Use CustomCPPForceImpl to simplify code (#70)

* Use CustomCPPForceImpl to simplify code

* Assorted cleanup

* Bug fix

* Remove obsolete references to CUDA and OpenCL in CI scripts

* Updated python versions for CI

.github/workflows/CI.yml

@@ -22,21 +22,15 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: Linux CPU CUDA 11.0 Python 3.6
-            python-version: "3.6"
+          - name: Linux CPU Python 3.12
+            python-version: "3.12"
             os: ubuntu-latest
             gcc-version: "9"
-            cuda-version: "11.0"
-            cdt-name: cos7  # CentOS sysroot: cuda 10.x needs cos6, 11+ needs cos7
-            CMAKE_FLAGS: |
-              -DPLUMED_BUILD_CUDA_LIB=ON \
-              -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
-              -DEXTRA_COMPILE_FLAGS="-L/usr/local/cuda/lib64/stubs -Wl,-rpath,/usr/local/cuda/lib64/stubs -Wl,-rpath-link,/usr/local/cuda/lib64/stubs"
-
-          - name: MacOS Intel CPU OpenCL Python 3.9
-            python-version: "3.9"
+            cdt-name: cos7
+
+          - name: MacOS Intel CPU OpenCL Python 3.10
+            python-version: "3.10"
             os: macos-latest
-            cuda-version: ""
             CMAKE_FLAGS: ""
 
     steps:
@@ -47,7 +41,6 @@ jobs:
         run: |
           sed -i -e "s/@CDT_NAME@/${{ matrix.cdt-name }}/g" \
                  -e "s/@GCC_VERSION@/${{ matrix.gcc-version }}.*/g" \
-                 -e "s/@CUDATOOLKIT_VERSION@/${{ matrix.cuda-version }}.*/g" \
                  devtools/conda-envs/build-${{ matrix.os }}.yml
 
       - uses: conda-incubator/setup-miniconda@v2
@@ -59,12 +52,6 @@ jobs:
           auto-activate-base: false
           channels: conda-forge
 
-      - name: "Install CUDA on Ubuntu (if needed)"
-        if: matrix.cuda-version != ''
-        env:
-          CUDA_VERSION: ${{ matrix.cuda-version }}
-        run: source devtools/scripts/install_cuda.sh
-
       - name: "Set SDK on MacOS (if needed)"
         if: startsWith(matrix.os, 'macos')
         run: source devtools/scripts/install_macos_sdk.sh
@@ -98,9 +85,6 @@ jobs:
             -DOPENMM_DIR=${CONDA_PREFIX} \
             -DPLUMED_INCLUDE_DIR=${CONDA_PREFIX}/include/plumed \
             -DPLUMED_LIBRARY_DIR=${CONDA_PREFIX}/lib \
-            -DPLUMED_BUILD_OPENCL_LIB=ON \
-            -DOPENCL_INCLUDE_DIR=${CONDA_PREFIX}/include \
-            -DOPENCL_LIBRARY=${CONDA_PREFIX}/lib/libOpenCL${SHLIB_EXT} \
             ${{ matrix.CMAKE_FLAGS }}
 
       - name: "Build"
@@ -131,12 +115,6 @@ jobs:
             fn=$(basename $f)
             echo "::group::$fn"
             summary+="\n${fn}: "
-            if [[ $fn == *Cuda* ]]; then
-              echo "Skipping $fn..."
-              summary+="Skipped"
-              echo "::endgroup::"
-              continue
-            fi
             echo "Running $fn..."
             ./${f}
             thisexitcode=$?

CMakeLists.txt

@@ -83,33 +83,9 @@ INSTALL (FILES ${API_ONLY_INCLUDE_FILES_INTERNAL} DESTINATION include/internal)
 # Enable testing
 
 ENABLE_TESTING()
+ADD_SUBDIRECTORY(tests)
 ADD_SUBDIRECTORY(serialization/tests)
 
-# Build the implementations for different platforms
-
-ADD_SUBDIRECTORY(platforms/reference)
-
-SET(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
-FIND_PACKAGE(OpenCL QUIET)
-IF(OPENCL_FOUND)
-    SET(PLUMED_BUILD_OPENCL_LIB ON CACHE BOOL "Build implementation for OpenCL")
-ELSE(OPENCL_FOUND)
-    SET(PLUMED_BUILD_OPENCL_LIB OFF CACHE BOOL "Build implementation for OpenCL")
-ENDIF(OPENCL_FOUND)
-IF(PLUMED_BUILD_OPENCL_LIB)
-    ADD_SUBDIRECTORY(platforms/opencl)
-ENDIF(PLUMED_BUILD_OPENCL_LIB)
-
-FIND_PACKAGE(CUDA QUIET)
-IF(CUDA_FOUND)
-    SET(PLUMED_BUILD_CUDA_LIB ON CACHE BOOL "Build implementation for CUDA")
-ELSE(CUDA_FOUND)
-    SET(PLUMED_BUILD_CUDA_LIB OFF CACHE BOOL "Build implementation for CUDA")
-ENDIF(CUDA_FOUND)
-IF(PLUMED_BUILD_CUDA_LIB)
-    ADD_SUBDIRECTORY(platforms/cuda)
-ENDIF(PLUMED_BUILD_CUDA_LIB)
-
 # Build the Python API
 
 FIND_PROGRAM(PYTHON_EXECUTABLE python)

README.md

@@ -43,15 +43,9 @@ files and libraries are installed.
 6. Set CMAKE_INSTALL_PREFIX to the directory where the plugin should be installed.  Usually,
 this will be the same as OPENMM_DIR, so the plugin will be added to your OpenMM installation.
 
-7. If you plan to build the OpenCL platform, make sure that OPENCL_INCLUDE_DIR and
-OPENCL_LIBRARY are set correctly, and that PLUMED_BUILD_OPENCL_LIB is selected.
+7. Press "Configure" again if necessary, then press "Generate".
 
-8. If you plan to build the CUDA platform, make sure that CUDA_TOOLKIT_ROOT_DIR is set correctly
-and that PLUMED_BUILD_CUDA_LIB is selected.
-
-9. Press "Configure" again if necessary, then press "Generate".
-
-10. Use the build system you selected to build and install the plugin.  For example, if you
+8. Use the build system you selected to build and install the plugin.  For example, if you
 selected Unix Makefiles, type `make install` to install the plugin, and `make PythonInstall` to
 install the Python wrapper.
 
@@ -81,7 +75,7 @@ Simbios, the NIH National Center for Physics-Based Simulation of
 Biological Structures at Stanford, funded under the NIH Roadmap for
 Medical Research, grant U54 GM072970. See https://simtk.org.
 
-Portions copyright (c) 2016 Stanford University and the Authors.
+Portions copyright (c) 2016-2023 Stanford University and the Authors.
 
 Authors: Peter Eastman
 

devtools/conda-envs/build-ubuntu-latest.yml

@@ -19,7 +19,6 @@ dependencies:
 - openmm
 - plumed >=2.7
 - ocl-icd
-- cudatoolkit @CUDATOOLKIT_VERSION@
 - pocl
 # test
 - pytest

openmmapi/include/internal/PlumedForceImpl.h

@@ -33,8 +33,9 @@
  * -------------------------------------------------------------------------- */
 
 #include "PlumedForce.h"
-#include "openmm/internal/ForceImpl.h"
-#include "openmm/Kernel.h"
+#include "openmm/internal/ContextImpl.h"
+#include "openmm/internal/CustomCPPForceImpl.h"
+#include "wrapper/Plumed.h"
 #include <utility>
 #include <set>
 #include <string>
@@ -47,26 +48,21 @@ class System;
  * This is the internal implementation of PlumedForce.
  */
 
-class OPENMM_EXPORT_PLUMED PlumedForceImpl : public OpenMM::ForceImpl {
+class OPENMM_EXPORT_PLUMED PlumedForceImpl : public OpenMM::CustomCPPForceImpl {
 public:
     PlumedForceImpl(const PlumedForce& owner);
     ~PlumedForceImpl();
     void initialize(OpenMM::ContextImpl& context);
     const PlumedForce& getOwner() const {
         return owner;
     }
-    void updateContextState(OpenMM::ContextImpl& context, bool& forcesInvalid) {
-        // This force field doesn't update the state directly.
-    }
-    double calcForcesAndEnergy(OpenMM::ContextImpl& context, bool includeForces, bool includeEnergy, int groups);
-    std::map<std::string, double> getDefaultParameters() {
-        return std::map<std::string, double>(); // This force field doesn't define any parameters.
-    }
-    std::vector<std::string> getKernelNames();
-    void updateParametersInContext(OpenMM::ContextImpl& context);
+    double computeForce(OpenMM::ContextImpl& context, const std::vector<OpenMM::Vec3>& positions, std::vector<OpenMM::Vec3>& forces);
 private:
     const PlumedForce& owner;
-    OpenMM::Kernel kernel;
+    plumed plumedmain;
+    bool hasInitialized, usesPeriodic;
+    int lastStepIndex;
+    std::vector<double> masses, charges;
 };
 
 } // namespace PlumedPlugin