moves and updates examples, adding new categorizations in EXAMPLES/ folder

.azure-pipelines.yml

@@ -216,6 +216,6 @@ jobs:
       BUILD: true
   - template: .azure-pipelines/test-template.yml
     parameters:
-      workingDirectory: EXAMPLES/simple_topography_and_also_a_simple_fluid_layer/
+      workingDirectory: EXAMPLES/applications/simple_topography_and_also_a_simple_fluid_layer/
 
 

.github/scripts/run_tests.sh

@@ -40,13 +40,13 @@ cd $dir
 #sed -i "s:^NTSTEP_BETWEEN_OUTPUT_INFO .*:NTSTEP_BETWEEN_OUTPUT_INFO    = 50:" DATA/Par_file
 
 # specific example setups
-if [ "${TESTDIR}" == "EXAMPLES/moving_sources_acoustic" ]; then
+if [ "${TESTDIR}" == "EXAMPLES/applications/moving_sources_acoustic" ]; then
   sed -i "s:^NSTEP .*:NSTEP    = 3000:" DATA/Par_file
 fi
-if [ "${TESTDIR}" == "EXAMPLES/Industrial_Format_SEP" ]; then
+if [ "${TESTDIR}" == "EXAMPLES/real_world/Industrial_Format_SEP" ]; then
   sed -i "s:^NPROC .*:NPROC    = 2:" DATA/Par_file
 fi
-if [ "${TESTDIR}" == "EXAMPLES/axisymmetric_case_AXISYM_option" ]; then
+if [ "${TESTDIR}" == "EXAMPLES/applications/axisymmetric_examples/axisymmetric_case_AXISYM_option" ]; then
   sed -i "s:^NPROC .*:NPROC    = 2:" DATA/Par_file
   sed -i "s:^NSTEP .*:NSTEP    = 1400:" DATA/Par_file
 fi
@@ -61,12 +61,12 @@ fi
 # selects kernel script for kernel benchmark examples
 do_kernel_script=0
 
-if [ "${TESTDIR}" == "EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC" ]; then do_kernel_script=1; fi
-if [ "${TESTDIR}" == "EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC" ]; then do_kernel_script=1; fi
-if [ "${TESTDIR}" == "EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC_ELASTIC" ]; then do_kernel_script=1; fi
+if [ "${TESTDIR}" == "EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC" ]; then do_kernel_script=1; fi
+if [ "${TESTDIR}" == "EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC" ]; then do_kernel_script=1; fi
+if [ "${TESTDIR}" == "EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC_ELASTIC" ]; then do_kernel_script=1; fi
 
 # setup elastic kernel for SH simulations
-if [ "${TESTDIR}" == "EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC" ] && [ "${TESTCASE}" == "SH" ]; then
+if [ "${TESTDIR}" == "EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC" ] && [ "${TESTCASE}" == "SH" ]; then
   # sets simulation type for SH-waves
   sed -i "s:^SIM_TYPE.*:SIM_TYPE=3:" run_this_example_kernel.sh
 fi

.github/workflows/CI.yml

@@ -187,7 +187,7 @@ jobs:
         #sudo -E apt-cache pkgnames intel | grep intel-oneapi
         #echo ""
         echo "installing packages intel oneapi:"
-        sudo apt-get install -y intel-oneapi-compiler-fortran-2023.2.2 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.2 intel-oneapi-mpi intel-oneapi-mpi-devel
+        sudo apt-get install -y intel-oneapi-compiler-fortran-2023.2.2 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.2 intel-oneapi-mpi-2021.14 intel-oneapi-mpi-devel-2021.14
         echo ""
 
     - name: compiler infos
@@ -294,6 +294,137 @@ jobs:
       run: |
         make tests
 
+  linuxCheck-Intel-ifx:
+    name: Test Intel ifx on ubuntu-latest
+    runs-on: ubuntu-latest
+    needs: changesCheck
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Cache Intel oneapi packages
+      id: cache-intel-oneapi-ifx
+      uses: actions/cache@v4
+      with:
+        path: /opt/intel/oneapi
+        key: install-${{ runner.os }}-ifx-all
+
+    - name: Install packages
+      if: steps.cache-intel-oneapi-ifx.outputs.cache-hit != 'true'
+      run: |
+        # new way
+        wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null
+        echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
+        echo ""
+        sudo apt-get update
+        echo ""
+        # info
+        #sudo -E apt-cache pkgnames intel | grep intel-oneapi
+        #echo ""
+        echo "installing packages intel oneapi:"
+        sudo apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp intel-oneapi-mpi intel-oneapi-mpi-devel
+        echo ""
+
+    - name: compiler infos
+      run: |
+        echo ""
+        source /opt/intel/oneapi/setvars.sh
+        echo ""
+        echo "compiler versions:"
+        echo "icx --version"
+        which icx
+        icx --version
+        echo ""
+        echo "ifx --version"
+        which ifx
+        ifx --version
+        echo ""
+        echo "mpiifx --version"
+        which mpiifx
+        mpiifx --version
+        echo ""
+        echo "mpif90 --version"
+        which mpif90
+        mpif90 --version
+        echo ""
+        # infos
+        which ifx
+        which icx
+        which mpiifx
+        echo "mpirun:"
+        which mpirun
+        echo ""
+        # intel setup for running tests
+        echo ""
+        echo "replacing mpif90 with mpiifx link:"
+        sudo ln -sf $(which mpiifx) $(which mpif90)
+        mpif90 --version
+        echo ""
+        # debug
+        #export I_MPI_DEBUG=5,pid,host
+        #export I_MPI_LIBRARY_KIND=debug
+        # remove -ftrapuv which leads to issues for running tests
+        sed -i "s/-ftrapuv//g" flags.guess
+        # environment setting
+        export TERM=xterm
+        # export info
+        echo "exports:"
+        export
+        echo ""
+        echo ""
+        printenv >> $GITHUB_ENV
+        echo "CXX=icx" >> $GITHUB_ENV
+        echo "CC=icx" >> $GITHUB_ENV
+        echo "FC=ifx" >> $GITHUB_ENV
+        echo ""
+
+    - name: configure debug
+      run: |
+        set +e # revert the default `set -e`
+        ./configure --enable-debug FC=ifx CC=icx
+        if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi
+
+    - name: make debug
+      run: |
+        make -j2 all
+        make -j2 all --always-make
+        make clean
+
+    - name: configure
+      run: |
+        ./configure FC=ifx CC=icx
+
+    - name: make
+      run: |
+        make -j2 all
+        make clean
+
+    - name: configure parallel debug
+      run: |
+        set +e # revert the default `set -e`
+        ./configure --enable-debug --with-mpi FC=ifx CC=icx MPIFC=mpiifx MPI_INC="${I_MPI_ROOT}/include"
+        if [[ $? -ne 0 ]]; then echo "configuration failed:"; cat config.log; echo ""; echo "exiting..."; exit 1; fi
+
+    - name: make parallel debug
+      run: |
+        make -j2 all
+        make -j2 all --always-make
+        make clean
+
+    - name: configure parallel
+      run: |
+        ./configure --with-mpi FC=ifx CC=icx MPIFC=mpiifx MPI_INC="${I_MPI_ROOT}/include"
+
+    - name: make parallel
+      run: |
+        make -j2 all
+        make clean
+
+    # note: fails with -ftrapuv flag due to MPI issue on virtual nodes
+    - name: make tests
+      run: |
+        make tests
+
 
   linuxTest_0:
     name: Test run example 0 - make tests
@@ -333,7 +464,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC
+        TESTDIR: EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -357,7 +488,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC
+        TESTDIR: EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC
         TESTCASE: P-SV
       run: ./.github/scripts/run_tests.sh
       shell: bash
@@ -382,7 +513,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC
+        TESTDIR: EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ELASTIC
         TESTCASE: SH
       run: ./.github/scripts/run_tests.sh
       shell: bash
@@ -407,7 +538,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC_ELASTIC
+        TESTDIR: EXAMPLES/benchmarks/BENCHMARK_CLAERBOUT_ADJOINT/ACOUSTIC_ELASTIC
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -431,7 +562,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/moving_sources_acoustic
+        TESTDIR: EXAMPLES/applications/moving_sources_acoustic
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -455,7 +586,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/anisotropic_isotropic_model
+        TESTDIR: EXAMPLES/applications/anisotropy/anisotropic_isotropic_model
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -480,7 +611,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/Industrial_Format_SEP
+        TESTDIR: EXAMPLES/real_world/Industrial_Format_SEP
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -504,7 +635,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/axisymmetric_case_AXISYM_option
+        TESTDIR: EXAMPLES/applications/axisymmetric_examples/axisymmetric_case_AXISYM_option
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -528,7 +659,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/simple_topography_and_also_a_simple_fluid_layer
+        TESTDIR: EXAMPLES/applications/simple_topography_and_also_a_simple_fluid_layer
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -552,7 +683,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/simple_topography_and_also_a_simple_fluid_layer
+        TESTDIR: EXAMPLES/applications/simple_topography_and_also_a_simple_fluid_layer
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -577,7 +708,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/tomographic_ocean_model
+        TESTDIR: EXAMPLES/applications/ocean_acoustics/tomographic_ocean_model
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -601,7 +732,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/Marmousi2
+        TESTDIR: EXAMPLES/real_world/Marmousi2
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -625,7 +756,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/Gmsh_example_Stacey_MPI
+        TESTDIR: EXAMPLES/applications/meshing/Gmsh_example_Stacey_MPI
       run: ./.github/scripts/run_tests.sh
       shell: bash
 
@@ -649,7 +780,7 @@ jobs:
 
     - name: Run test
       env:
-        TESTDIR: EXAMPLES/electromagnetic_GPR_TM
+        TESTDIR: EXAMPLES/reproducible_study/Morency2020_electromagnetic_GPR_TM
         DEBUG: true
       run: ./.github/scripts/run_tests.sh
       shell: bash