Improve CUDA codegen flags

- onnly generate PTX for an early and the latest arch (3.5 and 8.0)
- add binary 8.0 and 8.6 targets

diff --git a/api/gmxapi/CMakeLists.txt b/api/gmxapi/CMakeLists.txt
index 1fcf9b69ec88d1e96c6723e59890ffddbf91f8e6..865abe29253db45832529ed5c4e5378f7b7255a2 100644 (file)
--- a/api/gmxapi/CMakeLists.txt
+++ b/api/gmxapi/CMakeLists.txt
@@ -64,17 +64,12 @@ set_target_properties(gmxapi PROPERTIES
 
 if (GMX_LIB_MPI)
     # GROMACS is built against an MPI library.
-    # Clarification should be possible with resolution of #3672.
     set(_gmx_mpi_type "library")
-    # Ref https://cmake.org/cmake/help/v3.13/module/FindMPI.html#variables-for-using-mpi
-    find_package(MPI COMPONENTS CXX)
-    if (MPI_CXX_FOUND)
-target_link_libraries(gmxapi PRIVATE MPI::MPI_CXX)
-        # If clients also need to link this target, we need to provide help in gmxapi-config.cmake
-        set(_gmxapi_find_dependencies "find_dependency(MPI COMPONENTS CXX)")
-    else()
-        message(FATAL_ERROR "Building gmxapi for MPI-enabled GROMACS, but no MPI toolchain found.")
-    endif ()
+    # TODO: Normative solution with #3672.
+    # Do not target_link_options(gmxapi PRIVATE ${MPI_LINKER_FLAGS})
+    # because the root CMakeLists.txt sets CMAKE_SHARED_LINKER_FLAGS.
+    target_compile_options(gmxapi PUBLIC ${MPI_COMPILE_FLAGS})
+    target_link_libraries(gmxapi PUBLIC ${MPI_CXX_LIBRARIES})
 elseif(GMX_THREAD_MPI)
     # GROMACS is built with its internal thread-MPI implementation.
     set(_gmx_mpi_type "tmpi")

diff --git a/api/nblib/basicdefinitions.h b/api/nblib/basicdefinitions.h
index 41dabd32709734011cd3d048b15dec2e447ce897..ebb4d3f43dcaebaf0d222da17fc6ddf0479197b7 100644 (file)
--- a/api/nblib/basicdefinitions.h
+++ b/api/nblib/basicdefinitions.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2020, by the GROMACS development team, led by
+ * Copyright (c) 2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -88,6 +88,11 @@ constexpr const int N_IVEC  = (N_BOX_Z * N_BOX_Y * N_BOX_X);
 //! Needed for generating Bolzmann velocity distribution (kJ/(mol K))
 constexpr const real BOLTZ = (detail::RGAS / detail::KILO); /*  */
 
+#ifndef M_PI
+//! Required work-around for platforms that don't implement POSIX-style cmath header
+#    define M_PI 3.14159265358979323846
+#endif
+
 //! Charge multiplication factor for Coulomb interactions
 constexpr const real ONE_4PI_EPS0 = (1.0 / (4.0 * M_PI * detail::EPSILON0));
 

diff --git a/cmake/gmxManageNvccConfig.cmake b/cmake/gmxManageNvccConfig.cmake
index 12e54cb40efca94399964c7cff008d92dca0dd38..b5f5663f4c2757ee481d133ef453bdca745072ad 100644 (file)
--- a/cmake/gmxManageNvccConfig.cmake
+++ b/cmake/gmxManageNvccConfig.cmake
@@ -2,7 +2,7 @@
 # This file is part of the GROMACS molecular simulation package.
 #
 # Copyright (c) 2012,2013,2014,2015,2016 by the GROMACS development team.
-# Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 # and including many others, as listed in the AUTHORS file in the
 # top-level source directory and at http://www.gromacs.org.
@@ -101,11 +101,11 @@ if (GMX_CUDA_TARGET_SM OR GMX_CUDA_TARGET_COMPUTE)
 else()
     # Set the CUDA GPU architectures to compile for:
     # - with CUDA >=9.0         CC 7.0 is supported and CC 2.0 is no longer supported
-    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70 SASS, and compute_70 PTX
+    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70 SASS, and compute_35, compute_70 PTX
     # - with CUDA >=10.0        CC 7.5 is supported
-    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75 SASS, and compute_75 PTX
+    #     => compile sm_30, sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75 SASS, and compute_35, compute_75 PTX
     # - with CUDA >=11.0        CC 8.0 is supported
-    #     => compile sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75, sm_80 SASS, and compute_80 PTX
+    #     => compile sm_35, sm_37, sm_50, sm_52, sm_60, sm_61, sm_70, sm_75, sm_80 SASS, and compute_35, compute_80 PTX
 
     # First add flags that trigger SASS (binary) code generation for physical arch
     if(CUDA_VERSION VERSION_LESS "11.0")
@@ -118,22 +118,28 @@ else()
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=sm_60")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=sm_61")
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=sm_70")
+    if(NOT CUDA_VERSION VERSION_LESS "10.0")
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_75,code=sm_75")
+    endif()
     if(NOT CUDA_VERSION VERSION_LESS "11.0")
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=sm_80")
         # Requesting sm or compute 35, 37, or 50 triggers deprecation messages with
         # nvcc 11.0, which we need to suppress for use in CI
         list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-Wno-deprecated-gpu-targets")
     endif()
+    if(NOT CUDA_VERSION VERSION_LESS "11.1")
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_86,code=sm_86")
+    endif()
 
-    # Next add flags that trigger PTX code generation for the newest supported virtual arch
-    # that's useful to JIT to future architectures
+    # Next add flags that trigger PTX code generation for the
+    # newest supported virtual arch that's useful to JIT to future architectures
+    # as well as an older one suitable for JIT-ing to any rare intermediate arch
+    # (like that of Jetson / Drive PX devices)
     list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_35,code=compute_35")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_50,code=compute_50")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_52,code=compute_52")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_60,code=compute_60")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_61,code=compute_61")
-    list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_70,code=compute_70")
-    if(NOT CUDA_VERSION VERSION_LESS "10.0")
-        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_75,code=compute_75")
+    if(CUDA_VERSION VERSION_LESS "11.0")
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_32,code=compute_32")
+    else()
+        list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_53,code=compute_53")
     endif()
     if(NOT CUDA_VERSION VERSION_LESS "11.0")
         list (APPEND GMX_CUDA_NVCC_GENCODE_FLAGS "-gencode;arch=compute_80,code=compute_80")

diff --git a/cmake/gmxTestCompilerProblems.cmake b/cmake/gmxTestCompilerProblems.cmake
index edb8c4714257849e3608ac7a39691016169275c9..620f1767eda7c32b832e6a60faaa169539923fba 100644 (file)
--- a/cmake/gmxTestCompilerProblems.cmake
+++ b/cmake/gmxTestCompilerProblems.cmake
@@ -47,27 +47,27 @@ macro(gmx_test_compiler_problems)
         message(WARNING "The versions of the C and C++ compilers do not match (${CMAKE_C_COMPILER_VERSION} and ${CMAKE_CXX_COMPILER_VERSION}, respectively). Mixing different C/C++ compilers can cause problems.")
     endif()
 
-    # Error if compiler doesn't support required C++14 features.
+    # Error if compiler doesn't support required C++17 features.
     # cmake feature detection is currently inconsistent: gitlab.kitware.com/cmake/cmake/issues/18869
-    # When we use C++17 we might want to switch to using feature test macros.
+    # We might want to switch to using feature test macros some time.
     if(CMAKE_COMPILER_IS_GNUCXX)
-        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
-            set(cxx_required_version "GCC version 5")
+        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 7)
+            set(cxx_required_version "GCC version 7")
         endif()
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
         if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19.15)
             set(cxx_required_version "Visual Studio 2017")
         endif()
     elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.6) # For feature complete C++14 only 3.4 is needed.
-            set(cxx_required_version "Clang 3.6")        # But prior version have bugs (e.g. debug symbol support)
+        if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5)
+            set(cxx_required_version "Clang 5")
         endif()
     else()
-        message(WARNING "You are using an unsupported compiler. Please make sure it fully supports C++14.")
+        message(WARNING "You are using an unsupported compiler. Please make sure it fully supports C++17.")
     endif()
     if (cxx_required_version)
         message(FATAL_ERROR "${cxx_required_version} or later required. "
-                            "Earlier versions don't have full C++14 support.")
+                            "Earlier versions don't have full C++17 support.")
     endif()
 
     if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")

diff --git a/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg b/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg
index 703166eb70af22bd27d21426545f87cd057b0586..728403c7ea67a6857eef53e181118e2094baba8d 100644 (file)
--- a/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg
+++ b/docs/reference-manual/plots/GMX_logos/gmx_logo_black.svg
@@ -14,14 +14,14 @@
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    id="svg923"
-   sodipodi:docname="Gromacs Logo [Blue].svg"
+   sodipodi:docname="gmx_logo_black.svg"
    inkscape:version="0.92.3 (2405546, 2018-03-11)"
    inkscape:export-filename="/home/cathrine/Pictures/svg_files/gromacs_logo1.png"
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+         rdf:resource="http://purl.org/dc/dcmitype/StillImage" /><dc:title /></cc:Work></rdf:RDF></metadata><defs
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+   style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:40px;line-height:1.25;font-family:KannadaMN-Bold, 'Kannada MN';-inkscape-font-specification:'KannadaMN-Bold, Kannada MN';letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none"><flowRegion
+     id="flowRegion1715"><rect
+       id="rect1717"
+       width="829.83124"
+       height="284.51358"
+       x="1311.9237"
+       y="1882.0675" /></flowRegion><flowPara
+     id="flowPara1719" /></flowRoot></svg>
\ No newline at end of file

diff --git a/docs/release-notes/2021/2021.1.rst b/docs/release-notes/2021/2021.1.rst
index 4b884a69f36fa9eb9b694b853ff472924081cfb6..9eb10dae2c77d6be894e25fd730cd5919173cec5 100644 (file)
--- a/docs/release-notes/2021/2021.1.rst
+++ b/docs/release-notes/2021/2021.1.rst
@@ -19,9 +19,34 @@ Fixes where mdrun could behave incorrectly
 Fixes for ``gmx`` tools
 ^^^^^^^^^^^^^^^^^^^^^^^
 
+Fix periodic boundary conditions in analysis framework tools
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+There was a bug in the trajectory analysis framework which caused
+molecules that were broken over PBC not to be made whole. This would
+usually lead to obviously incorrect outliers in analysis output.
+
+:issue:`3900`
+
+Fix range checking bug in gmx covar
+"""""""""""""""""""""""""""""""""""
+
+A check was inverted causing range checking to be applied wrong.
+
+:issue:`3902`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Fixed compilation on Cygwin
+"""""""""""""""""""""""""""
+
+A |Gromacs| header file was not including the necessary standard
+header. A problem with the ``M_PI`` math constant defined only by
+POSIX and not by C++ was also worked around.
+
+:issue:`3890`
+
 Miscellaneous
 ^^^^^^^^^^^^^
-
+* Updated |Gromacs| logos

diff --git a/docs/release-notes/2021/major/miscellaneous.rst b/docs/release-notes/2021/major/miscellaneous.rst
index 91f8cca080fa528083c76d2dd3f0b83960cc83b7..dfa74e3dba3c31f8aedbf15b356520871d58cba4 100644 (file)
--- a/docs/release-notes/2021/major/miscellaneous.rst
+++ b/docs/release-notes/2021/major/miscellaneous.rst
@@ -52,6 +52,7 @@ The environment variables that had exactly the same meaning in OpenCL and CUDA w
 Dysfunctional parts of the QMMM interface has been removed
 """"""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-Currently, GROMACS supports QM/MM officially only via MiMiC. All other QM/MM
+Currently, GROMACS supports QM/MM officially only via MiMiC; a new CP2K QM/MM interface is being
+developed within BioExcel. All other QM/MM
 support has been untested and likely dysfunctional for years and has now been removed from .mdp
 input and output, resulting in smaller .mdp output files from grompp.

diff --git a/src/external/CMakeLists.txt b/src/external/CMakeLists.txt
index e850736ec45f0a4c378bb7cea7d87b0b29b8c2da..57f73c60d0e3247a737c8a64f3a47f5eeccdd8d1 100644 (file)
--- a/src/external/CMakeLists.txt
+++ b/src/external/CMakeLists.txt
@@ -61,8 +61,9 @@ if(BUILD_TESTING AND GMX_BUILD_UNITTESTS)
             )
     target_compile_definitions(gtest PUBLIC GTEST_LANG_CXX11)
     if (CYGWIN)
-        # Ensure GoogleTest can find POSIX things it needs
-        target_compile_definitions(gtest PRIVATE _POSIX_C_SOURCE=200809L)
+        # Ensure GoogleTest and things that use it can find
+        # POSIX things needed by GoogleTest
+        target_compile_definitions(gtest PUBLIC _POSIX_C_SOURCE=200809L)
     endif()
     gmx_target_warning_suppression(gmock -Wno-deprecated-copy HAVE_NO_DEPRECATED_COPY)
 

diff --git a/src/gromacs/domdec/partition.cpp b/src/gromacs/domdec/partition.cpp
index 06b4937cafcf0a6c98e288a5a8c1664b6c0734de..dca7464ba7813544b4d0aea99718e05943b74028 100644 (file)
--- a/src/gromacs/domdec/partition.cpp
+++ b/src/gromacs/domdec/partition.cpp
@@ -1125,7 +1125,7 @@ static void print_dd_load_av(FILE* fplog, gmx_domdec_t* dd)
     fprintf(fplog, "\n");
     fprintf(stderr, "\n");
 
-    if (lossFraction >= DD_PERF_LOSS_WARN)
+    if ((lossFraction >= DD_PERF_LOSS_WARN) && (dd->comm->dlbState != DlbState::offTemporarilyLocked))
     {
         std::string message = gmx::formatString(
                 "NOTE: %.1f %% of the available CPU time was lost due to load imbalance\n"
@@ -1133,9 +1133,16 @@ static void print_dd_load_av(FILE* fplog, gmx_domdec_t* dd)
                 lossFraction * 100);
 
         bool hadSuggestion = false;
-        if (!isDlbOn(comm))
+        if (dd->comm->dlbState == DlbState::offUser)
         {
-            message += "      You might want to use dynamic load balancing (option -dlb.)\n";
+            message += "      You might want to allow dynamic load balancing (option -dlb auto.)\n";
+            hadSuggestion = true;
+        }
+        else if (dd->comm->dlbState == DlbState::offCanTurnOn)
+        {
+            message +=
+                    "      Dynamic load balancing was automatically disabled, but it might be "
+                    "beneficial to manually tuning it on (option -dlb on.)\n";
             hadSuggestion = true;
         }
         else if (dlbWasLimited)
@@ -1151,7 +1158,6 @@ static void print_dd_load_av(FILE* fplog, gmx_domdec_t* dd)
                 "      considerable inhomogeneity in the simulated system.",
                 hadSuggestion ? "also " : "");
 
-
         fprintf(fplog, "%s\n", message.c_str());
         fprintf(stderr, "%s\n", message.c_str());
     }

diff --git a/src/gromacs/gmxana/gmx_covar.cpp b/src/gromacs/gmxana/gmx_covar.cpp
index a6a07535cac1a49034a085c2fcd2c787c59086b4..33c3fae1bc9bd96a9e3f53ec7756792af671354b 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.cpp
+++ b/src/gromacs/gmxana/gmx_covar.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -73,27 +73,25 @@ namespace
 /*! \brief Throw an error if any element in index exceeds a given number.
  *
  * \param[in] indices to be acessed
- * \param[in] largestOkayIndex to be accessed
+ * \param[in] numAtoms to be accessed
  * \param[in] indexUsagePurpose to be more explicit in the error message
  *
- * \throws RangeError if largestOkayIndex is larger than any element in indices
+ * \throws RangeError if any element in indices is larger than or equal numAtoms
  *
  */
-void throwErrorIfIndexOutOfBounds(ArrayRef<const int> indices,
-                                  const int           largestOkayIndex,
-                                  const std::string&  indexUsagePurpose)
+void throwErrorIfIndexOutOfBounds(ArrayRef<const int> indices, const int numAtoms, const std::string& indexUsagePurpose)
 {
     // do nothing if index is empty
-    if (indices.ssize() == 0)
+    if (indices.empty())
     {
         return;
     }
     const int largestIndex = *std::max_element(indices.begin(), indices.end());
-    if (largestIndex < largestOkayIndex)
+    if (largestIndex >= numAtoms)
     {
-        GMX_THROW(RangeError("The provided structure file only contains "
-                             + std::to_string(largestOkayIndex) + " coordinates, but coordinate index "
-                             + std::to_string(largestIndex) + " was requested for " + indexUsagePurpose
+        GMX_THROW(RangeError("The provided structure file only contains " + std::to_string(numAtoms)
+                             + " coordinates, but coordinate index " + std::to_string(largestIndex + 1)
+                             + " was requested for " + indexUsagePurpose
                              + ". Make sure to update structure files "
                                "and index files if you store only a part of your system."));
     }

diff --git a/src/gromacs/gmxpreprocess/genhydro.cpp b/src/gromacs/gmxpreprocess/genhydro.cpp
index af370d5e719ff270ea3f530b5f19613a715c3151..5ee31602a3bfa2be660374604f57ac2c7cc4d479 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.cpp
+++ b/src/gromacs/gmxpreprocess/genhydro.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013-2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -80,6 +80,21 @@ static int pdbasearch_atom(const char*              name,
     return search_atom(name, i, pdba, searchtype, bAllowMissing, cyclicBondsIndex);
 }
 
+/*! \brief Return the index of the first atom whose residue index
+ * matches and which has a patch with the given name.
+ *
+ * \param[out] ii      Index of the first atom in the residue that matches,
+ *                       -1 if no match occurs.
+ * \param[out] jj      Index of the patch that matches,
+ *                       unchanged if no match occurs.
+ * \param[in]  name    Name of the desired patch to match
+ * \param[in]  patches The patch database to search
+ * \param[in]  resind  The residue index to match
+ * \param[in]  pdba    The atoms to work with
+ *
+ * \todo The short-circuit logic will be simpler if this returned a
+ * std::pair<int, int> as soon as the first double match is found.
+ */
 static void hacksearch_atom(int*                                            ii,
                             int*                                            jj,
                             const char*                                     name,
@@ -105,6 +120,10 @@ static void hacksearch_atom(int*                                            ii,
             {
                 *ii = i;
                 *jj = j;
+                if (*ii >= 0)
+                {
+                    break;
+                }
             }
             j++;
         }
@@ -220,8 +239,11 @@ static void expand_hackblocks_one(const MoleculePatchDatabase& newPatch,
                 if (singlePatch.tp == 10 && k == 2)
                 {
                     /* This is a water virtual site, not a hydrogen */
-                    /* Ugly hardcoded name hack */
-                    patch->nname.assign("M");
+                    /* Ugly hardcoded name hack to replace 'H' with 'M' */
+                    GMX_RELEASE_ASSERT(
+                            !patch->nname.empty() && patch->nname[0] == 'H',
+                            "Water virtual site should be named starting with H at this point");
+                    patch->nname[0] = 'M';
                 }
                 else if (singlePatch.tp == 11 && k >= 2)
                 {

diff --git a/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp b/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
index f9bac4c8282411917c0e7fab95b2b0bbd5017e09..fd5fcfc7c69d58ac41f721eb330ecf515c0599ce 100644 (file)
--- a/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
+++ b/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -65,7 +65,7 @@ using test::CommandLine;
 
 //! Test parameter struct.
 using CommandLineOptionParams =
-        std::tuple<std::string, std::string, std::string, std::string, std::string, std::string, int>;
+        std::tuple<std::string, std::string, std::string, std::string, std::string, std::string, int, bool>;
 
 /*! \brief Strings containing regular expressions for lines to skip
  * when matching.
@@ -94,6 +94,8 @@ public:
     Pdb2gmxTest()
     {
         int outputFileType = std::get<6>(GetParam());
+        // If the file type of the output configuration is one
+        // commonly used (ie. pdb, gro), then check its content.
         if (outputFileType == efPDB)
         {
             // If we're writing PDB output, we are interested in
@@ -103,9 +105,9 @@ public:
             ExactTextMatch settings;
             setOutputFile("-o", outputfile.c_str(), TextFileMatch(settings));
         }
-        else
+        else if (outputFileType == efGRO)
         {
-            setOutputFile("-o", "conf.gro", ConfMatch());
+            setOutputFile("-o", "conf.gro", ConfMatch().matchFullConfiguration(std::get<7>(GetParam())));
         }
         setOutputFile("-p", "topol.top", TextFileMatch(c_textMatcher));
     }
@@ -151,7 +153,8 @@ INSTANTIATE_TEST_CASE_P(ForOplsaa,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
 #endif
 
 #if GROMOS
@@ -166,7 +169,8 @@ INSTANTIATE_TEST_CASE_P(ForGromos43a1,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
 
 INSTANTIATE_TEST_CASE_P(ForGromos53a6,
                         Pdb2gmxTest,
@@ -179,7 +183,8 @@ INSTANTIATE_TEST_CASE_P(ForGromos53a6,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
 #endif
 
 #if AMBER
@@ -194,7 +199,18 @@ INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildn,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
+INSTANTIATE_TEST_CASE_P(ForAmber99sb_ildnWithTip4p,
+                        Pdb2gmxTest,
+                        ::testing::Combine(::testing::Values("amber99sb-ildn"),
+                                           ::testing::Values("tip4p"),
+                                           ::testing::Values("none"),
+                                           ::testing::Values("id_or_ter"),
+                                           ::testing::Values("no"),
+                                           ::testing::Values("tip4p.pdb"),
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(true)));
 #endif
 
 #if CHARMM
@@ -209,7 +225,8 @@ INSTANTIATE_TEST_CASE_P(ForCharmm27,
                                                              "fragment2.pdb",
                                                              "fragment3.pdb",
                                                              "fragment4.pdb"),
-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
 
 
 INSTANTIATE_TEST_CASE_P(ChainSep,
@@ -220,7 +237,8 @@ INSTANTIATE_TEST_CASE_P(ChainSep,
                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
                                            ::testing::Values("all", "no"),
                                            ::testing::Values("chainTer.pdb"),
-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
 
 INSTANTIATE_TEST_CASE_P(ChainChanges,
                         Pdb2gmxTest,
@@ -230,7 +248,8 @@ INSTANTIATE_TEST_CASE_P(ChainChanges,
                                            ::testing::Values("id", "ter", "id_or_ter", "id_and_ter"),
                                            ::testing::Values("no"),
                                            ::testing::Values("two-fragments.pdb"),
-                                           ::testing::Values(efPDB)));
+                                           ::testing::Values(efPDB),
+                                           ::testing::Values(false)));
 
 INSTANTIATE_TEST_CASE_P(ForCharmm27CyclicSystem,
                         Pdb2gmxTest,
@@ -241,7 +260,8 @@ INSTANTIATE_TEST_CASE_P(ForCharmm27CyclicSystem,
                                            ::testing::Values("no", "all"),
                                            ::testing::Values("cyclic-rna.pdb",
                                                              "cyclic-protein-small.pdb"),
-                                           ::testing::Values(efGRO)));
+                                           ::testing::Values(efGRO),
+                                           ::testing::Values(false)));
 #endif
 
 } // namespace

diff --git a/src/gromacs/gmxpreprocess/tests/refdata/ForAmber99sb_ildnWithTip4p_Pdb2gmxTest_ProducesMatchingTopology_0.xml b/src/gromacs/gmxpreprocess/tests/refdata/ForAmber99sb_ildnWithTip4p_Pdb2gmxTest_ProducesMatchingTopology_0.xml
new file mode 100644 (file)
index 0000000..de032d5
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/refdata/ForAmber99sb_ildnWithTip4p_Pdb2gmxTest_ProducesMatchingTopology_0.xml
@@ -0,0 +1,60 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+  <OutputFiles Name="Files">
+    <File Name="-o">
+      <GroFile Name="Header">
+        <String Name="Title">TIP4p ice to test that MW is handled correctly</String>
+        <Int Name="Number of atoms">8</Int>
+      </GroFile>
+      <String Name="Configuration"><![CDATA[
+    1HO4     OW    1  -2.474  -5.526  -0.497
+    1HO4    HW1    2  -2.393  -5.526  -0.439
+    1HO4    HW2    3  -2.556  -5.526  -0.439
+    1HO4     MW    4  -2.484  -5.527  -0.485
+    2HO4     OW    5  -2.496  -5.242  -0.878
+    2HO4    HW1    6  -2.415  -5.242  -0.820
+    2HO4    HW2    7  -2.496  -5.160  -0.936
+    2HO4     MW    8  -2.482  -5.239  -0.874
+   0.16330   0.36715   0.49637
+]]></String>
+    </File>
+    <File Name="-p">
+      <String Name="Contents"><![CDATA[
+;
+;
+;      This is a standalone topology file
+;
+;      Created by:
+;      
+;      Command line:
+;      Force field was read from the standard GROMACS share directory.
+;
+
+; Include forcefield parameters
+#include "amber99sb-ildn.ff/forcefield.itp"
+
+; Include water topology
+#include "amber99sb-ildn.ff/tip4p.itp"
+
+#ifdef POSRES_WATER
+; Position restraint for each water oxygen
+[ position_restraints ]
+;  i funct       fcx        fcy        fcz
+   1    1       1000       1000       1000
+#endif
+
+; Include topology for ions
+#include "amber99sb-ildn.ff/ions.itp"
+
+[ system ]
+; Name
+TIP4p ice to test that MW is handled correctly
+
+[ molecules ]
+; Compound        #mols
+SOL                 2
+]]></String>
+    </File>
+  </OutputFiles>
+</ReferenceData>

diff --git a/src/gromacs/gmxpreprocess/tests/tip4p.pdb b/src/gromacs/gmxpreprocess/tests/tip4p.pdb
new file mode 100644 (file)
index 0000000..eb55c00
--- /dev/null
+++ b/src/gromacs/gmxpreprocess/tests/tip4p.pdb
@@ -0,0 +1,9 @@
+TITLE     TIP4p ice to test that MW is handled correctly
+ATOM      1  OW  SOL A   1     -24.744 -55.257  -4.969  1.00  1.00      A    O
+ATOM      2  HW1 SOL A   1     -25.692 -55.390  -4.996  1.00  0.00      A    H
+ATOM      3  HW2 SOL A   1     -24.532 -55.232  -4.035  1.00  0.00      A    H
+ATOM      4  MW  SOL A   1     -24.838 -55.271  -4.853  1.00  0.00      A    O
+ATOM      5  OW  SOL A   2     -24.964 -52.416  -8.778  1.00  1.00      A    O
+ATOM      6  HW1 SOL A   2     -24.502 -52.770  -8.018  1.00  0.00      A    H
+ATOM      7  HW2 SOL A   2     -24.314 -51.874  -9.224  1.00  0.00      A    H
+ATOM      8  MW  SOL A   2     -24.822 -52.393  -8.738  1.00  0.00      A    O

diff --git a/src/gromacs/mdlib/stat.h b/src/gromacs/mdlib/stat.h
index d3cf97713abce87ee2e31c8095b5926a31d7ba78..ad7c7657e761a775aa3e930aaa9f4686978c97cc 100644 (file)
--- a/src/gromacs/mdlib/stat.h
+++ b/src/gromacs/mdlib/stat.h
@@ -39,6 +39,8 @@
 #ifndef GMX_MDLIB_STAT_H
 #define GMX_MDLIB_STAT_H
 
+#include <cstdint>
+
 #include "gromacs/math/vectypes.h"
 
 struct gmx_ekindata_t;

diff --git a/src/gromacs/nbnxm/gpu_types_common.h b/src/gromacs/nbnxm/gpu_types_common.h
index 57d791be2a85f7d4945f9bd1db2173336ee677ee..2d2e90791e9833d227ee3640ab0483086da09da0 100644 (file)
--- a/src/gromacs/nbnxm/gpu_types_common.h
+++ b/src/gromacs/nbnxm/gpu_types_common.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -212,11 +212,11 @@ struct gpu_plist
     int excl_nalloc;
 
     /* parameter+variables for normal and rolling pruning */
-    //! true after search, indictes that initial pruning with outer prunning is needed
+    //! true after search, indicates that initial pruning with outer pruning is needed
     bool haveFreshList;
-    //! the number of parts/steps over which one cyle of roling pruning takes places
+    //! the number of parts/steps over which one cycle of rolling pruning takes places
     int rollingPruningNumParts;
-    //! the next part to which the roling pruning needs to be applied
+    //! the next part to which the rolling pruning needs to be applied
     int rollingPruningPart;
 };
 

diff --git a/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp b/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
index 2a2a394cae417fba976f71d7637425057d8dee48..9fe755c586006afabb0849d592cbd4fece5e83d5 100644 (file)
--- a/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
+++ b/src/gromacs/nbnxm/nbnxm_gpu_data_mgmt.cpp
@@ -191,16 +191,18 @@ void init_plist(gpu_plist* pl)
     pl->excl  = nullptr;
 
     /* size -1 indicates that the respective array hasn't been initialized yet */
-    pl->na_c          = -1;
-    pl->nsci          = -1;
-    pl->sci_nalloc    = -1;
-    pl->ncj4          = -1;
-    pl->cj4_nalloc    = -1;
-    pl->nimask        = -1;
-    pl->imask_nalloc  = -1;
-    pl->nexcl         = -1;
-    pl->excl_nalloc   = -1;
-    pl->haveFreshList = false;
+    pl->na_c                   = -1;
+    pl->nsci                   = -1;
+    pl->sci_nalloc             = -1;
+    pl->ncj4                   = -1;
+    pl->cj4_nalloc             = -1;
+    pl->nimask                 = -1;
+    pl->imask_nalloc           = -1;
+    pl->nexcl                  = -1;
+    pl->excl_nalloc            = -1;
+    pl->haveFreshList          = false;
+    pl->rollingPruningNumParts = 0;
+    pl->rollingPruningPart     = 0;
 }
 
 void init_timings(gmx_wallclock_gpu_nbnxn_t* t)

diff --git a/src/gromacs/pbcutil/rmpbc.cpp b/src/gromacs/pbcutil/rmpbc.cpp
index ee79717113fd60a3c101a52c99a8484aa7025082..9f8f591dd7e92f6509d05d9afc341c157f192817 100644 (file)
--- a/src/gromacs/pbcutil/rmpbc.cpp
+++ b/src/gromacs/pbcutil/rmpbc.cpp
@@ -4,7 +4,7 @@
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
  * Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -76,7 +76,8 @@ static t_graph* gmx_rmpbc_get_graph(gmx_rmpbc_t gpbc, PbcType pbcType, int natom
     int            i;
     rmpbc_graph_t* gr;
 
-    if (pbcType == PbcType::No || nullptr == gpbc || nullptr == gpbc->idef || gpbc->idef->ntypes <= 0)
+    if (pbcType == PbcType::No || nullptr == gpbc
+        || (nullptr == gpbc->interactionDefinitions && (nullptr == gpbc->idef || gpbc->idef->ntypes <= 0)))
     {
         return nullptr;
     }

diff --git a/src/testutils/conftest.cpp b/src/testutils/conftest.cpp
index 3fd50276cbfc93c058bef27e6c502842c4c94ca5..c9fe48523467e426b889df9df362528f6ec073e7 100644 (file)
--- a/src/testutils/conftest.cpp
+++ b/src/testutils/conftest.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -48,6 +48,7 @@
 
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textreader.h"
 #include "gromacs/utility/textstream.h"
 
 #include "testutils/refdata.h"
@@ -79,11 +80,11 @@ private:
 
 } // namespace
 
-void checkConfFile(TextInputStream* input, TestReferenceChecker* checker, const ConfMatchSettings& /*unused*/)
+void checkConfFile(TextInputStream* input, TestReferenceChecker* checker, const ConfMatchSettings& settings)
 {
 
     TestReferenceChecker groChecker(checker->checkCompound("GroFile", "Header"));
-    // Just check the first two lines of the output file
+    // Check the first two lines of the output file
     std::string line;
     EXPECT_TRUE(input->readLine(&line));
     line = stripSuffixIfPresent(line, "\n");
@@ -91,6 +92,12 @@ void checkConfFile(TextInputStream* input, TestReferenceChecker* checker, const
     EXPECT_TRUE(input->readLine(&line));
     line = stripSuffixIfPresent(line, "\n");
     groChecker.checkInteger(std::atoi(line.c_str()), "Number of atoms");
+    // Check the full configuration only if required
+    if (settings.matchFullConfiguration)
+    {
+        TextReader reader(input);
+        checker->checkTextBlock(reader.readAll(), "Configuration");
+    }
 }
 
 TextBlockMatcherPointer ConfMatch::createMatcher() const

diff --git a/src/testutils/include/testutils/conftest.h b/src/testutils/include/testutils/conftest.h
index d22033c53790bfc697fb2293077da3e9863bb1ea..144a60f436ef66d9c74cf9d9f85529d13329efc4 100644 (file)
--- a/src/testutils/include/testutils/conftest.h
+++ b/src/testutils/include/testutils/conftest.h
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2017,2018,2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 2017,2018,2019,2020,2021, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -60,9 +60,8 @@ class TestReferenceChecker;
 
 struct ConfMatchSettings
 {
-    ConfMatchSettings() : tolerance(defaultRealTolerance()) {}
-
-    FloatingPointTolerance tolerance;
+    FloatingPointTolerance tolerance              = defaultRealTolerance();
+    bool                   matchFullConfiguration = false;
 };
 
 /*! \brief
@@ -96,6 +95,12 @@ public:
         settings_.tolerance = tolerance;
         return *this;
     }
+    //! Sets whether the full file contents should be matched
+    ConfMatch& matchFullConfiguration(const bool flag)
+    {
+        settings_.matchFullConfiguration = flag;
+        return *this;
+    }
 
     TextBlockMatcherPointer createMatcher() const override;