Nektar++ workbook improvements

.gitlab-ci.yml

@@ -455,10 +455,7 @@ win10-mpi-default-build-and-test:
 # correct image version can be grabbed from the container registry.
 .dockerhub_build_template: &dockerhub_build_template
   image: docker:stable
-  only:
-    - master@nektar/nektar
-    - /^docker\/.*$/@nektar/nektar
-    - tags@nektar/nektar
+  <<: *execution-conditions
   script:
     - docker login -u "$CI_REGISTRY_USER" -p "$CI_REGISTRY_PASSWORD" $CI_REGISTRY
     - IMAGE=$CI_REGISTRY_IMAGE/${image_name}
@@ -473,11 +470,8 @@ win10-mpi-default-build-and-test:
 # registry on a particular SHA commit.
 .dockerhub-test-template: &dockerhub_test_template
   image: ${CI_REGISTRY_IMAGE}/${image_name}:$CI_COMMIT_SHORT_SHA
+  <<: *execution-conditions
   stage: package-test
-  only:
-    - master@nektar/nektar
-    - /^docker\/.*$/@nektar/nektar
-    - tags@nektar/nektar
 
 # Docker Hub deployment template. Only builds for master or tags on the main
 # Nektar repository. The strategy is to login to the container registry and pull
@@ -510,6 +504,7 @@ win10-mpi-default-build-and-test:
 dockerhub-build-env:
   <<: *dockerhub_build_template
   stage: package-env
+  needs: []
   variables:
     image_name: nektar-env
     dockerfile: docker/nektar-env/Dockerfile
@@ -560,7 +555,7 @@ dockerhub-test-nektar-dev:
     image_name: nektar-dev
   script:
     - cd $CI_PROJECT_DIR/templates/executable
-    - ./test.sh /usr/local/lib64/nektar++/cmake 3
+    - ./test.sh /usr/local/lib64/nektar++/cmake 3 /usr/bin/cmake
 
 # Deployment
 dockerhub-deploy-nektar:

CHANGELOG.md

 Changelog
 =========
 
+v5.1.1
+------
+**Python**
+- Updates to workbook, fix bugs in StdExpansion and SessionReader with MPI communication
+  being recreated. (!1296)
+
 v5.1.0
 ------
 **Library**

docker/nektar-workbook/Dockerfile

-FROM jupyter/scipy-notebook:42f4c82a07ff AS build
+FROM jupyter/scipy-notebook:hub-1.4.2 AS build
 
 LABEL maintainer="Nektar++ Development Team <nektar-users@imperial.ac.uk>"
 
 USER root
 RUN apt-get update && \
-    apt-get install -y libgl1-mesa-dev xvfb && \
+    apt-get install -y libgl1-mesa-dev xvfb openssh-client build-essential && \
     rm -rf /var/lib/apt/lists/*
 
 USER $NB_UID
-RUN conda install --quiet --yes cmake=3.19.1 boost=1.74.0 occt=7.4.0 gmsh=4.6.0 pyvista=0.27.2 itkwidgets=0.32.0 arpack=3.7.0 fftw=3.3.8 tinyxml jupyter_contrib_nbextensions && \
+RUN conda install --quiet --yes jupyterlab=2.3.1 cmake=3.19.1 boost=1.74.0 occt=7.4.0 gmsh=4.6.0 pyvista=0.31.3 \
+        arpack=3.7.0 fftw=3.3.8 scotch=6.0.9 openmpi=4.1.0 tinyxml=2.6.2 jupyter_contrib_nbextensions=0.5.1 \
+        ptscotch=6.0.9 hdf5=1.10.6=mpi_openmpi* && \
+    pip install --no-cache-dir nbgitpuller itkwidgets && \
     jupyter contrib nbextension install --sys-prefix && \
     jupyter nbextension enable --sys-prefix hide_input/main && \
     jupyter nbextension enable --sys-prefix hide_input_all/main && \
     jupyter nbextension enable --sys-prefix init_cell/main && \
-    jupyter nbextension enable --sys-prefix equation-numbering/main
+    jupyter nbextension enable --sys-prefix equation-numbering/main && \
+    jupyter labextension install @jupyter-widgets/jupyterlab-manager jupyter-matplotlib jupyterlab-datawidgets itkwidgets @jupyterlab/toc && \
+    conda clean --all -f -y && \
+    jupyter lab clean && \
+    rm -rf "/home/${NB_USER}/.cache/yarn" && \
+    fix-permissions "${CONDA_DIR}" && \
+    fix-permissions "/home/${NB_USER}"
 
 USER root
 COPY . /tmp/nektar
@@ -24,11 +33,17 @@ RUN cd /tmp/nektar && mkdir build && cd build && \
           -DNEKTAR_BUILD_UTILITIES=ON -DNEKTAR_BUILD_PYTHON=ON \
           -DNEKTAR_SOLVER_VORTEXWAVE=OFF -DNEKTAR_LIB_DIR=lib/x86_64-linux-gnu \
           -DNEKTAR_BUILD_TESTS=OFF -DNEKTAR_BUILD_UNIT_TESTS=OFF \
-          -DNEKTAR_BUILD_DEMOS=OFF -DNEKTAR_USE_SCOTCH=OFF -DNEKTAR_USE_MESHGEN=ON \
+          -DNEKTAR_BUILD_DEMOS=OFF -DNEKTAR_USE_SCOTCH=ON -DNEKTAR_USE_MESHGEN=ON \
           -DNEKTAR_USE_ARPACK=ON -DNEKTAR_USE_FFTW=ON \
-          -DCMAKE_INSTALL_PREFIX=/usr/local .. && \
+          -DNEKTAR_USE_MPI=ON -DNEKTAR_USE_HDF5=ON \
+          -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release .. && \
     make -j$(nproc) install && \
     chown -R $NB_UID:$NB_UID /tmp/nektar && \
     cd /tmp/nektar/build && sudo -u $NB_USER make nekpy-install-system && cd && ldconfig && rm -R /tmp/nektar
 
-USER $NB_UID
+USER root
+COPY docker/nektar-workbook/entrypoint.sh /
+RUN chmod +x /entrypoint.sh
+
+USER $NB_USER
+ENTRYPOINT ["/entrypoint.sh"]

docker/nektar-workbook/entrypoint.sh

+#!/bin/bash
+export DISPLAY=:99.0
+which Xvfb
+Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
+sleep 3
+exec "$@"

library/LibUtilities/Python/BasicUtils/SessionReader.cpp

@@ -37,6 +37,11 @@
 
 using namespace Nektar::LibUtilities;
 
+#ifdef NEKTAR_USE_MPI
+#include <LibUtilities/Communication/CommMpi.h>
+CommSharedPtr MPICOMM = CommSharedPtr();
+#endif
+
 /**
  * @brief Thin wrapper around SessionReader to provide a nicer Pythonic
  * interface.
@@ -75,8 +80,30 @@ SessionReaderSharedPtr SessionReader_CreateInstance(py::list &ns)
     // segfault.
     argv[argc] = NULL;
 
+#ifdef NEKTAR_USE_MPI
+    // In the case we're using MPI, it may already have been initialised. So to
+    // handle this, we'll construct our own CommMpi object and pass through to
+    // the SessionReader. This will persist indefinitely, or at least until the
+    // library is unloaded by Python.
+
+    if (!MPICOMM)
+    {
+        MPICOMM = GetCommFactory().CreateInstance("ParallelMPI", argc, argv);
+    }
+
+    std::vector<std::string> filenames(argc-1);
+    for (i = 1; i < argc; ++i)
+    {
+        filenames[i-1] = std::string(argv[i]);
+    }
+
+    // Create session reader.
+    SessionReaderSharedPtr sr = SessionReader::CreateInstance(
+        argc, argv, filenames, MPICOMM);
+#else
     // Create session reader.
     SessionReaderSharedPtr sr = SessionReader::CreateInstance(argc, argv);
+#endif
 
     // Clean up.
     delete [] argv;

library/StdRegions/Python/StdExpansion.cpp

@@ -61,7 +61,7 @@ Array<OneD, NekDouble> StdExpansion_IProductWRTBase(
     const Array<OneD, const NekDouble> &in)
 {
     Array<OneD, NekDouble> out(exp->GetNcoeffs());
-    exp->BwdTrans(in, out);
+    exp->IProductWRTBase(in, out);
     return out;
 }
 

templates/executable/test.sh

@@ -2,6 +2,14 @@
 
 set -e
 
+if [ "$#" -ne 3 ]; then
+    echo "Usage: test.sh /path/to/nektar++/cmake/dir ncpus /usr/bin/cmake"
+    echo ""
+    echo "Given a path to the Nektar++ CMake files, this script compiles and runs a simulation"
+    echo "using ncpus, using the CMake executable given in the third parameter."
+    exit 1
+fi
+
 # Create a build directory and compile against Nektar++
 rm -rf build && mkdir build && cd build
 $3 -DNektar++_DIR=$1 ..