Merge branch 'master' into actor

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,28 @@
+---
+name: Feature request
+about: Suggest adding a feature that is not yet in SeisSol  
+labels: feature
+
+---
+
+<!--*Please add a concise summary of your suggestion here.*-->
+
+### Rationale
+
+<!--*Is your feature request related to a problem? Please describe it!*-->
+
+### Description
+
+<!--*Describe the solution you'd like and the alternatives you have considered.*-->
+
+
+### Additional information
+<!--*Add any other context about the feature request here.*-->
+
+
+### General information
+
+- [ ] I have searched the issues of this repo and believe this is not a duplicate
+
+
+Other than that, thanks for taking the time to contribute to SeisSol!

.gitignore

@@ -60,3 +60,6 @@ postprocessing/validation/XDMFCubeCheck/build
 *.dblite
 config.log
 .sconf_temp
+/cmake-build-debug/
+/cmake-build-release/
+/cmake-build-relwithdebinfo/

.gitlab-ci.yml

@@ -0,0 +1,221 @@
+stages:
+    - pre_build
+    - build 
+    - test
+    - performance_eval
+
+ci_builder_pre:
+    stage: pre_build
+    tags:
+        - ci_testing_cc
+    variables:
+        GIT_STRATEGY: clone
+    before_script:
+        - git branch -vva
+        - echo $commit_author_name
+    script:
+        - echo "checking availability of ci_testing_cc"
+        - git --version
+        - git submodule set-url submodules/xdmfwriter https://github.com/TUM-I5/XdmfWriter.git
+        - git submodule set-url submodules/cxxtest https://github.com/CxxTest/cxxtest.git
+        - git submodule set-url submodules/utils https://github.com/TUM-I5/utils.git
+        - git submodule set-url submodules/async https://github.com/TUM-I5/ASYNC.git
+        - git submodule set-url submodules/scons-tools https://github.com/TUM-I5/scons-tools.git
+        - git submodule set-url submodules/PUML https://github.com/TUM-I5/PUML2.git
+        - git submodule set-url submodules/easi https://github.com/SeisSol/easi.git
+        - git submodule set-url submodules/yaml-cpp https://github.com/jbeder/yaml-cpp.git  
+        - git submodule set-url submodules/ImpalaJIT https://github.com/uphoffc/ImpalaJIT.git
+        - git submodule set-url submodules/yateto https://github.com/SeisSol/yateto.git
+        - git submodule set-url submodules/eigen3 https://github.com/eigenteam/eigen-git-mirror
+        - git submodule set-url submodules/Device https://github.com/SeisSol/Device.git
+        - git submodule --quiet update --init --recursive 
+        - wget -q https://syncandshare.lrz.de/dl/fiJNAokgbe2vNU66Ru17DAjT/netcdf-4.6.1.tar.gz
+        - wget -q https://github.com/hfp/libxsmm/archive/master.zip
+        - sudo apt-get install -qq --yes gcc-8 g++-8 gfortran-8 pkg-config cmake cmake-data 
+        - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-8 100
+        - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-8 100
+        - sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-8 100
+        - sudo apt-get install -qq --yes unzip openmpi-bin openmpi-common libopenmpi-dev hdf5-tools libhdf5-openmpi-dev python3 python3-pip libmetis-dev libparmetis-dev cxxtest libarmadillo-dev
+        - gfortran --version
+        - pip3 install --upgrade pip
+        - pip3 install 'numpy>=1.12.0'
+        - pip3 install lxml
+        - pip3 install setuptools
+        - pip3 install sphinx
+        - pip3 install sphinx_rtd_theme
+        - tar -xzf netcdf-4.6.1.tar.gz
+        - cd netcdf-4.6.1 && CC=h5pcc ./configure --prefix=/usr --enable-shared=no --disable-dap && make && sudo make install && cd ..
+        - unzip master.zip
+        - cd libxsmm-master && make generator && sudo cp bin/libxsmm_gemm_generator /usr/bin && cd ..
+
+ci_builder_build:
+    stage: build
+    tags:
+        - ci_testing_cc
+    needs:
+        - job: ci_builder_pre
+    before_script:
+        - cat .git/config
+    parallel:
+        matrix:
+             - precision: double
+             - precision: single
+    script:
+        - echo "now building"
+        - echo $CI_REGISTRY $CI_REGISTRY_IMAGE $CI_REGISTRY_USER
+        - git submodule update --init --recursive
+        - cmake --version
+        - set -euo pipefail
+        - export IFS=$'\n\t'
+        - export CTEST_OUTPUT_ON_FAILURE=1
+        - equation=elastic
+        - mechanisms=0
+        - for build_type in Release ; 
+             do for equation in elastic ;
+                 do dirname="build_${equation}_${precision}_${build_type}";
+                 echo "mkdir $dirname";
+                 if [ "$equation" = viscoelastic2 ]; then mechanisms=3; else mechanisms=0; fi;
+                 mkdir -p $dirname && cd $dirname ;
+                 pwd; 
+                 CMAKE_PREFIX_PATH=~ ;
+                 cmake -DNETCDF=OFF -DMETIS=ON -DCOMMTHREAD=ON -DASAGI=OFF -DHDF5=ON -DCMAKE_BUILD_TYPE=$build_type -DTESTING=ON -DLOG_LEVEL=warning -DLOG_LEVEL_MASTER=info -DARCH=hsw -DPRECISION=$precision -DEQUATIONS=$equation -DNUMBER_OF_MECHANISMS=$mechanisms -DGEMM_TOOLS_LIST=LIBXSMM .. ;
+                 make -j $(nproc);
+                 cd .. ; 
+             done; 
+          done;
+
+    artifacts:
+        paths:
+            - build_*
+
+ci_builder_test:
+        stage: test
+        tags:
+            - ci_testing_cc
+        allow_failure: true
+        needs:
+            - job: ci_builder_build
+        parallel:
+            matrix:
+                - DIR: build_elastic_double_Release
+                - DIR: build_elastic_single_Release
+        script: 
+            - echo "testing"
+            - pwd
+            - ls
+            - cd $DIR
+            - make test
+
+gpu_pre_build:
+    stage: pre_build
+    tags:
+        - atsccs68-docker-executor
+    allow_failure: true
+    variables:
+        GIT_STRATEGY: clone
+    image:
+        name: ravilmobile/seissol_base_amd64:ubuntu-1804_gcc-8.3.0_openmpi-3.1.5_cuda-10.1.243
+        entrypoint: [""]
+    before_script:
+        - git branch -vva
+        - echo $commit_author_name
+    script:
+        - echo "HOST arch.:" $HOST
+        - echo "GPU vendor:" $GPU_VENDOR ", GPU model:" $GPU_MODEL
+        - nvidia-smi
+
+gpu_build:
+    stage: build
+    tags:
+        -  atsccs68-docker-executor
+    allow_failure: false
+    needs:
+        - job: gpu_pre_build
+    image:
+        name: ravilmobile/seissol_base_amd64:ubuntu-1804_gcc-8.3.0_openmpi-3.1.5_cuda-10.1.243
+        entrypoint: [""]
+    before_script:
+        - git submodule init
+        - sed -i 's/\.\.\/\.\./https\:\/\/github\.com/g' .gitmodules
+        - git submodule sync
+        - git submodule --quiet update --init --recursive 
+    script:
+        - export CTEST_OUTPUT_ON_FAILURE=1
+        - . /opt/spack-environment/seissol_env.sh
+        - . /opt/spack-environment/cuda_env.sh
+        - pip3 install git+https://github.com/ravil-mobile/gemmforge.git
+        - set -euo pipefail
+        - for precision in double single; do
+            mkdir -p ./build_${precision} && cd ./build_${precision} ;
+            cmake ..
+            -DCMAKE_BUILD_TYPE=Release
+            -DDEVICE_ARCH=${GPU_VENDOR}
+            -DDEVICE_SUB_ARCH=${GPU_MODEL}
+            -DHOST_ARCH=${HOST}
+            -DPRECISION=${precision} ;
+            make -j ;
+            cd .. ;
+          done;
+        - set +u
+    artifacts:
+        paths:
+            - build_*
+
+gpu_convergence_test:
+    stage: test
+    tags:
+        -  atsccs68-docker-executor
+    allow_failure: false
+    needs:
+        - job: gpu_build
+    image:
+        name: ravilmobile/seissol_base_amd64:ubuntu-1804_gcc-8.3.0_openmpi-3.1.5_cuda-10.1.243
+        entrypoint: [""]
+    script:
+        - export CTEST_OUTPUT_ON_FAILURE=1
+        - . /opt/spack-environment/seissol_env.sh
+        - . /opt/spack-environment/cuda_env.sh
+        - git clone https://github.com/SeisSol/Examples.git tests
+        - pip3 install -r ./tests/convergence_elastic/requirements.txt
+        - set -euo pipefail
+        - for precision in double single; do
+            cd ./build_${precision} ;
+            echo "Elastic Convergence test with precision - " ${precision} ;
+            cp -r ../tests/convergence_elastic/* . ;
+            PYTHONPATH=$PWD python3 ./elastic_convergence_runner
+            --executable $PWD/SeisSol_Release_?nvidia_?_elastic
+            --tmp-dir /tmp/seissol
+            --sizes 4 8 16
+            --expected-errors 1e-2 1e-4 5e-5
+            --norm-type LInf
+            --end-time 0.5
+            --allow-run-as-root ;
+            cd .. ;
+          done;
+        - set +u
+    artifacts:
+        paths:
+            - build_*
+
+gpu_performance_test:
+    stage: performance_eval
+    tags:
+        -  atsccs68-docker-executor
+    allow_failure: true
+    needs:
+        - job: gpu_convergence_test
+    image:
+        name: ravilmobile/seissol_base_amd64:ubuntu-1804_gcc-8.3.0_openmpi-3.1.5_cuda-10.1.243
+        entrypoint: [""]
+    script:
+        - export CTEST_OUTPUT_ON_FAILURE=1
+        - . /opt/spack-environment/seissol_env.sh
+        - . /opt/spack-environment/cuda_env.sh
+        - set -euo pipefail
+        - for precision in double single; do
+            echo "Running SeiSol proxy with precision - " ${precision} ;
+            cd ./build_${precision} ;
+            ./SeisSol_proxy_Release_?${GPU_VENDOR}_?_elastic 100000 100 all ;
+            cd .. ;
+          done;
+        - set +u

.gitmodules

@@ -28,9 +28,9 @@
 [submodule "submodules/yateto"]
 	path = submodules/yateto
 	url = ../../SeisSol/yateto.git
-[submodule "submodules/pythonXdmfReader"]
-	path = submodules/pythonXdmfReader
-	url = ../../Thomas-Ulrich/pythonXdmfReader
 [submodule "submodules/eigen3"]
 	path = submodules/eigen3
 	url = ../../eigenteam/eigen-git-mirror
+[submodule "submodules/Device"]
+	path = submodules/Device
+	url = ../../SeisSol/Device.git