From 2fa0462f5354b3401f53f05a98fff626464efb61 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 10:41:49 -0800
Subject: [PATCH 01/25] CI for Windows

---
 .github/workflows/CI.yml               | 93 ++++++++++++++++++++++++++
 devtools/conda-envs/windows-latest.yml | 16 +++++
 2 files changed, 109 insertions(+)
 create mode 100644 devtools/conda-envs/windows-latest.yml

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c8b3b64f..e5020a10 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -140,3 +140,96 @@ jobs:
           export LD_LIBRARY_PATH="${CONDA_PREFIX}/lib/python${{ matrix.python-version }}/site-packages/torch/lib:${LD_LIBRARY_PATH}"
           cd python/tests
           pytest --verbose Test*
+
+
+  windows:
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.name }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Windows (CUDA 12.5, Python 3.12, PyTorch 2.5)
+            os: windows-latest
+            cuda-version: "12.5.0"
+            nvcc-version: "12.5"
+            python-version: "3.12"
+            pytorch-version: "2.5.*"
+
+    steps:
+      - name: "Check out"
+        uses: actions/checkout@v2
+
+      - name: "Install CUDA Toolkit"
+        uses: Jimver/cuda-toolkit@v0.2.16
+        id: cuda-toolkit
+        with:
+          cuda: ${{ matrix.cuda-version }}
+          method: 'network'
+          sub-packages: '["nvcc", "nvrtc", "nvrtc_dev", "cufft", "cufft_dev", "opencl", "cudart", "cuda_profiler_api"]'
+
+      - name: "Update the conda enviroment file"
+        uses: cschleiden/replace-tokens@v1
+        with:
+          tokenPrefix: '@'
+          tokenSuffix: '@'
+          files: devtools/conda-envs/build-${{ matrix.os }}.yml
+        env:
+          PYTORCH_VERSION: ${{ matrix.pytorch-version }}
+
+      - uses: conda-incubator/setup-miniconda@v2
+        name: "Install dependencies with Mamba"
+        with:
+          activate-environment: build
+          environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
+          miniforge-variant: Miniforge3
+          use-mamba: true
+          python-version: ${{ matrix.python-version }}
+        env:
+          # Override the CUDA detection as the CI hosts don't have NVIDIA drivers
+          CONDA_OVERRIDE_CUDA: ${{ matrix.nvcc-version }}
+
+      - name: "List conda packages"
+        shell: cmd /C call {0}
+        run: conda list
+
+      - name: "Configure"
+        shell: cmd /C call {0}
+        run: |
+          call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
+          mkdir build
+          cd build
+          for /f "usebackq delims==" %%v in (`python -c "import site; print(site.getsitepackages()[-1])"`) do set SITE_PACKAGES=%%v
+          cmake -G "NMake Makefiles JOM" ^
+            -DCMAKE_BUILD_TYPE=Release ^
+            -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX% ^
+            -DOPENMM_DIR=%CONDA_PREFIX% ^
+            -DTorch_DIR=%SITE_PACKAGES%/torch/share/cmake/Torch ^
+            -DNN_BUILD_OPENCL_LIB=ON ^
+            -DOPENCL_INCLUDE_DIR="${{steps.cuda-toolkit.outputs.CUDA_PATH}}/include" ^
+            -DOPENCL_LIBRARY="${{steps.cuda-toolkit.outputs.CUDA_PATH}}/lib/x64/OpenCL.lib" ^
+
+      - name: "Build"
+        shell: cmd /C call {0}
+        run: |
+          call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
+          cd build
+          jom -j 4 install
+          jom -j 4 PythonInstall
+
+      - name: "List plugins"
+        shell: cmd /C call {0}
+        run: |
+          python -c "import openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
+
+      - name: "Run C++ test"
+        shell: cmd /C call {0}
+        run: |
+          cd build
+          ctest --output-on-failure --exclude-regex "TestCuda|TestOpenCL"
+
+      - name: "Run Python test"
+        shell: cmd /C call {0}
+        run: |
+          cd python/tests
+          pytest --verbose Test*
diff --git a/devtools/conda-envs/windows-latest.yml b/devtools/conda-envs/windows-latest.yml
new file mode 100644
index 00000000..e53aada4
--- /dev/null
+++ b/devtools/conda-envs/windows-latest.yml
@@ -0,0 +1,16 @@
+name: build
+channels:
+- conda-forge
+dependencies:
+- jom
+- cmake
+- ccache
+- m2-coreutils
+- python
+- cython
+- swig
+- openmm >=8.2
+- nnpops
+- pytorch-gpu @PYTORCH_VERSION@
+- torchani
+- pytest

From b4a449d16b25d23274d0b16a00c680964f9ada4a Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 10:49:16 -0800
Subject: [PATCH 02/25] Fixed filename

---
 .../conda-envs/{windows-latest.yml => build-windows-latest.yml}   | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename devtools/conda-envs/{windows-latest.yml => build-windows-latest.yml} (100%)

diff --git a/devtools/conda-envs/windows-latest.yml b/devtools/conda-envs/build-windows-latest.yml
similarity index 100%
rename from devtools/conda-envs/windows-latest.yml
rename to devtools/conda-envs/build-windows-latest.yml

From 128ac15ae5e78d26a6fe9fee7056017c92dbbaf5 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 11:17:23 -0800
Subject: [PATCH 03/25] There are no nnpops packages for Windows

---
 devtools/conda-envs/build-windows-latest.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/devtools/conda-envs/build-windows-latest.yml b/devtools/conda-envs/build-windows-latest.yml
index e53aada4..d4bdacc2 100644
--- a/devtools/conda-envs/build-windows-latest.yml
+++ b/devtools/conda-envs/build-windows-latest.yml
@@ -10,7 +10,6 @@ dependencies:
 - cython
 - swig
 - openmm >=8.2
-- nnpops
 - pytorch-gpu @PYTORCH_VERSION@
 - torchani
 - pytest

From 7b26ee0e058983cf73e750300fa4c14d0626647b Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 11:29:01 -0800
Subject: [PATCH 04/25] Fixed cmake command

---
 .github/workflows/CI.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e5020a10..f959731a 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -200,14 +200,14 @@ jobs:
           mkdir build
           cd build
           for /f "usebackq delims==" %%v in (`python -c "import site; print(site.getsitepackages()[-1])"`) do set SITE_PACKAGES=%%v
-          cmake -G "NMake Makefiles JOM" ^
+          cmake .. -G "NMake Makefiles JOM" ^
             -DCMAKE_BUILD_TYPE=Release ^
             -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX% ^
             -DOPENMM_DIR=%CONDA_PREFIX% ^
             -DTorch_DIR=%SITE_PACKAGES%/torch/share/cmake/Torch ^
             -DNN_BUILD_OPENCL_LIB=ON ^
             -DOPENCL_INCLUDE_DIR="${{steps.cuda-toolkit.outputs.CUDA_PATH}}/include" ^
-            -DOPENCL_LIBRARY="${{steps.cuda-toolkit.outputs.CUDA_PATH}}/lib/x64/OpenCL.lib" ^
+            -DOPENCL_LIBRARY="${{steps.cuda-toolkit.outputs.CUDA_PATH}}/lib/x64/OpenCL.lib"
 
       - name: "Build"
         shell: cmd /C call {0}

From 54f0926dd7305b35950b1f7f02683bc13d104fbc Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 11:51:57 -0800
Subject: [PATCH 05/25] Newer method of finding CUDA libraries

---
 CMakeLists.txt                | 8 ++++----
 platforms/cuda/CMakeLists.txt | 9 +--------
 2 files changed, 5 insertions(+), 12 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 75095427..11666d20 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -139,12 +139,12 @@ IF(NN_BUILD_OPENCL_LIB)
     ADD_SUBDIRECTORY(platforms/opencl)
 ENDIF(NN_BUILD_OPENCL_LIB)
 
-FIND_PACKAGE(CUDA QUIET)
-IF(CUDA_FOUND)
+FIND_PACKAGE(CUDAToolkit QUIET)
+IF(CUDAToolkit_FOUND)
     SET(NN_BUILD_CUDA_LIB ON CACHE BOOL "Build implementation for CUDA")
-ELSE(CUDA_FOUND)
+ELSE(CUDAToolkit_FOUND)
     SET(NN_BUILD_CUDA_LIB OFF CACHE BOOL "Build implementation for CUDA")
-ENDIF(CUDA_FOUND)
+ENDIF(CUDAToolkit_FOUND)
 IF(NN_BUILD_CUDA_LIB)
     ADD_SUBDIRECTORY(platforms/cuda)
 ENDIF(NN_BUILD_CUDA_LIB)
diff --git a/platforms/cuda/CMakeLists.txt b/platforms/cuda/CMakeLists.txt
index 0eb9e831..030eecca 100644
--- a/platforms/cuda/CMakeLists.txt
+++ b/platforms/cuda/CMakeLists.txt
@@ -58,14 +58,7 @@ ADD_CUSTOM_COMMAND(OUTPUT ${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H}
 SET_SOURCE_FILES_PROPERTIES(${CUDA_KERNELS_CPP} ${CUDA_KERNELS_H} PROPERTIES GENERATED TRUE)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
 
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${CUDA_LIBRARIES})
-IF(WIN32)
-    FIND_LIBRARY(CUDA_DRIVER_LIBRARY cuda HINTS ${CUDA_DRIVER_LIBRARY_PATH})
-    IF(NOT CUDA_DRIVER_LIBRARY)
-        MESSAGE(FATAL_ERROR "Could not find CUDA driver library")
-    ENDIF()
-    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${CUDA_DRIVER_LIBRARY})
-ENDIF(WIN32)
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} CUDA::cuda_driver)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} OpenMM)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} OpenMMCUDA)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${NN_LIBRARY_NAME})

From 195a0e9bd2ec513a41776eac19aaffefb2f1ed92 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 12:17:22 -0800
Subject: [PATCH 06/25] Workaround for pytorch error

---
 CMakeLists.txt | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 11666d20..f64fc765 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -15,7 +15,6 @@ LINK_DIRECTORIES("${OPENMM_DIR}/lib" "${OPENMM_DIR}/lib/plugins")
 # We need to know where LibTorch is installed so we can access the headers and libraries.
 SET(PYTORCH_DIR "" CACHE PATH "Where the PyTorch C++ API is installed")
 SET(CMAKE_PREFIX_PATH "${PYTORCH_DIR}")
-FIND_PACKAGE(Torch REQUIRED)
 
 # Specify the C++ version we are building for.
 SET (CMAKE_CXX_STANDARD 17)
@@ -84,6 +83,30 @@ FOREACH(subdir ${NN_PLUGIN_SOURCE_SUBDIRS})
     INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
 ENDFOREACH(subdir)
 
+# The following is taken from https://discuss.pytorch.org/t/failed-to-find-nvtoolsext/179635.
+# CUDA 12 changed nvToolsExt from a library to just a header.  This broke compiling against
+# libtorch.  Almost two years later, they still haven't fixed it.  This is a workaround.
+
+FIND_PACKAGE(CUDAToolkit QUIET)
+if(
+    PYTORCH_VERSION VERSION_GREATER_EQUAL 2.5.0 AND
+    PYTORCH_CUDA_VERSION VERSION_GREATER_EQUAL 12
+)
+    message(STATUS "PyTorch NVTX headers workaround: Yes")
+    # only do this if nvToolsExt is not defined and CUDA::nvtx3 exists
+    if(NOT TARGET CUDA::nvToolsExt AND TARGET CUDA::nvtx3)
+        add_library(CUDA::nvToolsExt INTERFACE IMPORTED)
+        # ensure that PyTorch is told to use NVTX3 headers
+        target_compile_definitions(
+            CUDA::nvToolsExt INTERFACE
+            TORCH_CUDA_USE_NVTX3
+        )
+        target_link_libraries(CUDA::nvToolsExt INTERFACE CUDA::nvtx3)
+    endif()
+else()
+    message(STATUS "PyTorch NVTX headers workaround: No")
+endif()FIND_PACKAGE(Torch REQUIRED)
+
 # Create the library.
 
 ADD_LIBRARY(${SHARED_NN_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
@@ -139,7 +162,6 @@ IF(NN_BUILD_OPENCL_LIB)
     ADD_SUBDIRECTORY(platforms/opencl)
 ENDIF(NN_BUILD_OPENCL_LIB)
 
-FIND_PACKAGE(CUDAToolkit QUIET)
 IF(CUDAToolkit_FOUND)
     SET(NN_BUILD_CUDA_LIB ON CACHE BOOL "Build implementation for CUDA")
 ELSE(CUDAToolkit_FOUND)

From eeb1af8897cb130ce7bcf4a0772ef383cac24edb Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 12:18:27 -0800
Subject: [PATCH 07/25] Fixed typo

---
 CMakeLists.txt | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index f64fc765..4f5f81d8 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -105,7 +105,8 @@ if(
     endif()
 else()
     message(STATUS "PyTorch NVTX headers workaround: No")
-endif()FIND_PACKAGE(Torch REQUIRED)
+endif()
+FIND_PACKAGE(Torch REQUIRED)
 
 # Create the library.
 

From cccdf46097528dc8c0f27a219b609c7e9ad1ea55 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 12:36:43 -0800
Subject: [PATCH 08/25] Debugging

---
 CMakeLists.txt | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4f5f81d8..60e8b89c 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -88,10 +88,7 @@ ENDFOREACH(subdir)
 # libtorch.  Almost two years later, they still haven't fixed it.  This is a workaround.
 
 FIND_PACKAGE(CUDAToolkit QUIET)
-if(
-    PYTORCH_VERSION VERSION_GREATER_EQUAL 2.5.0 AND
-    PYTORCH_CUDA_VERSION VERSION_GREATER_EQUAL 12
-)
+if(CUDAToolkit_VERSION VERSION_GREATER_EQUAL 12)
     message(STATUS "PyTorch NVTX headers workaround: Yes")
     # only do this if nvToolsExt is not defined and CUDA::nvtx3 exists
     if(NOT TARGET CUDA::nvToolsExt AND TARGET CUDA::nvtx3)

From 6840be04807228f078814924b505c16be204769b Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 13:00:18 -0800
Subject: [PATCH 09/25] Debugging

---
 .github/workflows/CI.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index f959731a..6b0846b8 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -197,6 +197,7 @@ jobs:
         shell: cmd /C call {0}
         run: |
           call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
+          dir C:\Miniconda3\envs\build\lib
           mkdir build
           cd build
           for /f "usebackq delims==" %%v in (`python -c "import site; print(site.getsitepackages()[-1])"`) do set SITE_PACKAGES=%%v

From 3da4fb68db19ecf10840f11fa2781ab1d28b9e41 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 13:33:30 -0800
Subject: [PATCH 10/25] Debugging

---
 .github/workflows/CI.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 6b0846b8..c15d5dd7 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -197,14 +197,14 @@ jobs:
         shell: cmd /C call {0}
         run: |
           call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
-          dir C:\Miniconda3\envs\build\lib
+          dir C:\Miniconda3\envs\build\Library\lib
           mkdir build
           cd build
           for /f "usebackq delims==" %%v in (`python -c "import site; print(site.getsitepackages()[-1])"`) do set SITE_PACKAGES=%%v
           cmake .. -G "NMake Makefiles JOM" ^
             -DCMAKE_BUILD_TYPE=Release ^
             -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX% ^
-            -DOPENMM_DIR=%CONDA_PREFIX% ^
+            -DOPENMM_DIR=%CONDA_PREFIX%/Library ^
             -DTorch_DIR=%SITE_PACKAGES%/torch/share/cmake/Torch ^
             -DNN_BUILD_OPENCL_LIB=ON ^
             -DOPENCL_INCLUDE_DIR="${{steps.cuda-toolkit.outputs.CUDA_PATH}}/include" ^

From 4408b1fd8ba2df7b8951367a090fde6c58ab7ff8 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 13:47:30 -0800
Subject: [PATCH 11/25] Fixed install location

---
 .github/workflows/CI.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c15d5dd7..45bae9f1 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -197,13 +197,12 @@ jobs:
         shell: cmd /C call {0}
         run: |
           call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
-          dir C:\Miniconda3\envs\build\Library\lib
           mkdir build
           cd build
           for /f "usebackq delims==" %%v in (`python -c "import site; print(site.getsitepackages()[-1])"`) do set SITE_PACKAGES=%%v
           cmake .. -G "NMake Makefiles JOM" ^
             -DCMAKE_BUILD_TYPE=Release ^
-            -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX% ^
+            -DCMAKE_INSTALL_PREFIX=%CONDA_PREFIX%/Library ^
             -DOPENMM_DIR=%CONDA_PREFIX%/Library ^
             -DTorch_DIR=%SITE_PACKAGES%/torch/share/cmake/Torch ^
             -DNN_BUILD_OPENCL_LIB=ON ^

From f99e1b0880d62f098b4e2605260b7a2cd34d83ce Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 7 Mar 2025 14:48:32 -0800
Subject: [PATCH 12/25] Debugging

---
 .github/workflows/CI.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 45bae9f1..8a193f9a 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -214,8 +214,10 @@ jobs:
         run: |
           call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
           cd build
+          type CMakeCache.txt
           jom -j 4 install
           jom -j 4 PythonInstall
+          dir C:\Miniconda3\envs\build\Library\lib\plugins
 
       - name: "List plugins"
         shell: cmd /C call {0}

From 36a8a3df5476c2bbe77dc39f9a005290ab457329 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 10 Oct 2025 17:25:29 -0700
Subject: [PATCH 13/25] Debugging

---
 .github/workflows/CI.yml | 2 --
 1 file changed, 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 8a193f9a..45bae9f1 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -214,10 +214,8 @@ jobs:
         run: |
           call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" x64
           cd build
-          type CMakeCache.txt
           jom -j 4 install
           jom -j 4 PythonInstall
-          dir C:\Miniconda3\envs\build\Library\lib\plugins
 
       - name: "List plugins"
         shell: cmd /C call {0}

From 44769ba9a3ad131268b05d275545b31668520e34 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 10 Oct 2025 21:08:40 -0700
Subject: [PATCH 14/25] Debugging

---
 .github/workflows/CI.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 45bae9f1..481e7ad2 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -83,8 +83,6 @@ jobs:
         with:
           activate-environment: build
           environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
-          miniforge-variant: Miniforge3
-          use-mamba: true
           python-version: ${{ matrix.python-version }}
         env:
           # Override the CUDA detection as the CI hosts don't have NVIDIA drivers
@@ -182,8 +180,6 @@ jobs:
         with:
           activate-environment: build
           environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
-          miniforge-variant: Miniforge3
-          use-mamba: true
           python-version: ${{ matrix.python-version }}
         env:
           # Override the CUDA detection as the CI hosts don't have NVIDIA drivers

From 5b2fab8ed94da551c6c2f65b0566a45893355712 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Fri, 10 Oct 2025 21:11:55 -0700
Subject: [PATCH 15/25] Debugging

---
 .github/workflows/CI.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 481e7ad2..e8fa0fae 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -84,6 +84,7 @@ jobs:
           activate-environment: build
           environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
           python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
         env:
           # Override the CUDA detection as the CI hosts don't have NVIDIA drivers
           CONDA_OVERRIDE_CUDA: ${{ matrix.nvcc-version }}
@@ -181,6 +182,7 @@ jobs:
           activate-environment: build
           environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
           python-version: ${{ matrix.python-version }}
+          auto-activate-base: false
         env:
           # Override the CUDA detection as the CI hosts don't have NVIDIA drivers
           CONDA_OVERRIDE_CUDA: ${{ matrix.nvcc-version }}

From 8ec19b9024f78429045c65f1df7bf9ce0e2ce8c1 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Sat, 11 Oct 2025 21:15:13 -0700
Subject: [PATCH 16/25] Debugging

---
 .github/workflows/CI.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index e8fa0fae..5435a680 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -85,6 +85,8 @@ jobs:
           environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
           python-version: ${{ matrix.python-version }}
           auto-activate-base: false
+          miniforge-variant: Miniforge3
+          use-mamba: true
         env:
           # Override the CUDA detection as the CI hosts don't have NVIDIA drivers
           CONDA_OVERRIDE_CUDA: ${{ matrix.nvcc-version }}

From 57543f117de0d6bad5a9105240c6e60ba759fc38 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Sat, 11 Oct 2025 21:18:12 -0700
Subject: [PATCH 17/25] Debugging

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 5435a680..9b888916 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -78,7 +78,7 @@ jobs:
           NVCC_VERSION: ${{ matrix.nvcc-version }}
           PYTORCH_VERSION: ${{ matrix.pytorch-version }}
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         name: "Install dependencies with Mamba"
         with:
           activate-environment: build

From af807d61c13b77a8f77ece5c892ec65af9188cef Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Sun, 12 Oct 2025 11:00:50 -0700
Subject: [PATCH 18/25] Debugging

---
 .github/workflows/CI.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 9b888916..ffaf74d8 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -226,6 +226,7 @@ jobs:
         shell: cmd /C call {0}
         run: |
           cd build
+          set PATH=%PATH%;%CONDA_PREFIX%\lib\python${{ matrix.python-version }}\site-packages\torch\lib
           ctest --output-on-failure --exclude-regex "TestCuda|TestOpenCL"
 
       - name: "Run Python test"

From 31f2ca73361504e3176d17cecc9f93e6a306e337 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Sun, 12 Oct 2025 12:01:47 -0700
Subject: [PATCH 19/25] Debugging

---
 .github/workflows/CI.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index ffaf74d8..41906b44 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -227,6 +227,8 @@ jobs:
         run: |
           cd build
           set PATH=%PATH%;%CONDA_PREFIX%\lib\python${{ matrix.python-version }}\site-packages\torch\lib
+          set PATH
+          dir %CONDA_PREFIX%\lib\python${{ matrix.python-version }}\site-packages\torch\lib
           ctest --output-on-failure --exclude-regex "TestCuda|TestOpenCL"
 
       - name: "Run Python test"

From 56438b84b68ad5011d351e7dde7518146a18d86f Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Sun, 12 Oct 2025 21:12:19 -0700
Subject: [PATCH 20/25] Debugging

---
 .github/workflows/CI.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 41906b44..b4839920 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -226,9 +226,10 @@ jobs:
         shell: cmd /C call {0}
         run: |
           cd build
-          set PATH=%PATH%;%CONDA_PREFIX%\lib\python${{ matrix.python-version }}\site-packages\torch\lib
+          for /f "usebackq delims==" %%v in (`python -c "import site; print(site.getsitepackages()[-1])"`) do set SITE_PACKAGES=%%v
+          dir %SITE_PACKAGES%\torch
+          set PATH=%PATH%;%SITE_PACKAGES%\torch\lib
           set PATH
-          dir %CONDA_PREFIX%\lib\python${{ matrix.python-version }}\site-packages\torch\lib
           ctest --output-on-failure --exclude-regex "TestCuda|TestOpenCL"
 
       - name: "Run Python test"

From f795780ba4bef79a6c96874b5f826da92b9e7a62 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Sun, 12 Oct 2025 21:31:56 -0700
Subject: [PATCH 21/25] Debugging

---
 .github/workflows/CI.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index b4839920..c6707de0 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -227,8 +227,9 @@ jobs:
         run: |
           cd build
           for /f "usebackq delims==" %%v in (`python -c "import site; print(site.getsitepackages()[-1])"`) do set SITE_PACKAGES=%%v
-          dir %SITE_PACKAGES%\torch
-          set PATH=%PATH%;%SITE_PACKAGES%\torch\lib
+          dir %SITE_PACKAGES%\torch\lib
+          dir %CONDA_PREFIX%\Library\lib
+          set PATH=%PATH%;%SITE_PACKAGES%\torch\lib;%CONDA_PREFIX%\Library\lib
           set PATH
           ctest --output-on-failure --exclude-regex "TestCuda|TestOpenCL"
 

From 6687c4950ef044559129c05a42452665efd22734 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Mon, 13 Oct 2025 11:09:18 -0700
Subject: [PATCH 22/25] Debugging

---
 .github/workflows/CI.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c6707de0..891b0a09 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -52,10 +52,11 @@ jobs:
         uses: actions/checkout@v2
 
       - name: "Install CUDA Toolkit on Linux (if needed)"
-        uses: Jimver/cuda-toolkit@v0.2.15
+        uses: Jimver/cuda-toolkit@v0.2.24
         with:
           cuda: ${{ matrix.cuda-version }}
           linux-local-args: '["--toolkit", "--override"]'
+          use-github-cache: 'false'
         if: startsWith(matrix.os, 'ubuntu')
 
       - name: Manage disk space
@@ -162,7 +163,7 @@ jobs:
         uses: actions/checkout@v2
 
       - name: "Install CUDA Toolkit"
-        uses: Jimver/cuda-toolkit@v0.2.16
+        uses: Jimver/cuda-toolkit@v0.2.24
         id: cuda-toolkit
         with:
           cuda: ${{ matrix.cuda-version }}

From b87380b914b2887bd7d1763916bc5ab4b78fe95c Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Mon, 13 Oct 2025 11:27:13 -0700
Subject: [PATCH 23/25] Debugging

---
 .github/workflows/CI.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 891b0a09..0174b490 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -56,7 +56,6 @@ jobs:
         with:
           cuda: ${{ matrix.cuda-version }}
           linux-local-args: '["--toolkit", "--override"]'
-          use-github-cache: 'false'
         if: startsWith(matrix.os, 'ubuntu')
 
       - name: Manage disk space

From 57b4ff103e942c262335a94b2e73ecd4e3f33e29 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Mon, 13 Oct 2025 11:56:30 -0700
Subject: [PATCH 24/25] Update to newer Python/PyTorch/CUDA versions

---
 .github/workflows/CI.yml | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 0174b490..d2d16d0d 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -22,29 +22,29 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: Linux (CUDA 11.8, Python 3.10, PyTorch 2.1)
+          - name: Linux (CUDA 12.4, Python 3.13, PyTorch 2.8)
             os: ubuntu-22.04
-            cuda-version: "11.8.0"
+            cuda-version: "12.4"
             gcc-version: "10.3.*"
-            nvcc-version: "11.8"
-            python-version: "3.10"
-            pytorch-version: "2.1.*"
+            nvcc-version: "12.4"
+            python-version: "3.13"
+            pytorch-version: "2.8.*"
 
-          - name: MacOS ARM (Python 3.11, PyTorch 2.4)
+          - name: MacOS ARM (Python 3.13, PyTorch 2.5)
             os: macos-latest
             cuda-version: ""
             gcc-version: ""
             nvcc-version: ""
-            python-version: "3.11"
-            pytorch-version: "2.4.*"
+            python-version: "3.13"
+            pytorch-version: "2.5.*"
 
-          - name: MacOS Intel (Python 3.11, PyTorch 2.4)
+          - name: MacOS Intel (Python 3.13, PyTorch 2.5)
             os: macos-13
             cuda-version: ""
             gcc-version: ""
             nvcc-version: ""
-            python-version: "3.11"
-            pytorch-version: "2.4.*"
+            python-version: "3.13"
+            pytorch-version: "2.5.*"
 
 
     steps:

From 720541deb316abaebf9da4e10ce743e60f4b11f3 Mon Sep 17 00:00:00 2001
From: peastman <peastman@stanford.edu>
Date: Mon, 13 Oct 2025 11:58:55 -0700
Subject: [PATCH 25/25] Debugging

---
 .github/workflows/CI.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index d2d16d0d..c98b8283 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -24,7 +24,7 @@ jobs:
         include:
           - name: Linux (CUDA 12.4, Python 3.13, PyTorch 2.8)
             os: ubuntu-22.04
-            cuda-version: "12.4"
+            cuda-version: "12.5.0"
             gcc-version: "10.3.*"
             nvcc-version: "12.4"
             python-version: "3.13"