Merge branch 'develop' into feature_uncertainty

.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'

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``.
-

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 <https://docs.lammps.org/Build_extras.html#kokkos-package>`_)
       * ``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
 ********************************
 

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
+   <https://github.com/mala-project/mala/issues/468>`_. 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