta Bool controling if the theta derivative should be written to ++ * \tparam[in] writeSmDtheta Bool controlling if the theta derivative should be written to + * shared memory. Enables calculation of dtheta if set. + * \tparam[in] writeGlobal A boolean which tells if the theta values and gridlines should + * be written to global memory. Enables calculation of dtheta if + * set. + * \tparam[in] numGrids The number of grids using the splines. * \param[in] kernelParams Input PME CUDA data in constant memory. * \param[in] atomIndexOffset Starting atom index for the execution block w.r.t. global memory. * \param[in] atomX Atom coordinate of atom processed by thread. diff --cc src/gromacs/ewald/tests/pmetestcommon.cpp index 3eda383e7a,7cdabb9c49..a3c4409fca --- a/src/gromacs/ewald/tests/pmetestcommon.cpp +++ b/src/gromacs/ewald/tests/pmetestcommon.cpp @@@ -910,7 -889,8 +911,7 @@@ const char* codePathToString(CodePath c PmeTestHardwareContext::PmeTestHardwareContext() : codePath_(CodePath::CPU) {} PmeTestHardwareContext::PmeTestHardwareContext(TestDevice* testDevice) : - codePath_(CodePath::CPU), testDevice_(testDevice) - codePath_(CodePath::GPU), - testDevice_(testDevice) ++ codePath_(CodePath::GPU), testDevice_(testDevice) { setActiveDevice(testDevice_->deviceInfo()); pmeGpuProgram_ = buildPmeGpuProgram(testDevice_->deviceContext()); diff --cc src/gromacs/gmxana/gmx_wham.cpp index f747c89299,bcace1190f..5da2b4d1d7 --- a/src/gromacs/gmxana/gmx_wham.cpp +++ b/src/gromacs/gmxana/gmx_wham.cpp @@@ -133,17 -135,17 +133,17 @@@ enu bsMethod_trajGauss }; - //! Parameters of one pull coodinate + //! Parameters of one pull coordinate typedef struct { - int pull_type; //!< such as constraint, umbrella, ... - int geometry; //!< such as distance, direction, cylinder - int ngroup; //!< the number of pull groups involved - ivec dim; //!< pull dimension with geometry distance - int ndim; //!< nr of pull_dim != 0 - real k; //!< force constants in tpr file - real init_dist; //!< reference displacement - char coord_unit[256]; //!< unit of the displacement + PullingAlgorithm pull_type; //!< such as constraint, umbrella, ... + PullGroupGeometry geometry; //!< such as distance, direction, cylinder + int ngroup; //!< the number of pull groups involved + ivec dim; //!< pull dimension with geometry distance + int ndim; //!< nr of pull_dim != 0 + real k; //!< force constants in tpr file + real init_dist; //!< reference displacement + char coord_unit[256]; //!< unit of the displacement } t_pullcoord; //! Parameters of the umbrella potentials @@@ -1621,11 -2123,9 +1621,11 @@@ static void read_tpr_header(const char gmx_fatal(FARGS, "%s: Pull coordinate %d is of type \"%s\", expected \"umbrella\". Only " "umbrella coodinates can enter WHAM.\n" - "If you have umrella and non-umbrella coordinates, you can select the " + "If you have umbrella and non-umbrella coordinates, you can select the " "umbrella coordinates with gmx wham -is\n", - fn, i + 1, epull_names[header->pcrd[i].pull_type]); + fn, + i + 1, + enumValueToString(header->pcrd[i].pull_type)); } if (!geometryIsSet) { diff --cc src/gromacs/gmxpreprocess/gen_vsite.cpp index 6487348053,ffa7fde37e..b7e663640c --- a/src/gromacs/gmxpreprocess/gen_vsite.cpp +++ b/src/gromacs/gmxpreprocess/gen_vsite.cpp @@@ -373,8 -379,7 +373,8 @@@ static void read_vsite_database(const c break; default: gmx_fatal(FARGS, - "Didnt find a case for directive %s in read_vsite_database\n", - "Didn't find a case for directive %s in read_vsite_database\n", dirstr); ++ "Didn't find a case for directive %s in read_vsite_database\n", + dirstr); } } } diff --cc src/gromacs/gmxpreprocess/readir.cpp index 6b8c64ea3a,05c87c3786..28b4184f14 --- a/src/gromacs/gmxpreprocess/readir.cpp +++ b/src/gromacs/gmxpreprocess/readir.cpp @@@ -4342,7 -4227,7 +4342,7 @@@ void triple_check(const char* mdparin, set_warning_line(wi, mdparin, -1); - if (allTrue(haveAbsoluteReference(*ir)) && allTrue(havePositionRestraints(*sys))) - if (ir->comm_mode != ecmNO && allTrue(havePositionRestraints(*sys))) ++ if (ir->comm_mode != ComRemovalAlgorithm::No && allTrue(havePositionRestraints(*sys))) { warning_note(wi, "Removing center of mass motion in the presence of position restraints might " diff --cc src/gromacs/simd/support.cpp index 954a840529,146a28c8a3..71b7a8bec4 --- a/src/gromacs/simd/support.cpp +++ b/src/gromacs/simd/support.cpp @@@ -282,11 -313,10 +282,11 @@@ bool simdCheck(gmx::SimdType wanted, FI // the supported one, but AVX128Fma is an exception: AMD CPUs will (strongly) prefer // AVX128Fma, but they will work fine with AVX too. Thus, make an exception for this. logMsg = wrapper.wrapToString( - formatString("Highest SIMD level requested by all nodes in run: %s\n" + formatString("Highest SIMD level supported by all nodes in run: %s\n" "SIMD instructions selected at compile time: %s\n" - "Compiled SIMD newer than requested; program might crash.", + "Compiled SIMD newer than supported; program might crash.", - simdString(wanted).c_str(), simdString(compiled).c_str())); + simdString(wanted).c_str(), + simdString(compiled).c_str())); warnMsg = logMsg; } else if (wanted != compiled)