Merge branch 'master' into 6.0

.github/workflows/build_arch_docker_testing.yml.old

@@ -0,0 +1,18 @@
+name: Arch PASO unit testing
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: [self-hosted, linux, x64, meerkat]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Building the Docker image...
+      run: docker build . --file ./tools/unittesting/arch_py3 --tag esys-escript:$(date +%s)

.github/workflows/build_arch_trilinos_docker_testing.yml.old

@@ -0,0 +1,18 @@
+name: Arch Trilinos unit testing
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: [self-hosted, linux, x64, meerkat]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Building the Docker image...
+      run: docker build . --file ./tools/unittesting/arch_trilinos_py3 --tag esys-escript:$(date +%s)

.github/workflows/build_binder_image.yml

@@ -0,0 +1,38 @@
+name: Build Binder Image
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      -
+        name: Checkout code
+        uses: actions/checkout@v3
+      -
+        name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+      -
+        name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+      -
+        name: Build dockerfile
+        uses: docker/build-push-action@v3
+        with:
+          context: .
+          file: ./binder/DockerfileMain
+          platforms: linux/amd64
+          tags: ${{ secrets.DOCKERHUB_USERNAME }}/esys.escript.binder
+          push: true
+

.github/workflows/build_debian_docker_testing.yml.old

@@ -1,8 +1,8 @@
-name: Debian unit testing
+name: Debian PASO unit testing
 
 on:
   push:
-    branches: [ master, 6.0 ]
+    branches: [ master ]
   pull_request:
     branches: [ master ]
 
@@ -15,4 +15,5 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Building the Docker image...
-      run: docker build . --file ./tools/unittesting/debian_trilinos_py3
+      run: docker build . --file ./tools/unittesting/debian_py3 --tag esys-escript:$(date +%s)
+

.github/workflows/build_debian_trilinos_docker_hyb_testing.yml.old

@@ -15,4 +15,5 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Building the Docker image...
-      run: docker build . --file ./tools/unittesting/debian_trilinos_hyb_py3
+      run: docker build . --file ./tools/unittesting/debian_trilinos_hyb_py3 --tag esys-escript:$(date +%s)
+

.github/workflows/build_debian_trilinos_docker_testing.yml.old

@@ -15,4 +15,4 @@ jobs:
     steps:
     - uses: actions/checkout@v2
     - name: Building the Docker image...
-      run: docker build . --file ./tools/unittesting/debian_trilinos_py3
+      run: docker build . --file ./tools/unittesting/debian_trilinos_py3 --tag esys-escript:$(date +%s)

.github/workflows/build_docker_image.yml.old

@@ -0,0 +1,18 @@
+name: Build Docker Image
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Building the Docker image...
+      run: docker build . --file ./tools/docker/docker_trilinos --tag esys-escript:$(date +%s)

.github/workflows/build_flatpak.yml.old

@@ -0,0 +1,26 @@
+name: Build Flatpak
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+
+    - name: Installing dependencies
+      run: sudo apt-get install -y flatpak-builder
+
+    - name: Adding flatpak repo
+      run: sudo flatpak remote-add --if-not-exists flathub https://flathub.org/repo/flathub.flatpakrepo
+
+    - name: Installing freedesktop platform and sdk
+      run: sudo flatpak install -y flathub org.freedesktop.Platform//18.08 org.freedesktop.Sdk//18.08
+
+    - name: Building the flatpak...
+      run: sudo flatpak-builder ./build ./tools/flatpak/au.edu.uq.esys.escript.json

.github/workflows/build_nectarcloud.yml

@@ -2,9 +2,9 @@ name: Unit testing
 
 on:
   push:
-    branches: [ master, 6.0 ]
+    branches: [ master ]
   pull_request:
-    branches: [ master, 6.0 ]
+    branches: [ master ]
 
 jobs:
   build:
@@ -15,6 +15,6 @@ jobs:
       - name: Compile
         run: scons -j1 options_file=scons/nectar_options.py werror=0 verbose=0 build_full
       - name: Run testing
-        run: export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH; ./utest.sh `pwd`/build '-t2' > utestout
+        run: export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH; ./utest.sh `pwd`/build '-t2' > testout
 
 

.github/workflows/build_opensuse_docker_testing.yml.old

@@ -0,0 +1,18 @@
+name: openSUSE PASO unit testing
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: [self-hosted, linux, x64, meerkat]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Building the Docker image...
+      run: docker build . --file ./tools/unittesting/opensuse_py3 --tag esys-escript:$(date +%s)

.github/workflows/build_opensuse_trilinos_docker_testing.yml.old

@@ -0,0 +1,18 @@
+name: openSUSE Trilinos unit testing
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: [self-hosted, linux, x64, meerkat]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Building the Docker image...
+      run: docker build . --file ./tools/unittesting/opensuse_trilinos_py3 --tag esys-escript:$(date +%s)

.github/workflows/build_ubuntu_docker_testing.yml.old

@@ -0,0 +1,18 @@
+name: Ubuntu unit testing
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+
+  build:
+
+    runs-on: [self-hosted, linux, x64, meerkat]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Building the Docker image...
+      run: docker build . --file ./tools/unittesting/ubuntu_py3 --tag esys-escript:$(date +%s)

README.md

@@ -31,7 +31,7 @@ Further documentation including examples and a user guide for the latest release
 https://esys-escript.github.io/
 
 ## The project is funded by the
-   - [AuScope National Collaborative Research Infrastructure Strategy (NCRIS)](https://www.auscope.org.au/) (until mid of 2022),
+   - [AuScope National Collaborative Research Infrastructure Strategy (NCRIS)](https://www.auscope.org.au/) (until mid of 2023),
    - Australian Geophysical Observing System (AGOS) (ended 2014),
    - [The University of Queensland](https://www.uq.edu.au)
 
@@ -67,6 +67,10 @@ For information on a specific Linux distrobution, please consult the install gui
 To get started using escript please consult the user guide (user.pdf) and the (cookbook.pdf) cookbook. 
 All of these documents are available here and at https://esys-escript.github.io/
 
+Click on this button to try out escript in your web browser:
+
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/esys-escript/esys-escript.github.io/HEAD)
+
 ## Questions & Bugs 
 
 To raise a question or to report a bug please start a [github issue](https://github.com/esys-escript/esys-escript.github.io/issues).

SConstruct

@@ -70,6 +70,7 @@ build_trilinos_flavours = ( "check",      # check for unsuccessful make before s
                             "always",    # always build
                             "never", "False"  # never build
                             )
+
 #Note that scons construction vars the the following purposes:
 #  CPPFLAGS -> to the preprocessor
 #  CCFLAGS  -> flags for _both_ C and C++
@@ -441,7 +442,7 @@ elif cxx_name == 'mpic++':
     cc_debug     = "-g3 -O0  -DDOASSERT -DDOPROF -DBOUNDS_CHECK -DSLOWSHARECHECK --param=max-vartrack-size=100000000"
     #Removed because new netcdf doesn't seem to like it
     #cc_debug += ' -D_GLIBCXX_DEBUG  '
-    ld_extra += " -fPIC -lmpi "
+    ld_extra = " -fPIC -lmpi "
     if env['openmp']:
       ld_extra += " -lgomp"
     omp_flags    = "-fopenmp"

binder/Dockerfile

@@ -0,0 +1,24 @@
+FROM aellery/esys.escript.binder
+
+LABEL maintainer="[email protected]"
+
+# set up the user
+ARG NB_USER=jovyan
+ARG NB_UID=1000
+ENV USER ${NB_USER}
+ENV NB_UID ${NB_UID}
+ENV HOME /home/${NB_USER}
+
+RUN adduser --disabled-password \
+    --gecos "Default user" \
+    --uid ${NB_UID} \
+    ${NB_USER}
+
+COPY . ${HOME}
+USER root
+RUN chown -R ${NB_UID} ${HOME}
+USER ${NB_USER}
+
+ENV PYTHONPATH=/usr/
+
+CMD ["/bin/bash"]

binder/DockerfileMain

@@ -0,0 +1,22 @@
+FROM aellery/esys.escript.trilinos.nompi
+
+LABEL maintainer="[email protected]"
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# install escript
+WORKDIR /home/
+RUN git clone https://github.com/esys-escript/esys-escript.github.io --depth 1 .
+RUN scons openmp=1 \
+      pythoncmd=`which python3` \
+      pythonlibpath=/usr/lib/x86_64-linux-gnu/ \
+      pythonincpath=/usr/include/python3.9/ \
+      pythonlibname=python3.9 \
+      boost_libs=boost_python39 werror=0 \
+      paso=0 trilinos=1 trilinos_prefix=/usr/ build_full -j`nproc` \
+      prefix=/usr/ || cat config.log
+RUN rm -rf *
+
+WORKDIR /tmp
+
+CMD ["/bin/bash"]

docs/index.html

@@ -8,11 +8,18 @@
 
 <body>
 
-<h1> esys-escript </h1>
+<!-- <h1> esys-escript </h1> -->
+
+<center><img src="./au.edu.uq.esys.escript.png" alt="escript_logo" title="esys-escript"></center>
 
 <p>esys-escript is a programming tool for implementing mathematical models in python using the finite element method (FEM). As users do not access the data structures it is very easy to use and scripts can run on desktop computers as well as highly parallel supercomputer without changes. Application areas for escript include earth mantle convection, geophysical inversion, earthquakes, porous media flow, reactive transport, plate subduction, erosion, and tsunamis.</p>
 
-<center><img src="./au.edu.uq.esys.escript.png" alt="escript_logo" title="esys-escript logo"></center>
+<p></p>
+<p>
+Click on the Jupyter logo to try esys-escript online in a Jupyter Notebook. Choose your own username and password when you login.
+</p>
+
+<p><a href="http://203.101.225.133/hub/user-redirect/git-pull?repo=https%3A%2F%2Fgithub.com%2FAndreaCodd%2Feenotes&urlpath=tree%2Feenotes%2F&branch=main"><center><img src="./jupyter.png" alt="Jupyter_logo" title="Jupyter logo" width="200"></center></a></p>
 
 <p>esys-escript is designed as an easy-to-use environment for implementing mathematical models based on non-linear, coupled, time-dependent partial differential equations. It uses the finite element method (FEM) for spatial discretization and data representation. Escript is used through python and is suitable for rapid prototyping (e.g for a student project or thesis) as well as for large software projects. Scripts are executed in parallel using MPI, OpenMP and hybrid mode processing over 50 million unknowns on several thousand cores on a parallel computer.</p>
 
@@ -38,12 +45,13 @@ <h3>Main Features:</h3>
 
 <center>git clone https://github.com/esys-escript/esys-escript.github.io.git</center>
 
-<p>Please consult the <a href="https://github.com/esys-escript/esys-escript.github.io/raw/master/install.pdf">installation guide</a> as well as the other documentation.</a></p>
+<p>Please consult the <a href="https://github.com/esys-escript/esys-escript.github.io/raw/master/install.pdf">installation guide</a> and the <a href="https://github.com/esys-escript/esys-escript.github.io/raw/master/user.pdf">user guide</a> as well as the <a href="https://github.com/esys-escript/esys-escript.github.io/raw/master/docs.zip">other documentation</a>.</p>
+
 
 <h3>The project is funded by:</h3>
 
 <ul>
-<li>AuScope National Collaborative Research Infrastructure Strategy (NCRIS) (until end of 2019)</li>
+<li>AuScope National Collaborative Research Infrastructure Strategy (NCRIS) (until end of 2023)</li>
 <li>Australian Geophysical Observing System (AGOS) (ended 2014).</li>
 <li>School of Earth Sciences at the University of Queensland.</li>
 </ul>
@@ -92,3 +100,16 @@ <h3>The project is funded by:</h3>
         Ken Steube
 
 </body>
+
+
+<!-- <p><a href="https://www.uq.edu.au/"><center><img src="./UQ-logo.jpg" alt="UQ_logo" title="UQ logo"></center></a></p>
+ -->
+<div class="row">
+        <div class="column">
+                <p><a href="https://www.auscope.org.au/"><center><img src="./auscope.png" alt="Auscope_logo" title="Auscope logo" width=50%></center></a></p>
+        </div>
+
+        <!-- <div class="column">
+                <p><a href="https://www.uq.edu.au/"><center><img src="./UQ-logo.jpg" alt="UQ_logo" title="UQ logo" width=50%></center></a></p>
+        </div> -->
+</div>

docs/style.css

@@ -11,3 +11,14 @@ h1 {
 	text-align:center;
 }
 
+
+.row {
+  display: flex;
+  align-items: center;
+}
+
+.column {
+  flex: 50.00%;
+  padding: 5px;
+  align-items: center;
+}

escriptcore/src/Utils.cpp

@@ -1005,8 +1005,8 @@ boost::python::numpy::ndarray convertToNumpy(escript::Data data)
     bp::numpy::ndarray dataArray = bp::numpy::zeros(arrayshape, datatype);
 
     // Initialise variables
-    const DataTypes::cplx_t* samplesC;
-    const DataTypes::real_t* samplesR;
+    const DataTypes::cplx_t* samplesC=nullptr;
+    const DataTypes::real_t* samplesR=nullptr;
 
     // This is needed below in getSampleDataRO
     const DataTypes::cplx_t onlycomplex=(0);