From d505286312e104ba7e034c0f287a3ed77f535e9e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 16:20:22 +0100
Subject: [PATCH 01/22] add CI

---
 .github/workflows/CI.yml                    | 138 ++++++++++++++++++++
 devtools/conda-envs/build-macos-latest.yml  |  15 +++
 devtools/conda-envs/build-ubuntu-latest.yml |  23 ++++
 devtools/scripts/install_cuda.sh            |  44 +++++++
 devtools/scripts/install_macos_sdk.sh       |  31 +++++
 5 files changed, 251 insertions(+)
 create mode 100644 .github/workflows/CI.yml
 create mode 100644 devtools/conda-envs/build-macos-latest.yml
 create mode 100644 devtools/conda-envs/build-ubuntu-latest.yml
 create mode 100644 devtools/scripts/install_cuda.sh
 create mode 100644 devtools/scripts/install_macos_sdk.sh

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
new file mode 100644
index 0000000..f8c0a0b
--- /dev/null
+++ b/.github/workflows/CI.yml
@@ -0,0 +1,138 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - "master"
+  pull_request:
+    branches:
+      - "master"
+  schedule:
+    # Nightly tests run on master by default:
+    #   Scheduled workflows run on the latest commit on the default or base branch.
+    #   (from https://help.github.com/en/actions/reference/events-that-trigger-workflows#scheduled-events-schedule)
+    - cron: "0 0 * * *"
+
+
+jobs:
+  unix:
+    runs-on: ${{ matrix.os }}
+    name: ${{ matrix.name }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Linux CPU/CUDA Python 3.6
+            python-version: "3.6"
+            os: ubuntu-latest
+            gcc-version: "9"
+            cuda-version: "10.0"
+            cdt-name: cos6  # cuda 11+ requires cos7
+            CMAKE_FLAGS: |
+              -DPLUMED_BUILD_CUDA_LIB=ON \
+              -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \
+              -DEXTRA_COMPILE_FLAGS="-L/usr/local/cuda/lib64/stubs -Wl,-rpath,/usr/local/cuda/lib64/stubs -Wl,-rpath-link,/usr/local/cuda/lib64/stubs"
+
+          - name: MacOS Intel CPU/OpenCL Python 3.9
+            python-version: "3.9"
+            os: macos-latest
+            cuda-version: ""
+            CMAKE_FLAGS: ""
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: "Patch conda env (if needed)"
+        if: startsWith(matrix.os, 'ubuntu')
+        run: |
+          sed -i -e "s/@CDT_NAME@/${{ 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
+        name: "Prepare base dependencies"
+        with:
+          python-version: ${{ matrix.python-version }}
+          activate-environment: build
+          environment-file: devtools/conda-envs/build-${{ matrix.os }}.yml
+          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
+
+      - name: "Conda info"
+        shell: bash -l {0}
+        run: |
+          conda info -a
+          conda list
+
+      - name: Patch Plumed's Lepton location
+        shell: bash -l {0}
+        run: |
+          test -d ${CONDA_PREFIX}/include/plumed/lepton && mv ${CONDA_PREFIX}/include/plumed/lepton ${CONDA_PREFIX}/include/plumed/lepton.bak
+
+      - name: "Configure build with CMake"
+        shell: bash -l {0}
+        run: |
+          mkdir build
+          cd build
+
+          SHLIB_EXT=".so"
+          if [[ ${{ matrix.os }} == macos-* ]]; then
+            SHLIB_EXT=".dylib"
+          fi
+
+          cmake .. ${CMAKE_ARGS} \
+            -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} \
+            -DCMAKE_BUILD_TYPE=Release \
+            -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} \
+            ${{ matrix.CMAKE_FLAGS }}
+
+      - name: "Build"
+        shell: bash -l {0}
+        run: |
+          cd build
+          make -j2 install
+          make -j2 PythonInstall
+
+      - name: "Test"
+        shell: bash -l {0}
+        run: |
+          cd build
+          set +e
+          summary=""
+          exitcode=0
+          for f in Test*; do
+            echo "::group::$f"
+            summary+="\n${f}: "
+            if [[ $f == *Cuda* || $f == *OpenCL* ]]; then
+              echo "Skipping $f..."
+              summary+="Skipped"
+              continue
+            fi
+            echo "Running $f..."
+            ./${f}
+            thisexitcode=$?
+            if [[ $thisexitcode == 0 ]]; then summary+="OK"; else summary+="FAILED"; fi
+            ((exitcode+=$thisexitcode))
+            echo "::endgroup::"
+          done
+          echo "-------"
+          echo "Summary"
+          echo "-------"
+          echo -e "${summary}"
+          exit $exitcode
diff --git a/devtools/conda-envs/build-macos-latest.yml b/devtools/conda-envs/build-macos-latest.yml
new file mode 100644
index 0000000..00d0c8c
--- /dev/null
+++ b/devtools/conda-envs/build-macos-latest.yml
@@ -0,0 +1,15 @@
+name: build
+channels:
+- conda-forge
+dependencies:
+# build
+- cmake
+- make
+- compilers
+# host
+- python
+- pip
+- swig
+- openmm
+- plumed >=2.7
+- khronos-opencl-icd-loader
diff --git a/devtools/conda-envs/build-ubuntu-latest.yml b/devtools/conda-envs/build-ubuntu-latest.yml
new file mode 100644
index 0000000..4c66e87
--- /dev/null
+++ b/devtools/conda-envs/build-ubuntu-latest.yml
@@ -0,0 +1,23 @@
+name: build
+channels:
+- conda-forge
+dependencies:
+# build
+- cmake
+- make
+- gcc_linux-64 @GCC_VERSION@
+- gxx_linux-64 @GCC_VERSION@
+- libx11-common-@CDT_NAME@-x86_64
+- libx11-@CDT_NAME@-x86_64
+- mesa-dri-drivers-@CDT_NAME@-x86_64
+- mesa-dri1-drivers-@CDT_NAME@-x86_64
+- mesa-libgl-@CDT_NAME@-x86_64
+- mesa-libgl-devel-@CDT_NAME@-x86_64
+# host
+- python
+- pip
+- swig
+- openmm
+- plumed >=2.7
+- ocl-icd
+- cudatoolkit @CUDATOOLKIT_VERSION@
\ No newline at end of file
diff --git a/devtools/scripts/install_cuda.sh b/devtools/scripts/install_cuda.sh
new file mode 100644
index 0000000..48e741c
--- /dev/null
+++ b/devtools/scripts/install_cuda.sh
@@ -0,0 +1,44 @@
+# This script install CUDA on Ubuntu-based systemws
+# It uses the Nvidia repos for Ubuntu 18.04, which as of Dec 2020
+# includes packages for CUDA 10.0, 10.1, 10.2, 11.0, 11.1, 11.2
+# Future versions might require an updated repo (maybe Ubuntu 20)
+# It expects a $CUDA_VERSION environment variable set to major.minor (e.g. 10.0)
+
+set -euxo pipefail
+
+# Enable retrying
+echo 'APT::Acquire::Retries "5";' | sudo tee /etc/apt/apt.conf.d/80-retries
+
+sudo wget --retry-connrefused --waitretry=1 --read-timeout=20 --timeout=15 --tries 5 \
+    -O /etc/apt/preferences.d/cuda-repository-pin-600 \
+    https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
+sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
+sudo add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
+sudo apt-get update -qq
+
+CUDA_APT=${CUDA_VERSION/./-}
+## cufft changed package names in CUDA 11
+if [[ ${CUDA_VERSION} == 10.* ]]; then CUFFT="cuda-cufft"; else CUFFT="libcufft"; fi
+sudo apt-get install -y \
+    libgl1-mesa-dev cuda-compiler-${CUDA_APT} \
+    cuda-drivers cuda-driver-dev-${CUDA_APT} \
+    cuda-cudart-${CUDA_APT} cuda-cudart-dev-${CUDA_APT} \
+    ${CUFFT}-${CUDA_APT} ${CUFFT}-dev-${CUDA_APT} \
+    cuda-nvprof-${CUDA_APT} tree
+sudo apt-get clean
+
+if [[ ! -d /usr/local/cuda ]]; then
+    sudo ln -s /usr/local/cuda-${CUDA_VERSION} /usr/local/cuda
+fi
+
+if [[ -f /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so ]]; then
+    sudo ln -s /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so.1
+fi
+
+export CUDA_HOME="/usr/local/cuda"
+export CUDA_PATH="/usr/local/cuda"
+export PATH="${CUDA_HOME}/bin:${PATH}"
+
+echo "CUDA_HOME=${CUDA_HOME}" >> ${GITHUB_ENV}
+echo "CUDA_PATH=${CUDA_PATH}" >> ${GITHUB_ENV}
+echo "PATH=${PATH}" >> ${GITHUB_ENV}
diff --git a/devtools/scripts/install_macos_sdk.sh b/devtools/scripts/install_macos_sdk.sh
new file mode 100644
index 0000000..85b1616
--- /dev/null
+++ b/devtools/scripts/install_macos_sdk.sh
@@ -0,0 +1,31 @@
+# Install an older MacOS SDK
+# This should guarantee OpenMM builds with extended compatibility across MacOS versions
+# Adapted from conda-forge-ci-setup scripts:
+# * https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/dde296e/recipe/run_conda_forge_build_setup_osx
+# * https://github.com/conda-forge/conda-forge-ci-setup-feedstock/blob/dde296e/recipe/download_osx_sdk.sh
+#
+# Some possible updates might involve upgrading the download link to future MacOS releases (10.15 to something else),
+# depending on the version provided by the CI
+
+OSX_SDK_DIR="$(xcode-select -p)/Platforms/MacOSX.platform/Developer/SDKs"
+export MACOSX_DEPLOYMENT_TARGET=10.9
+export MACOSX_SDK_VERSION=10.9
+
+export CMAKE_OSX_SYSROOT="${OSX_SDK_DIR}/MacOSX${MACOSX_SDK_VERSION}.sdk"
+
+if [[ ! -d ${CMAKE_OSX_SYSROOT}} ]]; then
+    echo "Downloading ${MACOSX_SDK_VERSION} sdk"
+    curl -L -O --connect-timeout 5 --max-time 10 --retry 5  --retry-delay 0 --retry-max-time 40 --retry-connrefused --retry-all-errors \
+        https://github.com/phracker/MacOSX-SDKs/releases/download/10.15/MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz
+    tar -xf MacOSX${MACOSX_SDK_VERSION}.sdk.tar.xz -C "$(dirname ${CMAKE_OSX_SYSROOT})"
+fi
+
+if [[ "$MACOSX_DEPLOYMENT_TARGET" == 10.* ]]; then
+# set minimum sdk version to our target
+plutil -replace MinimumSDKVersion -string ${MACOSX_SDK_VERSION} $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+plutil -replace DTSDKName -string macosx${MACOSX_SDK_VERSION}internal $(xcode-select -p)/Platforms/MacOSX.platform/Info.plist
+fi
+
+echo "MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}" >> ${GITHUB_ENV}
+echo "CMAKE_OSX_SYSROOT=${MACOSX_DEPLOYMENT_TARGET}" >> ${GITHUB_ENV}
+echo "CMAKE_OSX_SYSROOT=${CMAKE_OSX_SYSROOT}" >> ${GITHUB_ENV}
\ No newline at end of file

From 8af524aff746b55449c8c94bde2d9720dad5c029 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 16:30:34 +0100
Subject: [PATCH 02/22] find Tests?

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index f8c0a0b..2271b54 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -113,6 +113,7 @@ jobs:
         shell: bash -l {0}
         run: |
           cd build
+          find . -name "Test*"
           set +e
           summary=""
           exitcode=0

From fbdbea568378c9dc7e7ac2871054fce718dab5fc Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 17:37:35 +0100
Subject: [PATCH 03/22] find tests

---
 .github/workflows/CI.yml | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 2271b54..a051449 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -112,20 +112,25 @@ jobs:
       - name: "Test"
         shell: bash -l {0}
         run: |
-          cd build
-          find . -name "Test*"
           set +e
+          cd build
+          if [[ ${{ matrix.os }} == ubuntu-* ]]; then
+            test_files=$(find . -name "Test*" -executable -type f)
+          else
+            test_files=$(find . -name "Test*" -perm +0111 -type f)
+          fi
           summary=""
           exitcode=0
-          for f in Test*; do
-            echo "::group::$f"
-            summary+="\n${f}: "
-            if [[ $f == *Cuda* || $f == *OpenCL* ]]; then
-              echo "Skipping $f..."
+          for f in $test_files; do
+            fn=$(basename $f)
+            echo "::group::$fn"
+            summary+="\n${fn}: "
+            if [[ $fn == *Cuda* || $f == *OpenCL* ]]; then
+              echo "Skipping $fn..."
               summary+="Skipped"
               continue
             fi
-            echo "Running $f..."
+            echo "Running $fn..."
             ./${f}
             thisexitcode=$?
             if [[ $thisexitcode == 0 ]]; then summary+="OK"; else summary+="FAILED"; fi

From bf28093515efdbb0f5826b2f702d18048fe516f9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 17:45:42 +0100
Subject: [PATCH 04/22] close skipped groups too

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index a051449..1f23cf8 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -128,6 +128,7 @@ jobs:
             if [[ $fn == *Cuda* || $f == *OpenCL* ]]; then
               echo "Skipping $fn..."
               summary+="Skipped"
+              echo "::endgroup::"
               continue
             fi
             echo "Running $fn..."

From 552c084d6a80f813e74c02cf2266fef6c8d5d7ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 17:51:25 +0100
Subject: [PATCH 05/22] update readme

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index ddcecc2..95156ab 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,7 @@
+[![GH Actions Status](https://github.com/openmm/openmm-plumed/workflows/CI/badge.svg)](https://github.com/openmm/openmm-plumed/actions?query=branch%3Amaster+workflow%3ACI)
+[![Conda](https://img.shields.io/conda/v/conda-forge/openmm-plumed.svg)](https://anaconda.org/conda-forge/openmm-plumed)
+[![Anaconda Cloud Badge](https://anaconda.org/conda-forge/openmm-plumed/badges/downloads.svg)](https://anaconda.org/conda-forge/openmm-plumed)
+
 OpenMM PLUMED Plugin
 =====================
 

From d79a3b85be833e34a82ba077ed5d11e131cb7d0d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 19:39:19 +0100
Subject: [PATCH 06/22] try pocl for opencl tests

---
 .github/workflows/CI.yml                    | 2 +-
 devtools/conda-envs/build-macos-latest.yml  | 1 +
 devtools/conda-envs/build-ubuntu-latest.yml | 3 ++-
 3 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 1f23cf8..0dfaaf8 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -125,7 +125,7 @@ jobs:
             fn=$(basename $f)
             echo "::group::$fn"
             summary+="\n${fn}: "
-            if [[ $fn == *Cuda* || $f == *OpenCL* ]]; then
+            if [[ $fn == *Cuda* ]]; then
               echo "Skipping $fn..."
               summary+="Skipped"
               echo "::endgroup::"
diff --git a/devtools/conda-envs/build-macos-latest.yml b/devtools/conda-envs/build-macos-latest.yml
index 00d0c8c..a443802 100644
--- a/devtools/conda-envs/build-macos-latest.yml
+++ b/devtools/conda-envs/build-macos-latest.yml
@@ -13,3 +13,4 @@ dependencies:
 - openmm
 - plumed >=2.7
 - khronos-opencl-icd-loader
+- pocl
diff --git a/devtools/conda-envs/build-ubuntu-latest.yml b/devtools/conda-envs/build-ubuntu-latest.yml
index 4c66e87..cadc3c8 100644
--- a/devtools/conda-envs/build-ubuntu-latest.yml
+++ b/devtools/conda-envs/build-ubuntu-latest.yml
@@ -20,4 +20,5 @@ dependencies:
 - openmm
 - plumed >=2.7
 - ocl-icd
-- cudatoolkit @CUDATOOLKIT_VERSION@
\ No newline at end of file
+- cudatoolkit @CUDATOOLKIT_VERSION@
+- pocl
\ No newline at end of file

From 28c92548a29e0100f6832f1fbb82f099a3f736b9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 19:48:52 +0100
Subject: [PATCH 07/22] try oclgrind

---
 devtools/conda-envs/build-ubuntu-latest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/build-ubuntu-latest.yml b/devtools/conda-envs/build-ubuntu-latest.yml
index cadc3c8..cb5880e 100644
--- a/devtools/conda-envs/build-ubuntu-latest.yml
+++ b/devtools/conda-envs/build-ubuntu-latest.yml
@@ -21,4 +21,4 @@ dependencies:
 - plumed >=2.7
 - ocl-icd
 - cudatoolkit @CUDATOOLKIT_VERSION@
-- pocl
\ No newline at end of file
+- oclgrind

From b2d87a00810123ca229e6d8e401fa9b387a8e746 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 20:04:08 +0100
Subject: [PATCH 08/22] debug opencl platforms on Linux

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 0dfaaf8..839589e 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -109,6 +109,11 @@ jobs:
           make -j2 install
           make -j2 PythonInstall
 
+      - name: "Debug platforms"
+        shell: bash -l {0}
+        run: |
+          python -m simtk.testInstallation
+
       - name: "Test"
         shell: bash -l {0}
         run: |

From 23e3deb433c5645bae687d31c0dc02846511cb66 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 20:13:34 +0100
Subject: [PATCH 09/22] more debugging

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 839589e..d9d2a0e 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -112,7 +112,9 @@ jobs:
       - name: "Debug platforms"
         shell: bash -l {0}
         run: |
+          set +e
           python -m simtk.testInstallation
+          python -c "import simtk.openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
 
       - name: "Test"
         shell: bash -l {0}

From b229774df2eeb2f268a48bcaac4aeed835d94058 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 20:23:26 +0100
Subject: [PATCH 10/22] pocl should work

---
 devtools/conda-envs/build-ubuntu-latest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/devtools/conda-envs/build-ubuntu-latest.yml b/devtools/conda-envs/build-ubuntu-latest.yml
index cb5880e..4fb1a35 100644
--- a/devtools/conda-envs/build-ubuntu-latest.yml
+++ b/devtools/conda-envs/build-ubuntu-latest.yml
@@ -21,4 +21,4 @@ dependencies:
 - plumed >=2.7
 - ocl-icd
 - cudatoolkit @CUDATOOLKIT_VERSION@
-- oclgrind
+- pocl

From 138a672d1cbd760c373cf31457541d63615774ff Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 20:41:51 +0100
Subject: [PATCH 11/22] Rename jobs

---
 .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 d9d2a0e..3e747a3 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: Linux CPU/CUDA Python 3.6
+          - name: Linux CPU CUDA 10.0 Python 3.6
             python-version: "3.6"
             os: ubuntu-latest
             gcc-version: "9"
@@ -33,7 +33,7 @@ jobs:
               -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
+          - name: MacOS Intel CPU OpenCL Python 3.9
             python-version: "3.9"
             os: macos-latest
             cuda-version: ""

From 264e9587335f7c44c9a5731ef35ec159b98ed8ae Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 20:42:41 +0100
Subject: [PATCH 12/22] print ldd info

---
 .github/workflows/CI.yml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 3e747a3..a5bbf30 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -109,12 +109,14 @@ jobs:
           make -j2 install
           make -j2 PythonInstall
 
-      - name: "Debug platforms"
+      - name: "Debug OpenCL on Linux"
         shell: bash -l {0}
+        if: startsWith(matrix.os, 'ubuntu')
         run: |
           set +e
           python -m simtk.testInstallation
           python -c "import simtk.openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
+          find build -name TestOpenCLPlumedForce -type f -exec ldd {} \;
 
       - name: "Test"
         shell: bash -l {0}

From e4ad862ae82195a14709fe92ccde72cc821b0d41 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 21:41:17 +0100
Subject: [PATCH 13/22] drop cmake_args

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index a5bbf30..a12345b 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -91,8 +91,9 @@ jobs:
             SHLIB_EXT=".dylib"
           fi
 
-          cmake .. ${CMAKE_ARGS} \
+          cmake .. \
             -DCMAKE_INSTALL_PREFIX=${CONDA_PREFIX} \
+            -DCMAKE_PREFIX_PATH=${CONDA_PREFIX} \
             -DCMAKE_BUILD_TYPE=Release \
             -DOPENMM_DIR=${CONDA_PREFIX} \
             -DPLUMED_INCLUDE_DIR=${CONDA_PREFIX}/include/plumed \

From faad7db851506676c47b3d2fac3e6b065e5581e5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 21:57:30 +0100
Subject: [PATCH 14/22] remove Nvidia's opencl

---
 devtools/scripts/install_cuda.sh | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/devtools/scripts/install_cuda.sh b/devtools/scripts/install_cuda.sh
index 48e741c..bab49f5 100644
--- a/devtools/scripts/install_cuda.sh
+++ b/devtools/scripts/install_cuda.sh
@@ -35,6 +35,9 @@ if [[ -f /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so ]]; then
     sudo ln -s /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so /usr/local/cuda-${CUDA_VERSION}/lib64/stubs/libcuda.so.1
 fi
 
+# Remove Nvidia's OpenCL
+sudo rm -rf /usr/local/cuda-${CUDA_VERSION}/lib64/libOpenCL.* /usr/local/cuda-${CUDA_VERSION}/include/CL /etc/OpenCL/vendors/nvidia.icd
+
 export CUDA_HOME="/usr/local/cuda"
 export CUDA_PATH="/usr/local/cuda"
 export PATH="${CUDA_HOME}/bin:${PATH}"

From 0b2d1880551d6c190cc71e2faae9cd96c788301a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 22:15:09 +0100
Subject: [PATCH 15/22] remove debug steps

---
 .github/workflows/CI.yml | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index a12345b..b450d68 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -110,15 +110,6 @@ jobs:
           make -j2 install
           make -j2 PythonInstall
 
-      - name: "Debug OpenCL on Linux"
-        shell: bash -l {0}
-        if: startsWith(matrix.os, 'ubuntu')
-        run: |
-          set +e
-          python -m simtk.testInstallation
-          python -c "import simtk.openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
-          find build -name TestOpenCLPlumedForce -type f -exec ldd {} \;
-
       - name: "Test"
         shell: bash -l {0}
         run: |

From 44075d5d45a48c64a8166220ab74e4b8999bbe33 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Mon, 1 Feb 2021 23:06:05 +0100
Subject: [PATCH 16/22] leave some useful debugging

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

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index b450d68..c25f321 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -110,6 +110,11 @@ jobs:
           make -j2 install
           make -j2 PythonInstall
 
+      - name: "Plugin information"
+        shell: bash -l {0}
+        run: |
+          python -c "import simtk.openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
+
       - name: "Test"
         shell: bash -l {0}
         run: |

From d3b8a30f070836881836f7f12a09404f2cdf7109 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Wed, 3 Feb 2021 12:54:46 +0100
Subject: [PATCH 17/22] add python tests runner

---
 .github/workflows/CI.yml                    | 8 +++++++-
 devtools/conda-envs/build-macos-latest.yml  | 2 ++
 devtools/conda-envs/build-ubuntu-latest.yml | 2 ++
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c25f321..85b4e83 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -115,7 +115,7 @@ jobs:
         run: |
           python -c "import simtk.openmm as mm; print('---Loaded---', *mm.pluginLoadedLibNames, '---Failed---', *mm.Platform.getPluginLoadFailures(), sep='\n')"
 
-      - name: "Test"
+      - name: "Test C++"
         shell: bash -l {0}
         run: |
           set +e
@@ -149,3 +149,9 @@ jobs:
           echo "-------"
           echo -e "${summary}"
           exit $exitcode
+
+      - name: "Test Python"
+        shell: bash -l {0}
+        run: |
+          cd python/tests
+          pytest -v Test*
diff --git a/devtools/conda-envs/build-macos-latest.yml b/devtools/conda-envs/build-macos-latest.yml
index a443802..4e9818e 100644
--- a/devtools/conda-envs/build-macos-latest.yml
+++ b/devtools/conda-envs/build-macos-latest.yml
@@ -14,3 +14,5 @@ dependencies:
 - plumed >=2.7
 - khronos-opencl-icd-loader
 - pocl
+# test
+- pytest
diff --git a/devtools/conda-envs/build-ubuntu-latest.yml b/devtools/conda-envs/build-ubuntu-latest.yml
index 4fb1a35..0095bc4 100644
--- a/devtools/conda-envs/build-ubuntu-latest.yml
+++ b/devtools/conda-envs/build-ubuntu-latest.yml
@@ -22,3 +22,5 @@ dependencies:
 - ocl-icd
 - cudatoolkit @CUDATOOLKIT_VERSION@
 - pocl
+# test
+- pytest

From 3285d1d2114e2e409e5ecbbfefc1422993830db0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Wed, 3 Feb 2021 12:55:18 +0100
Subject: [PATCH 18/22] bump cuda to 11.2

---
 .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 85b4e83..a7578e3 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -26,8 +26,8 @@ jobs:
             python-version: "3.6"
             os: ubuntu-latest
             gcc-version: "9"
-            cuda-version: "10.0"
-            cdt-name: cos6  # cuda 11+ requires cos7
+            cuda-version: "11.2"
+            cdt-name: cos7  # cuda 11+ requires cos7
             CMAKE_FLAGS: |
               -DPLUMED_BUILD_CUDA_LIB=ON \
               -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \

From 24439467bf7fbb65ba0014f4994c7583d1b70c01 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Wed, 3 Feb 2021 13:05:47 +0100
Subject: [PATCH 19/22] cos6?

---
 .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 a7578e3..bee81f5 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -27,7 +27,7 @@ jobs:
             os: ubuntu-latest
             gcc-version: "9"
             cuda-version: "11.2"
-            cdt-name: cos7  # cuda 11+ requires cos7
+            cdt-name: cos6
             CMAKE_FLAGS: |
               -DPLUMED_BUILD_CUDA_LIB=ON \
               -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda \

From 46cc15b7e3d1a65e3a212eda4edcfc2e66e03a64 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Wed, 3 Feb 2021 13:13:22 +0100
Subject: [PATCH 20/22] mesa-dri depends on mesa-dri1, no need to specify both

---
 .github/workflows/CI.yml                    | 2 +-
 devtools/conda-envs/build-ubuntu-latest.yml | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index bee81f5..5587094 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -27,7 +27,7 @@ jobs:
             os: ubuntu-latest
             gcc-version: "9"
             cuda-version: "11.2"
-            cdt-name: cos6
+            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 \
diff --git a/devtools/conda-envs/build-ubuntu-latest.yml b/devtools/conda-envs/build-ubuntu-latest.yml
index 0095bc4..d9431c9 100644
--- a/devtools/conda-envs/build-ubuntu-latest.yml
+++ b/devtools/conda-envs/build-ubuntu-latest.yml
@@ -10,7 +10,6 @@ dependencies:
 - libx11-common-@CDT_NAME@-x86_64
 - libx11-@CDT_NAME@-x86_64
 - mesa-dri-drivers-@CDT_NAME@-x86_64
-- mesa-dri1-drivers-@CDT_NAME@-x86_64
 - mesa-libgl-@CDT_NAME@-x86_64
 - mesa-libgl-devel-@CDT_NAME@-x86_64
 # host

From fd5e2a752e08bfb834c953b0c5a2f3669b8eda6c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Wed, 3 Feb 2021 13:31:33 +0100
Subject: [PATCH 21/22] 11.2 not yet deployed on CF

---
 .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 5587094..9a52df9 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -26,7 +26,7 @@ jobs:
             python-version: "3.6"
             os: ubuntu-latest
             gcc-version: "9"
-            cuda-version: "11.2"
+            cuda-version: "11.0"
             cdt-name: cos7  # CentOS sysroot: cuda 10.x needs cos6, 11+ needs cos7
             CMAKE_FLAGS: |
               -DPLUMED_BUILD_CUDA_LIB=ON \

From beea1b645282172190026d26ef5d019c1ed25b10 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jaime=20Rodr=C3=ADguez-Guerra?=
 <jaimergp@users.noreply.github.com>
Date: Wed, 3 Feb 2021 15:07:50 +0100
Subject: [PATCH 22/22] fix job name

---
 .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 9a52df9..cc25c05 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -22,7 +22,7 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - name: Linux CPU CUDA 10.0 Python 3.6
+          - name: Linux CPU CUDA 11.0 Python 3.6
             python-version: "3.6"
             os: ubuntu-latest
             gcc-version: "9"