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Merge release-2021 into master
authorAndrey Alekseenko <al42and@gmail.com>
Mon, 18 Oct 2021 14:31:36 +0000 (16:31 +0200)
committerAndrey Alekseenko <al42and@gmail.com>
Mon, 18 Oct 2021 14:39:47 +0000 (16:39 +0200)
Brings the following fixes from the release branch into master:

- #4148 (!1941)
- #4167 (!1966)
- #4190 (!2050)
- !2039

14 files changed:
docs/gmxapi/userguide/install.rst patch | blob | history
docs/release-notes/2021/2021.4.rst patch | blob | history
docs/release-notes/2021/major/portability.rst patch | blob | history
src/gromacs/ewald/pme.cpp patch | blob | history
src/gromacs/ewald/pme.h patch | blob | history
src/gromacs/mdlib/vsite.cpp patch | blob | history
src/gromacs/mdrun/runner.cpp patch | blob | history
src/gromacs/selection/evaluate.cpp patch | blob | history
src/gromacs/taskassignment/decidegpuusage.cpp patch | blob | history
src/gromacs/taskassignment/decidegpuusage.h patch | blob | history
src/gromacs/trajectoryanalysis/tests/distance.cpp patch | blob | history
src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml [new file with mode: 0644] patch | blob
src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml [new file with mode: 0644] patch | blob
src/gromacs/trajectoryanalysis/tests/simple.ndx [new file with mode: 0644] patch | blob

diff --git a/docs/gmxapi/userguide/install.rst b/docs/gmxapi/userguide/install.rst
index f0ab2210fb9ced25c1be0cb28f42833538b96ce8..e1994e9c74b343f80ed9c496eafad0eb6a494693 100644 (file)
--- a/docs/gmxapi/userguide/install.rst
+++ b/docs/gmxapi/userguide/install.rst
@@ -517,14 +517,14 @@ or
 
 Sometimes the build environment can choose a different Python interpreter than
 the one you intended.
-You can set the ``Python3_ROOT`` or ``CMAKE_PREFIX_PATH`` CMake variable to
+You can set the ``Python3_ROOT_DIR`` or ``CMAKE_PREFIX_PATH`` CMake variable to
 explicitly choose the Python installation or *venv* directory.
 
 If you use pyenv or pyenv-virtualenv to dynamically manage your Python version,
 you can help identify a particular version with ``pyenv version-name`` and the
 directory with ``pyenv prefix {version}``. For example::
 
-    -DPython3_ROOT=$(pyenv prefix $(pyenv version-name))
+    -DPython3_ROOT_DIR=$(pyenv prefix $(pyenv version-name))
 
 Docker web server
 -----------------
diff --git a/docs/release-notes/2021/2021.4.rst b/docs/release-notes/2021/2021.4.rst
index 69a9b7cabe8f7cae306c6821464b093559d8c994..d162efb241e54daab60cf1261f0a7d7e9347217b 100644 (file)
--- a/docs/release-notes/2021/2021.4.rst
+++ b/docs/release-notes/2021/2021.4.rst
@@ -16,6 +16,27 @@ in the :ref:`release-notes`.
 Fixes where mdrun could behave incorrectly
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Fixed crash for large system with virtual sites
+"""""""""""""""""""""""""""""""""""""""""""""""
+
+When large system with virtual sites were ran with domain decomposition
+and OpenMP threading, mdrun would crash when the number of atoms in
+a domain and its halo were more than 200000.
+
+:issue:`4167`
+
+Disabled the use of PME Mixed mode for FEP simulations
+""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+The use of Mixed mode PME (``-pme gpu -pmefft cpu``) led to incorrect
+computation of :math:`{\frac{\partial V}{\partial {\lambda}}}` in FEP
+simulations.
+
+Mixed mode is only used when explicitly requested by the user.
+
+:issue:`4190`
+
+
 Fixes for ``gmx`` tools
 ^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -24,6 +45,19 @@ grompp now prints a note again when combining center of mass motion removal and
 
 :issue:`4128`
 
+Static selections of large index groups now work
+""""""""""""""""""""""""""""""""""""""""""""""""
+
+Commands like ``gmx distance -f traj.xtc -n ndx.ndx -select "group
+\"Contacts\""`` only worked if the size of ``Contacts`` was less than
+the number of atoms. This restriction was a bug, and has been fixed so
+that ``Contacts`` make take any size.
+
+Other similar uses of static selections derived from index groups will
+also now work.
+
+:issue:`4148`
+
 Fixes that affect portability
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
diff --git a/docs/release-notes/2021/major/portability.rst b/docs/release-notes/2021/major/portability.rst
index f688a2b01d3b6aad133c4042b8763de0cd2bcd08..4c1a22e13eaa4d1b4c0d41d6362f50633c160489 100644 (file)
--- a/docs/release-notes/2021/major/portability.rst
+++ b/docs/release-notes/2021/major/portability.rst
@@ -12,7 +12,7 @@ CMake now detects Python using
 If you previously used ``PYTHON_EXECUTABLE`` to hint the location of the Python
 interpreter, you should instead specify the Python "root" or "prefix" path
 (the directory containing ``./bin/python3``) with CMake variable
-``Python3_ROOT`` or ``CMAKE_PREFIX_PATH``. As other infrastructure evolves,
+``Python3_ROOT_DIR`` or ``CMAKE_PREFIX_PATH``. As other infrastructure evolves,
 ``PYTHON_EXECUTABLE`` may cease to have the desired effect without warning.
 
 .. Note to developers!
diff --git a/src/gromacs/ewald/pme.cpp b/src/gromacs/ewald/pme.cpp
index 7438077d0b26031ecaf055243eea06eb928dc27a..e2c87459a0589403888d57fdfead803bbabb869f 100644 (file)
--- a/src/gromacs/ewald/pme.cpp
+++ b/src/gromacs/ewald/pme.cpp
@@ -180,6 +180,20 @@ bool pme_gpu_supports_input(const t_inputrec& ir, std::string* error)
     return errorReasons.isEmpty();
 }
 
+bool pme_gpu_mixed_mode_supports_input(const t_inputrec& ir, std::string* error)
+{
+    gmx::MessageStringCollector errorReasons;
+    // Before changing the prefix string, make sure that it is not searched for in regression tests.
+    errorReasons.startContext("PME GPU in Mixed mode does not support:");
+    errorReasons.appendIf(ir.efep != FreeEnergyPerturbationType::No, "Free Energy Perturbation.");
+    errorReasons.finishContext();
+    if (error != nullptr)
+    {
+        *error = errorReasons.toString();
+    }
+    return errorReasons.isEmpty();
+}
+
 /*! \brief \libinternal
  * Finds out if PME with given inputs is possible to run on GPU.
  * This function is an internal final check, validating the whole PME structure on creation,
diff --git a/src/gromacs/ewald/pme.h b/src/gromacs/ewald/pme.h
index 03d4da52c07097da2a8521823638d58f99902045..eb0c5651753535db601959d2101f7f8e12669ebd 100644 (file)
--- a/src/gromacs/ewald/pme.h
+++ b/src/gromacs/ewald/pme.h
@@ -300,6 +300,17 @@ bool pme_gpu_supports_hardware(const gmx_hw_info_t& hwinfo, std::string* error);
  */
 bool pme_gpu_supports_input(const t_inputrec& ir, std::string* error);
 
+/*! \brief Checks whether the input system allows to run PME on GPU in Mixed mode.
+ * Assumes that the input system is compatible with GPU PME otherwise, that is,
+ * before calling this function one should check that \ref pme_gpu_supports_input returns \c true.
+ *
+ * \param[in]  ir     Input system.
+ * \param[out] error  If non-null, the error message if the input is not supported.
+ *
+ * \returns true if PME can run on GPU in Mixed mode with this input, false otherwise.
+ */
+bool pme_gpu_mixed_mode_supports_input(const t_inputrec& ir, std::string* error);
+
 /*! \brief
  * Returns the active PME codepath (CPU, GPU, mixed).
  * \todo This is a rather static data that should be managed by the higher level task scheduler.
diff --git a/src/gromacs/mdlib/vsite.cpp b/src/gromacs/mdlib/vsite.cpp
index d030f9d4aba335b2e3f1b592663e9d27e320473e..c3f9edb3b27d65b522f598d0cfdac1f8fa4de1f7 100644 (file)
--- a/src/gromacs/mdlib/vsite.cpp
+++ b/src/gromacs/mdlib/vsite.cpp
@@ -2760,7 +2760,16 @@ static void assignVsitesToThread(VsiteThread*                    tData,
                                    "a constructing atom that does not belong to our task, such "
                                    "vsites should be assigned to the single 'master' task");
 
-                        task = nthread + thread;
+                        if (tData->useInterdependentTask)
+                        {
+                            // Assign to the interdependent task
+                            task = nthread + thread;
+                        }
+                        else
+                        {
+                            // Assign to the separate, non-parallel task
+                            task = 2 * nthread;
+                        }
                     }
                 }
             }
@@ -3000,12 +3009,13 @@ void ThreadingInfo::setVirtualSites(ArrayRef<const InteractionList> ilists,
             }
 
             /* To avoid large f_buf allocations of #threads*vsite_atom_range
-             * we don't use task2 with more than 200000 atoms. This doesn't
-             * affect performance, since with such a large range relatively few
-             * vsites will end up in the separate task.
-             * Note that useTask2 should be the same for all threads.
+             * we don't use the interdependent tasks with more than 200000 atoms.
+             * This doesn't affect performance, since with such a large range
+             * relatively few vsites will end up in the separate task.
+             * Note that useInterdependentTask should be the same for all threads.
              */
-            tData.useInterdependentTask = (vsite_atom_range <= 200000);
+            const int c_maxNumLocalAtomsForInterdependentTask = 200000;
+            tData.useInterdependentTask = (vsite_atom_range <= c_maxNumLocalAtomsForInterdependentTask);
             if (tData.useInterdependentTask)
             {
                 size_t              natoms_use_in_vsites = vsite_atom_range;
diff --git a/src/gromacs/mdrun/runner.cpp b/src/gromacs/mdrun/runner.cpp
index 3bf1d5071cd6d9d21bb56dd62ad182f178488c99..887e7ba7093ee95bbfddcea4cbdce399c1f34446 100644 (file)
--- a/src/gromacs/mdrun/runner.cpp
+++ b/src/gromacs/mdrun/runner.cpp
@@ -907,6 +907,7 @@ int Mdrunner::mdrunner()
                     hw_opt.nthreads_tmpi);
             useGpuForPme = decideWhetherToUseGpusForPmeWithThreadMpi(useGpuForNonbonded,
                                                                      pmeTarget,
+                                                                     pmeFftTarget,
                                                                      numAvailableDevices,
                                                                      userGpuTaskAssignment,
                                                                      *hwinfo_,
@@ -1012,6 +1013,7 @@ int Mdrunner::mdrunner()
                 gpusWereDetected);
         useGpuForPme    = decideWhetherToUseGpusForPme(useGpuForNonbonded,
                                                     pmeTarget,
+                                                    pmeFftTarget,
                                                     userGpuTaskAssignment,
                                                     *hwinfo_,
                                                     *inputrec,
diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp
index 23781cee8cfc0177dc1e85f98eefd9603273f17f..079f906cb9701b21d8c94381a1762c42f28a1fb9 100644 (file)
--- a/src/gromacs/selection/evaluate.cpp
+++ b/src/gromacs/selection/evaluate.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
  * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
- * Copyright (c) 2019,2020, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -522,6 +522,7 @@ void _gmx_sel_evaluate_static(gmx_sel_evaluate_t* /* data */,
 {
     if (sel->flags & SEL_UNSORTED)
     {
+        gmx_ana_index_reserve(sel->v.u.g, sel->u.cgrp.isize);
         // This only works if g contains all the atoms, but that is currently
         // the only supported case.
         gmx_ana_index_copy(sel->v.u.g, &sel->u.cgrp, false);
diff --git a/src/gromacs/taskassignment/decidegpuusage.cpp b/src/gromacs/taskassignment/decidegpuusage.cpp
index 36c4650f0649311fe23d213ec27e7a66f737e389..62010fe2697772148bdcdb604511933f4c06209b 100644 (file)
--- a/src/gromacs/taskassignment/decidegpuusage.cpp
+++ b/src/gromacs/taskassignment/decidegpuusage.cpp
@@ -157,6 +157,7 @@ bool decideWhetherToUseGpusForNonbondedWithThreadMpi(const TaskTarget        non
 
 bool decideWhetherToUseGpusForPmeWithThreadMpi(const bool              useGpuForNonbonded,
                                                const TaskTarget        pmeTarget,
+                                               const TaskTarget        pmeFftTarget,
                                                const int               numDevicesToUse,
                                                const std::vector<int>& userGpuTaskAssignment,
                                                const gmx_hw_info_t&    hardwareInfo,
@@ -168,8 +169,15 @@ bool decideWhetherToUseGpusForPmeWithThreadMpi(const bool              useGpuFor
     if ((pmeTarget == TaskTarget::Cpu) || !useGpuForNonbonded || !pme_gpu_supports_build(nullptr)
         || !pme_gpu_supports_hardware(hardwareInfo, nullptr) || !pme_gpu_supports_input(inputrec, nullptr))
     {
-        // PME can't run on a GPU. If the user required that, we issue
-        // an error later.
+        // PME can't run on a GPU. If the user required that, we issue an error later.
+        return false;
+    }
+
+    if (pmeFftTarget == TaskTarget::Cpu && !pme_gpu_mixed_mode_supports_input(inputrec, nullptr))
+    {
+        /* User requested PME FFT on CPU, but the current system is not compatible with Mixed mode,
+         * so we don't use GPUs at all.
+         * If the user had -pme gpu, we issue an error later. */
         return false;
     }
 
@@ -330,6 +338,7 @@ bool decideWhetherToUseGpusForNonbonded(const TaskTarget          nonbondedTarge
 
 bool decideWhetherToUseGpusForPme(const bool              useGpuForNonbonded,
                                   const TaskTarget        pmeTarget,
+                                  const TaskTarget        pmeFftTarget,
                                   const std::vector<int>& userGpuTaskAssignment,
                                   const gmx_hw_info_t&    hardwareInfo,
                                   const t_inputrec&       inputrec,
@@ -377,6 +386,16 @@ bool decideWhetherToUseGpusForPme(const bool              useGpuForNonbonded,
         }
         return false;
     }
+    if (pmeFftTarget == TaskTarget::Cpu && !pme_gpu_mixed_mode_supports_input(inputrec, &message))
+    {
+        /* User requested PME FFT on CPU, but the current system is not compatible with Mixed mode,
+         * so we don't use GPUs at all. */
+        if (pmeTarget == TaskTarget::Gpu)
+        {
+            GMX_THROW(NotImplementedError("Cannot compute PME interactions in Mixed mode, because " + message));
+        }
+        return false;
+    }
 
     if (pmeTarget == TaskTarget::Cpu)
     {
diff --git a/src/gromacs/taskassignment/decidegpuusage.h b/src/gromacs/taskassignment/decidegpuusage.h
index 3404bebb6af6f6c6e8bc3097dd8d77695fb6768e..76b6f40042a0fec1ecd7bcec55482aec9d3ac72d 100644 (file)
--- a/src/gromacs/taskassignment/decidegpuusage.h
+++ b/src/gromacs/taskassignment/decidegpuusage.h
@@ -137,6 +137,7 @@ bool decideWhetherToUseGpusForNonbondedWithThreadMpi(TaskTarget              non
  * \param[in]  useGpuForNonbonded        Whether GPUs will be used for nonbonded interactions.
  * \param[in]  pmeTarget                 The user's choice for mdrun -pme for where to assign
  *                                       long-ranged PME nonbonded interaction tasks.
+ * \param[in]  pmeFftTarget              The user's choice for mdrun -pmefft for where to run FFT.
  * \param[in]  numDevicesToUse           The number of compatible GPUs that the user permitted us to use.
  * \param[in]  userGpuTaskAssignment     The user-specified assignment of GPU tasks to device IDs.
  * \param[in]  hardwareInfo              Hardware information
@@ -150,6 +151,7 @@ bool decideWhetherToUseGpusForNonbondedWithThreadMpi(TaskTarget              non
  *             InconsistentInputError  If the user requirements are inconsistent. */
 bool decideWhetherToUseGpusForPmeWithThreadMpi(bool                    useGpuForNonbonded,
                                                TaskTarget              pmeTarget,
+                                               TaskTarget              pmeFftTarget,
                                                int                     numDevicesToUse,
                                                const std::vector<int>& userGpuTaskAssignment,
                                                const gmx_hw_info_t&    hardwareInfo,
@@ -209,6 +211,7 @@ bool decideWhetherToUseGpusForNonbonded(TaskTarget              nonbondedTarget,
  *
  * \param[in]  useGpuForNonbonded        Whether GPUs will be used for nonbonded interactions.
  * \param[in]  pmeTarget                 The user's choice for mdrun -pme for where to assign long-ranged PME nonbonded interaction tasks.
+ * \param[in]  pmeFftTarget              The user's choice for mdrun -pmefft for where to do FFT for PME.
  * \param[in]  userGpuTaskAssignment     The user-specified assignment of GPU tasks to device IDs.
  * \param[in]  hardwareInfo              Hardware information
  * \param[in]  inputrec                  The user input
@@ -222,6 +225,7 @@ bool decideWhetherToUseGpusForNonbonded(TaskTarget              nonbondedTarget,
  *             InconsistentInputError  If the user requirements are inconsistent. */
 bool decideWhetherToUseGpusForPme(bool                    useGpuForNonbonded,
                                   TaskTarget              pmeTarget,
+                                  TaskTarget              pmeFftTarget,
                                   const std::vector<int>& userGpuTaskAssignment,
                                   const gmx_hw_info_t&    hardwareInfo,
                                   const t_inputrec&       inputrec,
diff --git a/src/gromacs/trajectoryanalysis/tests/distance.cpp b/src/gromacs/trajectoryanalysis/tests/distance.cpp
index 49b0f8cb6309f1f998bc18d55025740f889f9044..95706b6426f9f46341413791bf1d99c9b4c4cc5b 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/distance.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/distance.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2013,2014,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2019,2021, 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.
@@ -90,4 +90,20 @@ TEST_F(DistanceModuleTest, HandlesDynamicSelections)
     runTest(CommandLine(cmdline));
 }
 
+TEST_F(DistanceModuleTest, HandlesSelectionFromGroup)
+{
+    const char* const cmdline[] = { "distance", "-select", "group \"Contacts\"" };
+    setInputFile("-n", "simple.ndx");
+    setTopology("simple.gro");
+    runTest(CommandLine(cmdline));
+}
+
+TEST_F(DistanceModuleTest, HandlesSelectionFromLargeGroup)
+{
+    const char* const cmdline[] = { "distance", "-select", "group \"ManyContacts\"" };
+    setInputFile("-n", "simple.ndx");
+    setTopology("simple.gro");
+    runTest(CommandLine(cmdline));
+}
+
 } // namespace
diff --git a/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml
new file mode 100644 (file)
index 0000000..7301870
--- /dev/null
+++ b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromGroup.xml
@@ -0,0 +1,2094 @@
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
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diff --git a/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml
new file mode 100644 (file)
index 0000000..01ed5a1
--- /dev/null
+++ b/src/gromacs/trajectoryanalysis/tests/refdata/DistanceModuleTest_HandlesSelectionFromLargeGroup.xml
@@ -0,0 +1,2270 @@
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+            <Real Name="Value">-1</Real>
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+            <Real Name="Value">0</Real>
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+  </OutputData>
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diff --git a/src/gromacs/trajectoryanalysis/tests/simple.ndx b/src/gromacs/trajectoryanalysis/tests/simple.ndx
new file mode 100644 (file)
index 0000000..5f1dde8
--- /dev/null
+++ b/src/gromacs/trajectoryanalysis/tests/simple.ndx
@@ -0,0 +1,37 @@
+[ System ]
+   1    2    3    4    5    6    7    8    9   10   11   12   13   14   15
+[ RNA ]
+   1    2    3    7    8    9   10   11   12
+[ RB ]
+   4    5    6
+[ RD ]
+  13   14   15
+[ Ion ]
+   4    5    6
+[ RB ]
+   4    5    6
+[ RD ]
+  13   14   15
+[ Other ]
+  13   14   15
+[ RB ]
+   4    5    6
+[ RD ]
+  13   14   15
+[ Contacts ]
+   2    3
+   1    2
+[ SuccessiveContacts ]
+   1    2
+   2    3
+[ ManyContacts ]
+   1    2
+   1    6
+   1    8
+   1   10
+   1   11
+  10   12
+   2    3
+   2    6
+   2    7
+   2    9
Local GROMACS mirror with custom stuff