Merge pull request #20 from prashjha/remove_hpx

Removed HPX and Boost dependencies and added mesh partitioning and MPI and Multithreading parallelism

.circleci/Docker/Dockerfile-bionic

@@ -5,25 +5,48 @@
 # Distributed under the Boost Software License, Version 1.0. (See accompanying
 # file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
 
-# base ubuntu image with petsc, libmesh, hpx
+# base ubuntu image with essentials and vtk
 FROM prashjha/peridem-base-bionic:latest
 
 # Set metadata
 LABEL maintainer="Prashant K. Jha <[email protected]>"
 LABEL description="PeriDEM docker image"
 
-WORKDIR /
+## build command
+## docker build -t prashjha/peridem-bionic:latest -f ./Dockerfile-bionic . 2>&1 | tee log-peridem-bionic.txt
 
-RUN git clone  https://github.com/prashjha/PeriDEM.git
+# -----------------------
+# setup user (for mpi tests)
+# username - user
+# password - password
+# add only if the user does not exist
+# -----------------------
+RUN if id user >/dev/null 2>&1; then echo "User 'user' already exists"; else echo "User 'user' does not exist so creating user 'user'" && useradd -m user && yes password | passwd user && usermod -s /bin/bash user; fi
 
-RUN cd /PeriDEM && \
-		mkdir build && \
-		cd build && \
-		cmake -DHPX_IGNORE_COMPILER_COMPATIBILITY=ON \
-					-DCMAKE_BUILD_TYPE=Release \
-					-DEnable_Tests=ON \
-					-DHPX_DIR=${HPX_DIR}/lib/cmake/HPX \
-					.. && \
-		make -j 2 && \
-		make install
+# change user
+USER user
+WORKDIR /home/user
+
+# -----------------------
+# setup git pull method
+# -----------------------
+RUN git config --global url."https://github.com/".insteadOf [email protected]: && \
+    git config --global url."https://".insteadOf git://
+
+# -----------------------
+# build peridem
+# -----------------------
+RUN git clone https://github.com/prashjha/PeriDEM.git &&\
+    cd PeriDEM &&\
+    git submodule update --init --recursive && \
+    mkdir -p build && \
+    cd build && \
+    cmake -DCMAKE_BUILD_TYPE=Release \
+          -DEnable_Tests=ON \
+          -DDisable_Docker_MPI_Tests=OFF \
+          -DVTK_DIR=/usr/local/lib/cmake/vtk-9.3 \
+          -DMETIS_DIR=/usr/lib \
+          .. && \
+    make -j 2 && \
+    make install
 

.circleci/Docker/Dockerfile-focal

@@ -5,25 +5,48 @@
 # Distributed under the Boost Software License, Version 1.0. (See accompanying
 # file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
 
-# base ubuntu image with petsc, libmesh, hpx
+# base ubuntu image with essentials and vtk
 FROM prashjha/peridem-base-focal:latest
 
 # Set metadata
 LABEL maintainer="Prashant K. Jha <[email protected]>"
 LABEL description="PeriDEM docker image"
 
-WORKDIR /
+## build command
+## docker build -t prashjha/peridem-focal:latest -f ./Dockerfile-focal . 2>&1 | tee log-peridem-focal.txt
 
-RUN git clone  https://github.com/prashjha/PeriDEM.git
+# -----------------------
+# setup user (for mpi tests)
+# username - user
+# password - password
+# add only if the user does not exist
+# -----------------------
+RUN if id user >/dev/null 2>&1; then echo "User 'user' already exists"; else echo "User 'user' does not exist so creating user 'user'" && useradd -m user && yes password | passwd user && usermod -s /bin/bash user; fi
 
-RUN cd /PeriDEM && \
-		mkdir build && \
-		cd build && \
-		cmake -DHPX_IGNORE_COMPILER_COMPATIBILITY=ON \
-					-DCMAKE_BUILD_TYPE=Release \
-					-DEnable_Tests=ON \
-					-DHPX_DIR=${HPX_DIR}/lib/cmake/HPX \
-					.. && \
-		make -j 2 && \
-		make install
+# change user
+USER user
+WORKDIR /home/user
+
+# -----------------------
+# setup git pull method
+# -----------------------
+RUN git config --global url."https://github.com/".insteadOf [email protected]: && \
+    git config --global url."https://".insteadOf git://
+
+# -----------------------
+# build peridem
+# -----------------------
+RUN git clone https://github.com/prashjha/PeriDEM.git &&\
+    cd PeriDEM &&\
+    git submodule update --init --recursive && \
+    mkdir -p build && \
+    cd build && \
+    cmake -DCMAKE_BUILD_TYPE=Release \
+          -DEnable_Tests=ON \
+          -DDisable_Docker_MPI_Tests=OFF \
+          -DVTK_DIR=/usr/local/lib/cmake/vtk-9.3 \
+          -DMETIS_DIR=/usr/lib \
+          .. && \
+    make -j 2 && \
+    make install
 

.circleci/config.yml

@@ -9,14 +9,23 @@ version: 2.1
 parameters:
   docker-img-os:
     type: string
-    default: bionic
-
+    default: focal
+  cmake-include-dirs:
+    type: string
+    default: -DVTK_DIR=/usr/local/lib/cmake/vtk-9.3 -DMETIS_DIR=/usr/lib
+
 commands:
+  postcheckout:
+    steps:
+      - run:
+          name: "Pull submodules"
+          command: |
+            git submodule update --init --recursive
   libcmake:
     parameters:
       cmake-args:
         type: string
-        default: -DCMAKE_BUILD_TYPE=Release -DEnable_Tests=ON -DHPX_DIR=${HPX_DIR}/lib/cmake/HPX
+        default: -DCMAKE_BUILD_TYPE=Release -DEnable_Tests=ON -DEnable_Documentation=OFF -DDisable_Docker_MPI_Tests=OFF <<pipeline.parameters.cmake-include-dirs>>
     steps:
       - run: 
           name: Configure
@@ -35,7 +44,7 @@ commands:
     parameters:
       verb-flag:
         type: string
-        default: --verbose
+        default: --extra-verbose
     steps:
       - run: 
           name: Test
@@ -54,18 +63,22 @@ jobs:
     build:
         docker:
           - image: prashjha/peridem-base-<<pipeline.parameters.docker-img-os>>:latest
+            user: user
         steps:
-            - checkout
-            - libcmake
-            - libmake
-            - libtest
+          - checkout
+          - postcheckout
+          - libcmake
+          - libmake
+          - libtest
     documentation:
       docker:
         - image: prashjha/peridem-base-<<pipeline.parameters.docker-img-os>>:latest
+          user: user
       steps:
         - checkout
+        - postcheckout
         - libcmake:
-            cmake-args: -DCMAKE_BUILD_TYPE=Release -DEnable_Documentation=ON -DHPX_DIR=${HPX_DIR}/lib/cmake/HPX
+            cmake-args: -DCMAKE_BUILD_TYPE=Release -DEnable_Tests=ON -DEnable_Documentation=ON <<pipeline.parameters.cmake-include-dirs>>
         - libdoc
     deploy:
       machine:
@@ -75,6 +88,7 @@ jobs:
         IMAGE_NAME: peridem-<<pipeline.parameters.docker-img-os>>:latest
       steps:
         - checkout
+        - postcheckout
         - run:
             name: Build docker
             command: |
@@ -98,10 +112,12 @@ jobs:
     codecoverage:
       docker:
         - image: prashjha/peridem-base-<<pipeline.parameters.docker-img-os>>:latest
+          user: user
       steps:
         - checkout
+        - postcheckout
         - libcmake:
-            cmake-args: -DCMAKE_BUILD_TYPE=Release -DEnable_Tests=ON -DHPX_DIR=${HPX_DIR}/lib/cmake/HPX -DCMAKE_CXX_FLAGS="-g -O0 -fprofile-arcs -ftest-coverage -fpic"
+            cmake-args: -DCMAKE_BUILD_TYPE=Release -DEnable_Tests=ON -DCMAKE_CXX_FLAGS="-g -O0 -fprofile-arcs -ftest-coverage -fpic" <<pipeline.parameters.cmake-include-dirs>>
         - libmake
         - libtest:
             verb-flag: ""
@@ -122,27 +138,29 @@ jobs:
               fi
 workflows:
   version: 2
-  build_doc_deploy_cov:
+  build_doc_deploy_codecov:
     jobs:
       - build:
           filters:
             branches:
               ignore: gh-pages
-      # - documentation:
-      #     filters:
-      #       branches:
-      #         ignore: gh-pages
-      #     requires:
-      #       - build
+      - documentation:
+         filters:
+           branches:
+             only: main
+         requires:
+           - build
       - deploy:
           filters:
             branches:
-              ignore: gh-pages
+              only: main
           requires:
+            - documentation
             - build
       - codecoverage:
           filters:
             branches:
-              ignore: gh-pages
+              only: main
           requires:
+            - documentation
             - build

.gitignore

@@ -40,10 +40,14 @@
 # build directory
 build
 build_2
+build2
+build*
+cmake-build*
 
 # ide directory
 .idea
 .idea/workspace.xml
+.vscode
 
 
 # docs directory
@@ -70,4 +74,4 @@ __pycache__
 */__pycache__/*
 
 # ignore specific test directory
-test_ignored_dir
+test_ignored_dir