Add wheels

recipe/0001-wheels.patch

@@ -0,0 +1,73 @@
+From 20d1d14ed17e5e6e2badfe94b08bac53a59fc5eb Mon Sep 17 00:00:00 2001
+From: Isuru Fernando <[email protected]>
+Date: Fri, 8 Mar 2024 08:56:04 -0600
+Subject: [PATCH] wheels
+
+---
+ wrappers/python/CMakeLists.txt       |  2 ++
+ wrappers/python/openmm-cuda/setup.py | 12 ++++++++++++
+ wrappers/python/setup.py             |  4 +++-
+ 3 files changed, 17 insertions(+), 1 deletion(-)
+ create mode 100644 wrappers/python/openmm-cuda/setup.py
+
+diff --git a/wrappers/python/CMakeLists.txt b/wrappers/python/CMakeLists.txt
+index 5e8355cad..16ed4d4a6 100644
+--- a/wrappers/python/CMakeLists.txt
++++ b/wrappers/python/CMakeLists.txt
+@@ -294,6 +294,8 @@ else()
+ endif()
+ configure_file(pysetup.cmake.in
+     "${CMAKE_CURRENT_BINARY_DIR}/pysetupinstall.cmake" @ONLY)
++configure_file(openmm-cuda/setup.py
++    "${OPENMM_PYTHON_STAGING_DIR}/openmm-cuda/setup.py" @ONLY)
+ add_custom_target(PythonInstall
+     COMMAND ${CMAKE_COMMAND}
+         -P "${CMAKE_CURRENT_BINARY_DIR}/pysetupinstall.cmake"
+diff --git a/wrappers/python/openmm-cuda/setup.py b/wrappers/python/openmm-cuda/setup.py
+new file mode 100644
+index 000000000..82d74ad7a
+--- /dev/null
++++ b/wrappers/python/openmm-cuda/setup.py
+@@ -0,0 +1,12 @@
++from setuptools import setup, find_packages
++
++cuda_ver = r"@CUDAToolkit_VERSION@"
++cuda_vers = cuda_ver.split(".")
++
++cuda_ver = cuda_vers[0] if int(cuda_vers[0]) > 11 else ".".join(cuda_vers[:2])
++
++setup(
++    name=f"openmm-cuda",
++    version=f"@OPENMM_VERSION@.{cuda_ver}",
++    packages=find_packages(),
++)
+diff --git a/wrappers/python/setup.py b/wrappers/python/setup.py
+index d2a147065..4cbac13a8 100644
+--- a/wrappers/python/setup.py
++++ b/wrappers/python/setup.py
+@@ -85,12 +85,13 @@ def writeVersionPy(filename="openmm/version.py", major_version_num=MAJOR_VERSION
+
+     cnt = """
+ # THIS FILE IS GENERATED FROM OPENMM SETUP.PY
++import os
+ short_version = '%(version)s'
+ version = '%(version)s'
+ full_version = '%(full_version)s'
+ git_revision = '%(git_revision)s'
+ release = %(isrelease)s
+-openmm_library_path = r'%(path)s'
++openmm_library_path = os.path.join(os.path.dirname(__file__), "..", "OpenMM.libs", "lib")
+
+ if not release:
+     version = full_version
+@@ -164,6 +165,7 @@ def buildKeywordDictionary(major_version_num=MAJOR_VERSION_NUM,
+     (through custom forces and integrators), openness, and high performance
+     (especially on recent GPUs) that make it truly unique among simulation codes.
+     """
++    setupKeywords["extras_require"]         = {"cuda12": f"openmm-cuda=={__version__}.12", "cuda11.2": f"openmm-cuda=={__version__}.11.2"}
+
+     define_macros = [('MAJOR_VERSION', major_version_num),
+                      ('MINOR_VERSION', minor_version_num)]
+-- 
+2.42.0
+

recipe/build_openmm.sh

@@ -46,40 +46,88 @@ elif [[ "$target_platform" == osx* ]]; then
     #   /System/Library/Frameworks/OpenCL.framework/OpenCL
 fi
 
-# Set location for FFTW3 on both linux and mac
-CMAKE_FLAGS+=" -DFFTW_INCLUDES=${PREFIX}/include/"
-CMAKE_FLAGS+=" -DFFTW_LIBRARY=${PREFIX}/lib/libfftw3f${SHLIB_EXT}"
-CMAKE_FLAGS+=" -DFFTW_THREADS_LIBRARY=${PREFIX}/lib/libfftw3f_threads${SHLIB_EXT}"
 # Disambiguate swig location
 CMAKE_FLAGS+=" -DSWIG_EXECUTABLE=$(which swig)"
 
+if [[ "$target_platform" == linux-* ]]; then
+    export LDFLAGS="$LDFLAGS -static-libstdc++ -Wl,--exclude-libs,ALL -Wl,-rpath,$ORIGIN/../OpenMM.libs/lib"
+fi
+
 # Build in subdirectory and install.
 mkdir -p build
 cd build
 cmake ${CMAKE_FLAGS} ${SRC_DIR}
 make -j$CPU_COUNT
-make -j$CPU_COUNT install PythonInstall
+make install
 
-# Put examples into an appropriate subdirectory.
-mkdir -p ${PREFIX}/share/openmm/
-mv ${PREFIX}/examples ${PREFIX}/share/openmm/
+cd python
+rm -rf dist
+rm -rf fixed_wheels
+export OPENMM_LIB_PATH=$PREFIX/lib
+export OPENMM_INCLUDE_PATH=$PREFIX/include
+$PYTHON -m pip wheel . --wheel-dir=dist
 
-# Fix some overlinking warnings/errors
-for lib in ${PREFIX}/lib/plugins/*${SHLIB_EXT}; do
-    ln -s $lib ${PREFIX}/lib/$(basename $lib) || true
+# vendor include directories and libraries
+for whl in $PWD/dist/*.whl; do
+  pushd $PREFIX
+    plugins=""
+    for plugin in lib/plugins/*.so; do
+      if [[ "$plugin" != *CUDA.so ]]; then
+        plugins="$plugins $plugin"
+      fi
+    done
+    $BUILD_PREFIX/bin/python $RECIPE_DIR/vendor_wheel.py $whl include/openmm include/lepton lib/libOpenMM.so lib/libOpenMM.so.8.1 lib/libOpenMMRPMD.so lib/libOpenMMAmoeba.so lib/libOpenMMDrude.so $plugins
+  popd
 done
 
-if [[ "$with_test_suite" == "true" ]]; then
-    mkdir -p ${PREFIX}/share/openmm/tests/
-    # BSD find vs GNU find: -executable is only available in GNU find
-    # +0111 is somehow equivalent in BSD, but that's not compatible in GNU
-    # so we use different commands for each...
-    if [[ "$target_platform" == osx* ]]; then
-        find . -name "Test*" -perm +0111 -type f \
-            -exec python $RECIPE_DIR/patch_osx_tests.py "{}" \; \
-            -exec cp "{}" $PREFIX/share/openmm/tests/ \;
-    else
-        find . -name "Test*" -executable -type f -exec cp "{}" $PREFIX/share/openmm/tests/ \;
-    fi
-    cp -r python/tests $PREFIX/share/openmm/tests/python
-fi
+function repair() {
+  # Repair the wheels in dist
+  if [[ "$target_platform" == linux-64 ]]; then
+    rm -rf $PREFIX/lib/libstdc++.*
+    rm -rf $PREFIX/lib/libgcc*
+    auditwheel repair dist/*.whl -w $PWD/fixed_wheels --plat manylinux2014_x86_64 --exclude libOpenMM.so.8.1 --exclude libOpenMMOpenCL.so --exclude libOpenMMDrude.so --exclude libOpenMMAmoeba.so --exclude libOpenMMRPMD.so --exclude libOpenCL.so.1 --exclude libcuda.so.1 --exclude libcufft.so.11 --exclude libnvrtc.so.12 --exclude libcufft.so.10 --exclude libnvrtc.so.11.2 --lib-sdir=$LIB_SDIR
+  elif [[ "$target_platform" == linux-* ]]; then
+    rm -rf $PREFIX/lib/libstdc++.*
+    rm -rf $PREFIX/lib/libgcc*
+    auditwheel repair dist/*.whl -w $PWD/fixed_wheels --plat manylinux2014_$ARCH
+  else
+    python -m pip install "https://github.com/isuruf/delocate/archive/sanitize_rpaths2.tar.gz#egg=delocate"
+    python $(which delocate-wheel) -w fixed_wheels --sanitize-rpaths -v dist/*.whl
+  fi
+}
+
+LIB_SDIR=".libs/lib" repair
+rm -rf dist
+mkdir dist
+for whl in fixed_wheels/*.whl; do
+  whl_tag="${whl##*-}"
+done
+
+pushd openmm-cuda
+  $PYTHON -m pip wheel .
+  for whl in $PWD/*.whl; do
+    whl_name=$(basename $whl)
+    whl_name="${whl_name::${#whl_name}-7}$whl_tag"
+    pushd $PREFIX
+        $BUILD_PREFIX/bin/python $RECIPE_DIR/vendor_wheel.py $whl lib/plugins/libOpenMMCUDA.so
+    popd
+    cp $whl ../dist/$whl_name
+  done
+popd
+LIB_SDIR=".libs" repair
+
+# Copy the wheel to destination
+for whl in fixed_wheels/*.whl; do
+  if [[ "$build_platform" == "osx-"* ]]; then
+    WHL_DEST=$RECIPE_DIR/../build_artifacts/pypi_wheels
+  elif [[ "$build_platform" == "linux-"* ]]; then
+    WHL_DEST=/home/conda/feedstock_root/build_artifacts/pypi_wheels
+  fi
+  mkdir -p $WHL_DEST
+  cp $whl $WHL_DEST
+done
+
+# Install the wheel
+for whl in fixed_wheels/*.whl; do
+  $PYTHON -m pip install $whl
+done

recipe/conda_build_config.yaml

@@ -1,6 +1,5 @@
 opencl_impl:  # [osx]
 - apple       # [osx]
-- khronos     # [osx]
 channel_targets:
 - conda-forge main
 MACOSX_SDK_VERSION:        # [osx and x86_64]

recipe/meta.yaml

@@ -17,6 +17,8 @@ package:
 source:
   git_url: https://github.com/openmm/{{ name }}.git
   git_rev: "ec797ac"
+  patches:
+    - 0001-wheels.patch
 
 build:
   number: {{ build }}
@@ -58,9 +60,17 @@ requirements:
     - m2-findutils  # [win]
     - m2-coreutils  # [win]
 {% endif %}
+    # START WHEEL CHANGES
+    - auditwheel      # [linux]
+    - setuptools      # [linux]
+    - unzip           # [unix]
+    - patchelf        # [linux]
+    - delocate
+    # END WHEEL CHANGES
 
   host:
     - python
+    - pip
     - swig
     - pthread-stubs
     - lxml

recipe/recipe-scripts-license.txt

@@ -0,0 +1,27 @@
+BSD-3-Clause license
+Copyright (c) 2015-2022, conda-forge contributors
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  1. Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+  2. Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+  3. Neither the name of the copyright holder nor the names of its
+     contributors may be used to endorse or promote products derived from
+     this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.

recipe/vendor_wheel.py

@@ -0,0 +1,32 @@
+import sys
+from os.path import join as pjoin
+import os
+import shutil
+from glob import glob
+import tempfile
+import subprocess
+
+from delocate import wheeltools
+
+cwd = os.getcwd()
+
+def add_library(lib_paths, wheel_name):
+    print('Processing', wheel_name)
+    with wheeltools.InWheel(wheel_name, wheel_name):
+        for lib_path in lib_paths:
+            d = os.path.dirname(pjoin('OpenMM.libs', lib_path))
+            os.makedirs(d, exist_ok=True)
+            f = pjoin(cwd, lib_path)
+            if os.path.isdir(f):
+                shutil.copytree(f, pjoin('OpenMM.libs', lib_path), dirs_exist_ok=True)
+            else:
+                shutil.copy2(f, pjoin('OpenMM.libs', lib_path))
+
+def main():
+    args = list(sys.argv)
+    args.pop(0)
+    dist_path = args.pop(0)
+    add_library(args, dist_path)
+
+if __name__ == '__main__':
+    main()