Merge pull request #41 from luca-heltai/new-image

.github/workflows/docker.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:          
       - name: Checkout code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v1
@@ -21,7 +21,7 @@ jobs:
           password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Build and push Docker image of master 
-        uses: docker/build-push-action@v2
+        uses: docker/build-push-action@v3
         with:
           context: ./docker/
           file: ./docker/Dockerfile.fsi-suite

.github/workflows/doxygen.yml

@@ -7,7 +7,9 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    container: heltai/dealii:vscode
+    container: 
+      image: heltai/dealii:vscode
+      options: --user root
 
     steps:
     - uses: actions/checkout@v2

.github/workflows/indentation.yml

@@ -1,19 +1,29 @@
 name: Indent
 
-on:
-  push:
-    branches: [ main ]
-  pull_request:
-    branches: [ main ]
+on: [push, pull_request]
+
+concurrency:
+  group: ${ {github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
+permissions:
+  contents: read
 
 jobs:
-  build:
+  indent:
+    # run the indent checks
 
-    runs-on: ubuntu-latest
-    container: heltai/dealii:vscode
+    name: indent
+    runs-on: [ubuntu-20.04]
+    container: 
+      image: heltai/dealii:vscode
+      options: --user root
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 100
     - name: Check indentation
       run: |
-         ./scripts/check_indentation.sh 
+         git config --global --add safe.directory "$GITHUB_WORKSPACE"
+         ./scripts/check_indentation.sh 

.github/workflows/tests.yml

@@ -10,10 +10,12 @@ jobs:
   debug:
 
     runs-on: ubuntu-latest
-    container: heltai/dealii:vscode
+    container: 
+      image: heltai/dealii:vscode
+      options: --user root
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Build debug
       run: |
          rm -rf build_linux_debug
@@ -31,10 +33,12 @@ jobs:
   release:
 
     runs-on: ubuntu-latest
-    container: heltai/dealii:vscode
+    container: 
+      image: heltai/dealii:vscode
+      options: --user root
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Build release
       run: |
           rm -rf build_linux_release

.vscode/settings.json

@@ -107,7 +107,8 @@
         "titleBar.activeBackground": "#dd0531",
         "titleBar.activeForeground": "#e7e7e7",
         "titleBar.inactiveBackground": "#dd053199",
-        "titleBar.inactiveForeground": "#e7e7e799"
+        "titleBar.inactiveForeground": "#e7e7e799",
+        "commandCenter.border": "#e7e7e799"
     },
     "editor.tokenColorCustomizations": {
         "textMateRules": [

docker/Dockerfile

@@ -1,5 +1,5 @@
 # This image is pushed to heltai/dealii:vscode
-FROM dealii/dealii:master-focal
+FROM dealii/dealii:master-jammy
 
 LABEL maintainer="[email protected]"
 
@@ -12,7 +12,6 @@ RUN apt-get update \
     doxygen \
     gdb \
     graphviz \
-    libcgal-dev \
     linux-tools-common \
     linux-tools-generic \
     valgrind \
@@ -21,23 +20,6 @@ RUN apt-get update \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
-RUN mkdir -p /root/.vscode-server/extensions \
-    /root/.vscode-server-insiders/extensions 
-
-ENV OMPI_ALLOW_RUN_AS_ROOT 1
-
-ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM 1
-
-ENV HOME /root
-
-RUN mkdir /root/.ssh
-
-ADD dotgdbinit.py /root/.gdbinit
-
-ADD  build.sh copy_test.sh copy_output.sh d2check.sh cwdiff /usr/bin/
-
-RUN mv /usr/local/bin/clang-format /usr/bin/clang-format
-
 # Now install parmoonlith
 RUN cd /usr/src/ && \
     git clone https://bitbucket.org/zulianp/par_moonolith.git && \
@@ -46,6 +28,29 @@ RUN cd /usr/src/ && \
     cd build && \
     cmake .. -G Ninja \
         -DBUILD_SHARED_LIBS=ON && \
+    sed -i '/#include <vector>/a #include <limits>' _deps/benchmark-src/src/benchmark_register.h &&\
     ninja && \
     ninja install && \
     cd ../ && rm -rf build
+
+RUN mkdir -p /root/.vscode-server/extensions \
+    /root/.vscode-server-insiders/extensions 
+
+ENV OMPI_ALLOW_RUN_AS_ROOT 1
+
+ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM 1
+
+ADD dotgdbinit.py /root/.gdbinit
+
+RUN mv /usr/local/bin/clang-format /usr/bin/clang-format
+
+ADD  	\
+	build.sh \
+	copy_output.sh \
+	copy_test.sh \
+	d2check.sh \
+    cwdiff \
+    newdocentry.sh \
+    work_on_test.sh \
+    /usr/bin/
+

docker/Dockerfile.fsi-suite

@@ -8,4 +8,5 @@ RUN cd /usr/local/src \
     -DCMAKE_BUILD_TYPE=DebugRelease \
     .. \  
     && ninja install \
-    && cd ../ && rm -rf .git build
+    && cd ../ && rm -rf .git build
+

docker/build.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
-docker pull dealii/dealii:master-focal
+docker pull dealii/dealii:master-jammy
 docker build -t heltai/dealii:vscode .
 docker push heltai/dealii:vscode

docker/copy_output.sh

@@ -1,5 +1,10 @@
+#!/bin/bash
+snippetdir=$SNIPPET_DIR
+if [ -z "$snippetdir" ];  then
+        snippetdir=~/c++/snippets/
+fi
 echo copying 
-echo ~/c++/snippets/build/output
+echo `pwd`/output
 echo to 
-echo `cat /workspace/snippets/.dealii_output_file`
-sed  's/^JobId.*//g' ~/c++/snippets/build/output > `cat /workspace/snippets/.dealii_output_file`
+echo `cat $snippetdir/.dealii_output_file`
+sed  's/^JobId.*//g' `pwd`/output > `cat $snippetdir/.dealii_output_file`

docker/copy_test.sh

@@ -1,7 +1,13 @@
+#!/bin/bash
 oldtestrel=$1
 newtestrel=$2
 oldtest="$(cd "$(dirname "$oldtestrel")"; pwd)/$(basename "$oldtestrel")"
 newtest="$(cd "$(dirname "$newtestrel")"; pwd)/$(basename "$newtestrel")"
+snippetdir=$SNIPPET_DIR
+if [ -z "$snippetdir" ];  then 
+	snippetdir=~/c++/snippets/
+fi
+echo Using snippet dir: $snippetdir
 if [ -f $oldtest ]; then 
   extension=""
   for option in "${@:3}"; do
@@ -19,8 +25,8 @@ if [ -f $oldtest ]; then
   touch $output
   git add $newtest
   git add $output
-  echo $output >  /workspace/snippets/.dealii_output_file
-  ln -sf $newtest /workspace/snippets/snippet.cc
+  echo $output > $SNIPPET_DIR/.dealii_output_file
+  ln -sf $newtest $SNIPPET_DIR/snippet.cc
 else
     echo File 
     echo $oldtest 

docker/newdocentry.sh

@@ -0,0 +1,22 @@
+#!/bin/sh
+case $2 in
+major)
+    type=major
+    ;;
+incompatibilities)
+    type=incompatibilities
+    ;;
+*)
+    type=minor
+    ;;
+esac
+
+filename=../doc/news/changes/$type/`date "+%Y%m%d"`LucaHeltai
+
+echo Writing to $filename
+message="$1
+<br>
+(Luca Heltai, `date "+%Y/%m/%d"`)"
+
+echo "$message" > $filename
+git add $filename

docker/work_on_test.sh

@@ -0,0 +1,38 @@
+#!/bin/bash
+newtestrel=$1
+newtest="$(cd "$(dirname "$newtestrel")"; pwd)/$(basename "$newtestrel")"
+snippetdir=$SNIPPET_DIR
+if [ -z "$snippetdir" ];  then
+	snippetdir=~/c++/snippets/
+fi
+echo Using snippet dir: $snippetdir
+if [ -f $newtest ]; then 
+  ln -sf $newtest $snippetdir/snippet.cc
+  echo Linked 
+  echo $newtest 
+  echo to 
+  echo $snippetdir/snippet.cc
+  echo 
+  extension=""
+  for option in "${@:2}"; do
+      if [[ $option == *"mpirun"* ]]; then
+  	extension=$extension.$option
+      else
+  	extension=$extension.with_$option=on
+      fi
+  done
+  output=${newtest/\.cc/$extension.output}
+  if [ -f $output ]; then
+  	echo $output >  $snippetdir/.dealii_output_file
+	echo Stored output name 
+	echo $output 
+	echo in  
+	echo $snippetdir/.dealii_output_file
+  else
+	echo Could not find $output file! Did not store its name anywhere
+  fi
+else
+    echo File 
+    echo $newtest 
+    echo does not exist. Make sure you specify an existing test.
+fi

include/parsed_tools/grid_info.h

@@ -126,7 +126,7 @@ namespace dealii
                  const dealii::Patterns::PatternBase &pattern =
                    *Convert<T>::to_pattern())
         {
-          return dealii::internal::ReferenceCell::make_reference_cell_from_int(
+          return dealii::internal::make_reference_cell_from_int(
             Convert<int>::to_value(s, pattern));
         }
       };
@@ -203,36 +203,36 @@ namespace ParsedTools
           reference_cell_types = tria.get_reference_cells();
 
           std::set<dealii::types::material_id> m_ids;
-          for (const auto cell : tria.active_cell_iterators())
+          for (const auto &cell : tria.active_cell_iterators())
             m_ids.insert(cell->material_id());
           material_ids.insert(material_ids.end(), m_ids.begin(), m_ids.end());
         }
 
       if (info_level > 2)
         {
-          for (const auto id : boundary_ids)
+          for (const auto &id : boundary_ids)
             faces_per_boundary_id[id] = 0;
 
-          for (const auto id : material_ids)
+          for (const auto &id : material_ids)
             cells_per_material_id[id] = 0;
 
-          for (const auto id : manifold_ids)
+          for (const auto &id : manifold_ids)
             {
               faces_per_manifold_id[id] = 0;
               cells_per_manifold_id[id] = 0;
             }
 
-          for (const auto id : reference_cell_types)
+          for (const auto &id : reference_cell_types)
             cells_per_reference_cell_type[id] = 0;
 
-          for (const auto cell : tria.active_cell_iterators())
+          for (const auto &cell : tria.active_cell_iterators())
             {
               ++cells_per_material_id[cell->material_id()];
               ++cells_per_manifold_id[cell->manifold_id()];
               ++cells_per_reference_cell_type[cell->reference_cell()];
             }
 
-          for (const auto f : tria.active_face_iterators())
+          for (const auto &f : tria.active_face_iterators())
             {
               if (f->at_boundary())
                 ++faces_per_boundary_id[f->boundary_id()];

include/parsed_tools/grid_refinement.h

@@ -282,7 +282,7 @@ namespace ParsedTools
           }
       }
     else if (strategy == RefinementStrategy::global)
-      for (const auto cell : tria.active_cell_iterators())
+      for (const auto &cell : tria.active_cell_iterators())
         cell->set_refine_flag();
     else
       Assert(false, dealii::ExcInternalError());
@@ -338,7 +338,7 @@ namespace ParsedTools
       }
     else if (strategy == RefinementStrategy::global)
       {
-        for (const auto cell : tria.active_cell_iterators())
+        for (const auto &cell : tria.active_cell_iterators())
           if (cell->is_locally_owned())
             cell->set_refine_flag();
       }
@@ -354,7 +354,7 @@ namespace ParsedTools
   GridRefinement::limit_levels(dealii::Triangulation<dim, spacedim> &tria) const
   {
     if (min_level != 0 || max_level != 0)
-      for (const auto cell : tria.active_cell_iterators())
+      for (const auto &cell : tria.active_cell_iterators())
         if (cell->is_locally_owned())
           {
             if (min_level != 0 && cell->level() < min_level)