Use PocketFFT (openmm#3667)

* Use PocketFFT instead of FFTW * Minor cleanup * Use PocketFFT instead of fftpack for reference platform * Remove FFTW as a dependency * Converted a test case to use PocketFFT * Fixed an incorrect comment
erbad · Jun 30, 2022 · 1dac981 · 1dac981
1 parent 583471a
commit 1dac981
Show file tree

Hide file tree

Showing 33 changed files with 3,888 additions and 1,741 deletions.
diff --git a/.azure-pipelines/azure-pipelines-windows.yml b/.azure-pipelines/azure-pipelines-windows.yml
@@ -42,7 +42,6 @@ jobs:
       - script: |
           conda install cmake ^
                         cython ^
-                        fftw ^
                         ninja ^
                         numpy ^
                         swig ^

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -88,7 +88,7 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
 
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
-SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 platforms/reference serialization libraries/irrxml)
+SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs libraries/hilbert libraries/csha1 libraries/pocketfft platforms/reference serialization libraries/irrxml)
 IF(X86 OR ARM)
     SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/vecmath)
 ENDIF()
@@ -392,12 +392,7 @@ ENDIF(OPENMM_BUILD_DRUDE_PLUGIN)
 
 # CPU PME plugin
 
-FIND_PACKAGE(FFTW QUIET)
-IF(FFTW_FOUND)
-    SET(OPENMM_BUILD_PME_PLUGIN ON CACHE BOOL "Build CPU PME plugin")
-ELSE(FFTW_FOUND)
-    SET(OPENMM_BUILD_PME_PLUGIN OFF CACHE BOOL "Build CPU PME plugin")
-ENDIF(FFTW_FOUND)
+SET(OPENMM_BUILD_PME_PLUGIN ON CACHE BOOL "Build CPU PME plugin")
 SET(OPENMM_BUILD_PME_PATH)
 IF(OPENMM_BUILD_PME_PLUGIN)
    SET(OPENMM_BUILD_PME_PATH ${CMAKE_CURRENT_SOURCE_DIR}/plugins/cpupme)

diff --git a/appveyor.yml b/appveyor.yml
@@ -19,14 +19,6 @@ install:
   - "set PATH=%APPVEYOR_BUILD_FOLDER%\\cclash-0.3.14;%PATH%"
   - "set CCLASH_DIR=C:\\ProgramData\\cclash"
 
-# Download FFTW3 for PME plugin
-  - ps: Invoke-WebRequest ftp://ftp.fftw.org/pub/fftw/fftw-3.3.4-dll64.zip -OutFile fftw-3.3.4-dll64.zip
-  - 7z x fftw-3.3.4-dll64.zip -oC:\fftw > null
-  - cd C:\fftw
-  - lib /def:libfftw3f-3.def
-  - cd %APPVEYOR_BUILD_FOLDER%
-  - "set PATH=C:\\fftw;%PATH%"
-
 # Download and install some OpenMM build dependencies (doxygen, swig)
   - choco install -y doxygen.install swig > null
 
@@ -53,8 +45,6 @@ build_script:
       "-DOPENMM_BUILD_PME_PLUGIN=ON
        -DOPENCL_INCLUDE_DIR=C:/opencl/inc
        -DOPENCL_LIBRARY=C:/opencl/lib/OpenCL.lib
-       -DFFTW_LIBRARY=C:/fftw/libfftw3f-3.lib
-       -DFFTW_INCLUDES=C:/fftw
        -DOPENMM_BUILD_EXAMPLES=OFF
        -DOPENMM_BUILD_OPENCL_TESTS=OFF
        -DCMAKE_BUILD_TYPE=Release

diff --git a/cmake_modules/FindFFTW.cmake b/cmake_modules/FindFFTW.cmake
diff --git a/devtools/ci/gh-actions/conda-envs/build-M1-arm64.yml b/devtools/ci/gh-actions/conda-envs/build-M1-arm64.yml
@@ -10,7 +10,6 @@ dependencies:
 - python
 - cython
 - swig
-- fftw
 - numpy
 - doxygen 1.9.1
 # test

diff --git a/devtools/ci/gh-actions/conda-envs/build-macos-latest.yml b/devtools/ci/gh-actions/conda-envs/build-macos-latest.yml
@@ -10,7 +10,6 @@ dependencies:
 - python
 - cython
 - swig
-- fftw
 - numpy
 - doxygen 1.8.14
 # test

diff --git a/devtools/ci/gh-actions/conda-envs/build-ubuntu-latest.yml b/devtools/ci/gh-actions/conda-envs/build-ubuntu-latest.yml
@@ -12,7 +12,6 @@ dependencies:
 - python
 - cython
 - swig
-- fftw
 - numpy
 - ocl-icd-system
 - doxygen 1.8.14

diff --git a/devtools/ci/gh-actions/conda-envs/build-windows-latest.yml b/devtools/ci/gh-actions/conda-envs/build-windows-latest.yml
@@ -12,7 +12,6 @@ dependencies:
 - python
 - cython
 - swig
-- fftw
 - numpy
 - doxygen 1.8.14
 - khronos-opencl-icd-loader

diff --git a/devtools/packaging/scripts/linux/build.sh b/devtools/packaging/scripts/linux/build.sh
@@ -71,8 +71,6 @@ CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=$CLANG_PREFIX/bin/clang -DCMAKE_CXX_COMPILER=$
 # Ensure we build a release
 CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=Release"
 
-# setting the rpath so that libOpenMMPME.so finds the right libfftw3
-#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
 # Use NVIDIA CUDA 8.0
 CMAKE_FLAGS+=" -DCUDA_CUDART_LIBRARY=/usr/local/cuda-8.0/lib64/libcudart.so"
 CMAKE_FLAGS+=" -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-8.0/bin/nvcc"
@@ -84,11 +82,6 @@ CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/opt/AMDAPPSDK-3.0/include/"
 CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so"
 # Generate API docs
 CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
-# Set location for FFTW3
-PREFIX="$WORKSPACE/miniconda"
-CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
-CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
-CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
 # Necessary to find GL headers
 CMAKE_FLAGS+=" -DCMAKE_CXX_FLAGS_RELEASE=-I/usr/include/nvidia/"
 

diff --git a/devtools/packaging/scripts/linux/prepare.sh b/devtools/packaging/scripts/linux/prepare.sh
@@ -29,4 +29,4 @@ yum install -y libgcrypt
 
 # Ensure configuration is up to date.
 conda config --add channels omnia
-conda install --yes --quiet swig fftw3f pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
+conda install --yes --quiet swig pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
diff --git a/devtools/packaging/scripts/osx/build.sh b/devtools/packaging/scripts/osx/build.sh
@@ -17,20 +17,11 @@ fi
 
 CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=$INSTALL"
 
-# setting the rpath so that libOpenMMPME.so finds the right libfftw3
-#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
 CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++"
 CMAKE_FLAGS+=" -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9"
 CMAKE_FLAGS+=" -DCMAKE_OSX_SYSROOT=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk"
 CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
 
-# Build in subdirectory.
-# Set location for FFTW3
-PREFIX="$WORKSPACE/miniconda"
-CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
-CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.dylib"
-CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.dylib"
-
 # Build in subdirectory.
 if [ -e build ]; then
     rm -rf build

diff --git a/devtools/packaging/scripts/osx/prepare.sh b/devtools/packaging/scripts/osx/prepare.sh
@@ -26,5 +26,5 @@ export PATH=$WORKSPACE/miniconda/bin:$PATH
 
 # Ensure configuration is up to date.
 conda config --add channels http://conda.binstar.org/omnia
-conda install --yes --quiet swig fftw3f pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
+conda install --yes --quiet swig pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
 pip install sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen
diff --git a/devtools/packaging/scripts/source/build.sh b/devtools/packaging/scripts/source/build.sh
@@ -71,8 +71,6 @@ CMAKE_FLAGS+=" -DCMAKE_C_COMPILER=$CLANG_PREFIX/bin/clang -DCMAKE_CXX_COMPILER=$
 # Ensure we build a release
 CMAKE_FLAGS+=" -DCMAKE_BUILD_TYPE=Release"
 
-# setting the rpath so that libOpenMMPME.so finds the right libfftw3
-#CMAKE_FLAGS+=" -DCMAKE_INSTALL_RPATH=.."
 # Use NVIDIA CUDA 8.0
 CMAKE_FLAGS+=" -DCUDA_CUDART_LIBRARY=/usr/local/cuda-8.0/lib64/libcudart.so"
 CMAKE_FLAGS+=" -DCUDA_NVCC_EXECUTABLE=/usr/local/cuda-8.0/bin/nvcc"
@@ -84,11 +82,6 @@ CMAKE_FLAGS+=" -DOPENCL_INCLUDE_DIR=/opt/AMDAPPSDK-3.0/include/"
 CMAKE_FLAGS+=" -DOPENCL_LIBRARY=/opt/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so"
 # Generate API docs
 CMAKE_FLAGS+=" -DOPENMM_GENERATE_API_DOCS=ON"
-# Set location for FFTW3
-PREFIX="$WORKSPACE/miniconda"
-CMAKE_FLAGS+=" -DFFTW_INCLUDES=$PREFIX/include"
-CMAKE_FLAGS+=" -DFFTW_LIBRARY=$PREFIX/lib/libfftw3f.so"
-CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=$PREFIX/lib/libfftw3f_threads.so"
 # Necessary to find GL headers
 CMAKE_FLAGS+=" -DCMAKE_CXX_FLAGS_RELEASE=-I/usr/include/nvidia/"
 

diff --git a/devtools/packaging/scripts/source/prepare.sh b/devtools/packaging/scripts/source/prepare.sh
@@ -29,4 +29,4 @@ yum install -y libgcrypt
 
 # Ensure configuration is up to date.
 conda config --add channels omnia
-conda install --yes --quiet swig fftw3f pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
+conda install --yes --quiet swig pip doxygen sphinx sphinxcontrib-bibtex sphinxcontrib-lunrsearch sphinxcontrib-autodoc_doxygen lxml cmake
diff --git a/devtools/packaging/scripts/windows/build.bat b/devtools/packaging/scripts/windows/build.bat
@@ -1,11 +1,9 @@
 mkdir build
 cd build
 
-set FFTW=C:\Miniconda3\pkgs\fftw3f-3.3.4-vc14_2\Library
 set APPSDK=C:\Program Files (x86)\AMD APP SDK\2.9-1
 "C:\Program Files\CMake\bin\cmake.exe" .. -G "NMake Makefiles JOM" -DCMAKE_BUILD_TYPE=Release -DOPENMM_GENERATE_API_DOCS=ON ^
-    -DOPENCL_INCLUDE_DIR="%APPSDK%\include" -DOPENCL_LIBRARY="%APPSDK%\lib\x86_64\OpenCL.lib" ^
-    -DFFTW_INCLUDES="%FFTW%/include" -DFFTW_LIBRARY="%FFTW%/lib/libfftw3f-3.lib"
+    -DOPENCL_INCLUDE_DIR="%APPSDK%\include" -DOPENCL_LIBRARY="%APPSDK%\lib\x86_64\OpenCL.lib"
 
 jom
 jom PythonInstall

diff --git a/devtools/packaging/scripts/windows/prepare.ps1 b/devtools/packaging/scripts/windows/prepare.ps1
@@ -19,7 +19,7 @@ wget https://repo.continuum.io/miniconda/Miniconda3-latest-Windows-x86_64.exe -U
 # Install software with conda.
 
 & "C:\Miniconda3\Scripts\conda.exe" config --add channels omnia --add channels conda-forge
-& "C:\Miniconda3\Scripts\conda.exe" install -y fftw3f==3.3.4=vc14_2 jinja2 lxml sphinx sphinxcontrib-autodoc_doxygen sphinxcontrib-lunrsearch conda-build anaconda-client
+& "C:\Miniconda3\Scripts\conda.exe" install -y jinja2 lxml sphinx sphinxcontrib-autodoc_doxygen sphinxcontrib-lunrsearch conda-build anaconda-client
 & "C:\Miniconda3\Scripts\pip.exe" install sphinxcontrib.bibtex
 
 # Install software with choco.

diff --git a/docs-source/usersguide/library/02_compiling.rst b/docs-source/usersguide/library/02_compiling.rst
@@ -78,7 +78,7 @@ them is with conda.  The following command will install everything needed to
 build OpenMM.
 ::
 
-    conda install -c conda-forge cmake make cython swig fftw doxygen numpy
+    conda install -c conda-forge cmake make cython swig doxygen numpy
 
 Step 1: Configure with CMake
 ============================
@@ -213,7 +213,7 @@ Before building OpenMM from source, you will need certain tools.
 C++ compiler
 ------------
 
-On Windows systems, use the C++ compiler in Visual Studio 2015 or later.  You
+On Windows systems, use the C++ compiler in Visual Studio 2017 or later.  You
 can download a free version of Visual Studio from https://visualstudio.microsoft.com.
 
 Python
@@ -267,7 +267,7 @@ It will open a command window that is preconfigured for conda.  Enter the
 following command to install everything needed to build OpenMM.
 ::
 
-    conda install -c conda-forge cython swig fftw doxygen numpy
+    conda install -c conda-forge cython swig doxygen numpy
 
 Step 1: Configure with CMake
 ============================

diff --git a/docs-source/usersguide/library/04_platform_specifics.rst b/docs-source/usersguide/library/04_platform_specifics.rst
@@ -35,9 +35,7 @@ The OpenCL Platform recognizes the following Platform-specific properties:
   is the most accurate option, but is usually much slower than the others.
 * UseCpuPme: This selects whether to use the CPU-based PME
   implementation.  The allowed values are “true” or “false”.  Depending on your
-  hardware, this might (or might not) improve performance.  To use this option,
-  you must have FFTW (single precision, multithreaded) installed, and your CPU
-  must support SSE 4.1.
+  hardware, this might (or might not) improve performance.
 * OpenCLPlatformIndex: When multiple OpenCL implementations are installed on
   your computer, this is used to select which one to use.  The value is the
   zero-based index of the platform (in the OpenCL sense, not the OpenMM sense) to use,
@@ -74,9 +72,7 @@ The CUDA Platform recognizes the following Platform-specific properties:
   is the most accurate option, but is usually much slower than the others.
 * UseCpuPme: This selects whether to use the CPU-based PME implementation.
   The allowed values are “true” or “false”.  Depending on your hardware, this
-  might (or might not) improve performance.  To use this option, you must have
-  FFTW (single precision, multithreaded) installed, and your CPU must support SSE
-  4.1.
+  might (or might not) improve performance.
 * CudaCompiler: This specifies the path to the CUDA kernel compiler.  Versions
   of CUDA before 7.0 require a separate compiler executable.  If you do
   not specify this, OpenMM will try to locate the compiler itself.  Specify this
-Original file line number
+Diff line change
@@ Expand Up / @@ -42,7 +42,6 @@ jobs: @@
           - script: |
               conda install cmake ^
                             cython ^
-                            fftw ^
                             ninja ^
                             numpy ^
                             swig ^
@@ Expand Down @@