Merge pull request #134 from OpenBioSim/feature_optimise_lever

Feature optimise lever
OpenBioSim · Dec 8, 2023 · 825c7c7 · 825c7c7
2 parents ae2f36d + 07e8dea
commit 825c7c7
Show file tree

Hide file tree

Showing 6 changed files with 331 additions and 77 deletions.
diff --git a/corelib/src/libs/SireIO/moleculeparser.cpp b/corelib/src/libs/SireIO/moleculeparser.cpp
@@ -1929,8 +1929,19 @@ MoleculeParserPtr MoleculeParser::parse(const System &system, const QString &for
     cannot be recognised, or if there is an error in parsing. */
 MoleculeParserPtr MoleculeParser::parse(const QString &filename, const PropertyMap &map)
 {
-    MoleculeParserPtr parser = MoleculeParser::_pvt_parse(filename, map);
-    getFileCache()->clear();
+    MoleculeParserPtr parser;
+
+    try
+    {
+        parser = MoleculeParser::_pvt_parse(filename, map);
+        getFileCache()->clear();
+    }
+    catch (...)
+    {
+        getFileCache()->clear();
+        throw;
+    }
+
     return parser;
 }
 
@@ -1939,48 +1950,56 @@ QList<MoleculeParserPtr> MoleculeParser::parse(const QStringList &filenames, con
 {
     QList<MoleculeParserPtr> result;
 
-    if (filenames.count() == 1)
-    {
-        result.append(MoleculeParser::_pvt_parse(filenames[0], map));
-    }
-    else
+    try
     {
-        QVector<MoleculeParserPtr> parsers(filenames.count());
-
-        bool run_parallel = true;
-
-        if (map["parallel"].hasValue())
+        if (filenames.count() == 1)
         {
-            run_parallel = map["parallel"].value().asA<BooleanProperty>().value();
-        }
-
-        if (run_parallel)
-        {
-            // parse the files in parallel - we use a grain size of 1
-            // as each file can be pretty big, and there won't be many of them
-            tbb::parallel_for(
-                tbb::blocked_range<int>(0, filenames.count(), 1),
-                [&](tbb::blocked_range<int> r)
-                {
-                    for (int i = r.begin(); i < r.end(); ++i)
-                    {
-                        parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
-                    }
-                },
-                tbb::simple_partitioner());
+            result.append(MoleculeParser::_pvt_parse(filenames[0], map));
         }
         else
         {
-            for (int i = 0; i < filenames.count(); ++i)
+            QVector<MoleculeParserPtr> parsers(filenames.count());
+
+            bool run_parallel = true;
+
+            if (map["parallel"].hasValue())
+            {
+                run_parallel = map["parallel"].value().asA<BooleanProperty>().value();
+            }
+
+            if (run_parallel)
             {
-                parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
+                // parse the files in parallel - we use a grain size of 1
+                // as each file can be pretty big, and there won't be many of them
+                tbb::parallel_for(
+                    tbb::blocked_range<int>(0, filenames.count(), 1),
+                    [&](tbb::blocked_range<int> r)
+                    {
+                        for (int i = r.begin(); i < r.end(); ++i)
+                        {
+                            parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
+                        }
+                    },
+                    tbb::simple_partitioner());
             }
+            else
+            {
+                for (int i = 0; i < filenames.count(); ++i)
+                {
+                    parsers[i] = MoleculeParser::_pvt_parse(filenames[i], map);
+                }
+            }
+
+            result = parsers.toList();
         }
 
-        result = parsers.toList();
+        getFileCache()->clear();
+    }
+    catch (...)
+    {
+        getFileCache()->clear();
+        throw;
     }
-
-    getFileCache()->clear();
 
     return result;
 }

diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
@@ -57,6 +57,15 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
   a zero sigma value. They will either be sigma=1/epsilon=0 for non-perturbable
   atoms, or sigma=1e-9/epsilon=1e-9 for perturbable atoms.
 
+* Optimised the ``LambaLever`` class so that it caches the forcefield parameters
+  calculated at different lambda values. This means that we don't have to
+  re-calculate the parameters at each lambda update step. This is a
+  significant speed-up for alchemical free energy simulations.
+
+* Now catch ``std::bad_alloc`` and raise it as a ``MemoryError``. This
+  means that we can catch out-of-memory errors and raise a more
+  informative exception.
+
 * Please add an item to this changelog when you create your PR
 
 `2023.4.1 <https://github.com/openbiosim/sire/compare/2023.4.0...2023.4.1>`__ - October 2023

diff --git a/wrapper/Convert/SireOpenMM/CMakeLists.txt b/wrapper/Convert/SireOpenMM/CMakeLists.txt
@@ -24,6 +24,25 @@ if (${SIRE_USE_OPENMM})
     # Other python wrapping directories
     include_directories(${CMAKE_SOURCE_DIR})
 
+    # Check to see if we have support for updating some parameters in context
+    include(CheckCXXSourceCompiles)
+    check_cxx_source_compiles( "#include <openmm/CustomNonbondedForce.h>
+                                 int main() {
+                                   OpenMM::CustomNonbondedForce *force;
+                                   OpenMM::Context *context;
+                                   force->updateSomeParametersInContext(0, 0, *context);
+                                   return 0;
+                                 }"
+                               SIREOPENMM_HAS_UPDATESOMEPARAMETERSINCONTEXT )
+
+    if ( ${SIREOPENMM_HAS_UPDATESOMEPARAMETERSINCONTEXT} )
+      message( STATUS "OpenMM has support for updating some parameters in context")
+      add_definitions("-DSIRE_HAS_UPDATE_SOME_IN_CONTEXT")
+    else()
+      message( STATUS "OpenMM does not have support for updating some parameters in context")
+      message( STATUS "The free energy code will be a little slower.")
+    endif()
+
     # Define the sources in SireOpenMM
     set ( SIREOPENMM_SOURCES