diff --git a/.github/workflows/cpu-tests.yml b/.github/workflows/cpu-tests.yml index 48f0a456c..48dc91a34 100644 --- a/.github/workflows/cpu-tests.yml +++ b/.github/workflows/cpu-tests.yml @@ -35,6 +35,8 @@ jobs: steps: - name: Check out repository uses: actions/checkout@v4 + with: + fetch-depth: '1' - name: Set environment variables run: | @@ -62,7 +64,7 @@ jobs: fi - name: Pull latest image from container registry - run: docker pull $IMAGE_REPO/$IMAGE_NAME || true + run: docker pull $IMAGE_REPO/$IMAGE_NAME --quiet || true - name: Build temporary Docker image run: | @@ -131,12 +133,12 @@ jobs: - name: "Prepare environment: Load Docker image from cache" if: env.DOCKER_TAG != 'latest' - run: docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz + run: docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz --quiet - name: "Prepare environment: Pull latest image from container registry" if: env.DOCKER_TAG == 'latest' run: | - docker pull $IMAGE_REPO/$IMAGE_NAME:latest + docker pull $IMAGE_REPO/$IMAGE_NAME:latest --quiet docker image tag $IMAGE_REPO/$IMAGE_NAME:latest $IMAGE_NAME:latest - name: "Prepare environment: Run Docker container" @@ -155,6 +157,8 @@ jobs: - name: Check out repository (mala) uses: actions/checkout@v4 + with: + fetch-depth: '1' - name: Install mala package # Exec all commands inside the mala-cpu container @@ -174,7 +178,13 @@ jobs: # if comparison fails, `install/mala_cpu_[base]_environment.yml` needs to be aligned with # `requirements.txt` and/or extra dependencies are missing in the Docker Conda environment - diff --side-by-side --color=always env_before.yml env_after.yml + + if diff --brief env_before.yml env_after.yml + then + echo "Files env_before.yml and env_after.yml do not differ." + else + diff --side-by-side --color-always env_before.yml env_after.yml + fi - name: Download test data repository from RODARE shell: 'bash -c "docker exec -i mala-cpu python < {0}"' @@ -229,9 +239,6 @@ jobs: ((contains(github.ref_name, 'develop') || contains(github.ref_name, 'master')) && needs.build-docker-image-cpu.outputs.docker-tag != 'latest') || startsWith(github.ref, 'refs/tags/') steps: - - name: Check out repository - uses: actions/checkout@v4 - - name: "Prepare environment: Restore cache" if: env.DOCKER_TAG != 'latest' uses: actions/cache@v4 @@ -242,21 +249,19 @@ jobs: - name: "Prepare environment: Load Docker image from cache" if: env.DOCKER_TAG != 'latest' - run: docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz + run: docker load -i $DOCKER_CACHE_PATH/docker-image.tar.gz --quiet - name: "Prepare environment: Pull latest image from container registry" if: env.DOCKER_TAG == 'latest' - run: docker pull $IMAGE_REPO/$IMAGE_NAME:latest + run: docker pull $IMAGE_REPO/$IMAGE_NAME:latest --quiet - name: Tag Docker image run: | # Execute on change of Docker image if [[ "$DOCKER_TAG" != 'latest' ]]; then - GIT_SHA=${GITHUB_REF_NAME}-$(git rev-parse --short "$GITHUB_SHA") - echo "GIT_SHA=$GIT_SHA" docker tag $IMAGE_NAME:$GITHUB_RUN_ID $IMAGE_REPO/$IMAGE_NAME:latest - docker tag $IMAGE_NAME:$GITHUB_RUN_ID $IMAGE_REPO/$IMAGE_NAME:$GIT_SHA + docker tag $IMAGE_NAME:$GITHUB_RUN_ID $IMAGE_REPO/$IMAGE_NAME:${GITHUB_REF_NAME}-${GITHUB_SHA:0:7} fi # Execute on push of git tag @@ -272,4 +277,4 @@ jobs: run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login ghcr.io -u ${{ github.actor }} --password-stdin - name: Push Docker image - run: docker push $IMAGE_REPO/$IMAGE_NAME --all-tags + run: docker push $IMAGE_REPO/$IMAGE_NAME --all-tags | grep -v -E 'Waiting|Layer already|Preparing|Pushed' diff --git a/docs/source/advanced_usage/predictions.rst b/docs/source/advanced_usage/predictions.rst index 7058f17de..20e82494b 100644 --- a/docs/source/advanced_usage/predictions.rst +++ b/docs/source/advanced_usage/predictions.rst @@ -40,6 +40,8 @@ Likewise, you can adjust the inference temperature via calculator.data_handler.target_calculator.temperature = ... +.. _production_gpu: + Predictions on GPU ******************* @@ -137,4 +139,3 @@ With the exception of the electronic density, which is saved into the ``.cube`` format for visualization with regular electronic structure visualization software, all of these observables can be plotted with Python based visualization libraries such as ``matplotlib``. - diff --git a/docs/source/install/installing_lammps.rst b/docs/source/install/installing_lammps.rst index 50fb41cef..28affb950 100644 --- a/docs/source/install/installing_lammps.rst +++ b/docs/source/install/installing_lammps.rst @@ -41,18 +41,24 @@ The MALA team recommends to build LAMMPS with ``cmake``. To do so * ``Kokkos_ARCH_GPUARCH=???``: Your GPU architecture (see see `Kokkos instructions `_) * ``CMAKE_CXX_COMPILER=???``: Path to the ``nvcc_wrapper`` executable shipped with the LAMMPS code, should be at ``/your/path/to/lammps/lib/kokkos/bin/nvcc_wrapper`` -* For example, this configures the LAMMPS cmake build with Kokkos support - for an Intel Haswell CPU and an Nvidia Volta GPU, with MPI support: + + For example, this configures the LAMMPS cmake build with Kokkos support + for an Intel Haswell CPU and an Nvidia Volta GPU, with MPI support: .. code-block:: bash cmake ../cmake -D PKG_KOKKOS=yes -D BUILD_MPI=yes -D PKG_ML-SNAP=yes -D Kokkos_ENABLE_CUDA=yes -D Kokkos_ARCH_HSW=yes -D Kokkos_ARCH_VOLTA70=yes -D CMAKE_CXX_COMPILER=/path/to/lammps/lib/kokkos/bin/nvcc_wrapper -D BUILD_SHARED_LIBS=yes + .. note:: + When using a GPU by setting ``parameters.use_gpu = True``, you *need* to + have a GPU version of ``LAMMPS`` installed. See :ref:`production_gpu` for + details. * Build the library and executable with ``cmake --build .`` (Add ``--parallel=8`` for a faster build) + Installing the Python extension ******************************** diff --git a/docs/source/install/installing_qe.rst b/docs/source/install/installing_qe.rst index 3b426ba48..9ff514c7a 100644 --- a/docs/source/install/installing_qe.rst +++ b/docs/source/install/installing_qe.rst @@ -4,24 +4,25 @@ Installing Quantum ESPRESSO (total energy module) Prerequisites ************* -To run the total energy module, you need a full Quantum ESPRESSO installation, -for which to install the Python bindings. This module has been tested with -version ``7.2.``, the most recent version at the time of this release of MALA. -Newer versions may work (untested), but installation instructions may vary. +To build and run the total energy module, you need a full Quantum ESPRESSO +installation, for which to install the Python bindings. This module has been +tested with version ``7.2.``, the most recent version at the time of this +release of MALA. Newer versions may work (untested), but installation +instructions may vary. Make sure you have an (MPI-aware) F90 compiler such as ``mpif90`` (e.g. Debian-ish machine: ``apt install openmpi-bin``, on an HPC cluster something like ``module load openmpi gcc``). Make sure to use the same compiler for QE and the extension. This should be the default case, but if problems arise you can manually select the compiler via -``--f90exec=`` in ``build_total_energy_energy_module.sh`` +``--f90exec=`` in ``build_total_energy_module.sh`` We assume that QE's ``configure`` script will find your system libs, e.g. use ``-lblas``, ``-llapack`` and ``-lfftw3``. We use those by default in -``build_total_energy_energy_module.sh``. If you have, say, the MKL library, +``build_total_energy_module.sh``. If you have, say, the MKL library, you may see ``configure`` use something like ``-lmkl_intel_lp64 -lmkl_sequential -lmkl_core`` when building QE. In this case you have to modify -``build_total_energy_energy_module.sh`` to use the same libraries! +``build_total_energy_module.sh`` to use the same libraries! Build Quantum ESPRESSO ********************** @@ -35,10 +36,16 @@ Build Quantum ESPRESSO * Change to the ``external_modules/total_energy_module`` directory of the MALA repository +.. note:: + At the moment, building QE using ``cmake`` `doesn't work together with the + build_total_energy_module.sh script + `_. Please use the + ``configure`` + ``make`` build workflow. + Installing the Python extension ******************************** -* Run ``build_total_energy_energy_module.sh /path/to/your/q-e``. +* Run ``build_total_energy_module.sh /path/to/your/q-e``. * If the build is successful, a file named something like ``total_energy.cpython-39m-x86_64-linux-gnu.so`` will be generated. This is