update CUPyDO script

build_CUPyDO.sh

 #!/bin/bash
+# build CUPyDO and all related solvers / run ctest
+#
+# usage: build_CUPyDO.sh -b -j 2  : build (using 2 cores)
+#        build_CUPyDO.sh -b -t    : build and test
+#        build_CUPyDO.sh -b -t -q : build and test (batch mode)
 
-function build_CUPyDO()
+# profile should be sourced if in batch mode
+source ~/.profile
+# bash: enable more errors
+set -eu
+
+GEOGEN_VERSION=2.0.0
+SOL2_VERSION=3.2.2
+MODALI_VERSION=v2.0
+NATIVESOLID_VERSION=romain  # v1.1
+PYBEAM_VERSION=master
+VLM_VERSION=v2.0
+SU2_VERSION=fix_wrap_strong
+PFEM3D_VERSION=v2.0.0
+# WAVES_VERSION=v2.2.2 # AttributeError: module 'flow' has no attribute 'F0PsPhiInf'
+WAVES_VERSION=v2.1.1
+PFEM_VERSION=v1.19
+METAFOR_VERSION=v3492
+CUPYDO_VERSION=lacroix
+
+# Gmsh
+#   https://gmsh.info/
+
+function get_last_Gmsh()
 {
-    # clone/build CUPyDO
-    if [ ! -d CUPyDO ] ; then
-        git clone git@github.com:ulgltas/CUPyDO.git
+    if [ ! -d Gmsh ] ; then
+        echo "Gmsh: retrieving gmsh-git-Linux64-sdk.tgz"
+        wget -q https://gmsh.info/bin/Linux/gmsh-git-Linux64-sdk.tgz
+        tar -xzf gmsh-git-Linux64-sdk.tgz 
+        mv gmsh-git-Linux64-sdk Gmsh
+        rm gmsh-git-Linux64-sdk.tgz 
+    else
+        echo "Gmsh: found"
     fi
+}
 
-    cd CUPyDO
-    git pull
-    git checkout pfem_compatibility_update
-    git pull
-    if [ -d build ] ; then
-        rm -rf build
+# geoGen (for VLM) 
+#   https://github.com/acrovato/geoGen
+#   full python 
+
+function get_geoGen() 
+{
+    if [ ! -d geoGen ] ; then
+        echo "geoGen: retrieving geoGen ${GEOGEN_VERSION}"
+        wget -q https://github.com/acrovato/geoGen/archive/refs/tags/v${GEOGEN_VERSION}.tar.gz
+        tar -xf v${GEOGEN_VERSION}.tar.gz 
+        mv geoGen-${GEOGEN_VERSION} geoGen
+        rm v${GEOGEN_VERSION}.tar.gz
+    else
+        echo "geoGen: found"
     fi
-    mkdir build
-    cd build
-    cmake ..
-    make -j 6
-    make install
-    cd ../..
 }
 
-function build_waves()
+# sol2 (for PFEM3D)
+#   https://github.com/ThePhD/sol2
+
+function build_sol2() # 
 {
-    # clone/build waves
-    if [ ! -d waves ] ; then
-	git clone git@gitlab.uliege.be:am-dept/waves.git
+    if [ ! -d sol2 ] ; then
+        echo "sol2: retrieving sol2 ${SOL2_VERSION}"
+
+        SOL2_INSTALL_PREFIX=`pwd`/sol2
+
+        wget -q https://github.com/ThePhD/sol2/archive/refs/tags/v${SOL2_VERSION}.tar.gz
+        tar -xf v${SOL2_VERSION}.tar.gz
+        rm v${SOL2_VERSION}.tar.gz
+
+        echo "sol2: building"
+        cd sol2-${SOL2_VERSION}
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        cd build
+        cmake .. -DCMAKE_INSTALL_PREFIX=${SOL2_INSTALL_PREFIX} #>sol2.cmake.log
+        cmake --build . --target install -- -j ${NCORES} #>sol2.build.log
+        cd ../..
+        rm -rf sol2-${SOL2_VERSION}
+    else
+        echo "sol2: found"
     fi
+}
+
+# modali: Modal integrator for fluid-structure computations
+#   https://github.com/ulgltas/modali
+#   full python - no build
 
-    cd waves
-    if [ -d build ] ; then
-        rm -rf build
+function build_modali()
+{
+    if [ ! -d modali ] ; then
+        echo "modali: cloning modali ${MODALI_VERSION}"
+        git -c advice.detachedHead=false \
+            clone --quiet \
+            --branch ${MODALI_VERSION} \
+            git@github.com:ulgltas/modali.git
+    else
+        echo "modali: already cloned"
     fi
-    mkdir build
-    cd build
-    cmake -DUSE_PY3=OFF -C../CMake/disable-trilinos.cmake ..
-    make -j 6
-    cd ../..
 }
 
-function build_PFEM()
+# NativeSolid (RBM?)
+#   https://github.com/ulgltas/NativeSolid
+
+function build_NativeSolid()
 {
-    # clone/build PFEM
-    if [ ! -d PFEM ] ; then
-        git clone git@gitlab.uliege.be:am-dept/PFEM.git
+    if [ ! -d NativeSolid ] ; then
+        echo "NativeSolid: cloning NativeSolid ${NATIVESOLID_VERSION}"
+        git -c advice.detachedHead=false \
+            clone --quiet git@github.com:ulgltas/NativeSolid.git \
+            --branch ${NATIVESOLID_VERSION} 
+    else
+        echo "NativeSolid: already cloned"     
     fi
 
-    cd PFEM
-    git pull
-    git checkout reorganize_schemes_and_algos
-    git pull
-    if [ -d build ] ; then
-        rm -rf build
+    # requires lapacke/cblas
+    #   lapacke: (sudo apt install liblapacke-dev)
+    #   cblas/blas: (sudo apt-get install libopenblas-dev)
+
+    if [ ! -f ./NativeSolid/bin/TestCVector ] ; then
+        echo "NativeSolid: building"
+        cd NativeSolid
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        cd build
+        cmake -DCMAKE_BUILD_TYPE=Release -Wno-dev .. #>NativeSolid.cmake.log
+        make -j ${NCORES} #>NativeSolid.make.log
+        cd ../..
+    else
+        echo "NativeSolid: already built"
     fi
-    mkdir build
-    cd build
-    cmake ..
-    make -j 6
-    cd ../..
 }
 
+# pyBeam:
+#   https://github.com/pyBeam/pyBeam
+#   requires meson/ninja: sudo apt install meson
 
-function build_NativeSolid()
+function build_pyBeam()
 {
-    # clone/build NativeSolid
-    if [ ! -d NativeSolid ] ; then
-        git clone git@github.com:ulgltas/NativeSolid.git
+    if [ ! -d pyBeam ] ; then
+        echo "pyBeam: cloning pyBeam"
+        git -c advice.detachedHead=false \
+            clone --depth 1 --recursive \
+            git@github.com:pyBeam/pyBeam.git \
+            --branch ${PYBEAM_VERSION}
+        ver=$(python3 -V 2>&1 | sed 's/.* \([0-9]\).\([0-9]\).*/\1\2/')
+        if [ "$ver" -gt "37" ]; then    
+            # fix meson build file for python3.8
+            #   see https://github.com/mesonbuild/meson/issues/5629
+            sed -i "s/dependency('python3')/dependency('python3-embed')/g" \
+                pyBeam/meson.build
+        fi
+    else
+        echo "pyBeam: already cloned"
     fi
 
-    cd NativeSolid
-    if [ -d build ] ; then
-        rm -rf build
+    if [ ! -f pyBeam/build/bin/pyBeam.py ] ; then
+        echo "pyBeam: building"
+        cd pyBeam
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        meson build --prefix=$PWD/build
+        ninja -C build install
+        cd ..
+    else
+        echo "pyBeam: already installed"
     fi
-    mkdir build
-    cd build
-    cmake ..
-    make -j 6
-    cd ../..
 }
 
+# VLM
+#   https://github.com/ulgltas/VLM
 
-function build_modali()
+function build_VLM()
 {
-    # clone modali
-    if [ ! -d modali ] ; then
-        git clone git@github.com:ulgltas/modali.git
+    if [ ! -d VLM ] ; then
+        echo "VLM: cloning VLM ${VLM_VERSION}"
+        git -c advice.detachedHead=false \
+            clone --quiet \
+            --branch ${VLM_VERSION} \
+            git@github.com:ulgltas/VLM.git
+    else
+        echo "VLM: already cloned" 
+    fi
+
+    if [ ! -f VLM/bin/VLM ] ; then
+        echo "VLM: building"
+        cd VLM
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        cd build
+        cmake -Wno-dev -DCMAKE_BUILD_TYPE=Release -DPYTHON_WRAPPER=ON ..
+        make -j ${NCORES}
+        make install
+        cd ../..
+    else
+        echo "VLM: already built"
     fi
 }
 
+# SU2
+#   https://github.com/ulgltas/SU2
+
+function build_SU2()
+{
+    if [ ! -d SU2 ] ; then
+        echo "SU2: cloning SU2"
+        git clone --depth 1 git@github.com:ulgltas/SU2.git \
+            --branch ${SU2_VERSION}
+    else
+        echo "SU2: srcs found"
+    fi
+
+    if [ ! -f SU2/build/bin/SU2_CFD ] ; then
+        echo "SU2: building"
+        cd SU2
+        export CXXFLAGS="-O3"
+        python3 meson.py setup build \
+            -Denable-pywrapper=true \
+            -Denable-cgns=false \
+            -Denable-tecio=false \
+            -Dwith-mpi=disabled \
+            -Denable-tests=false \
+            -Denable-autodiff=true \
+            --prefix=$PWD/build
+        ./ninja -C build install
+        cd ..
+    else
+        echo "SU2: already installed"
+    fi
+}
+
+# PFEM3D
+#   https://github.com/ImperatorS79/PFEM3D
+#   sudo apt install libcgal-dev liblua5.3-dev 
+#
+# ctest runtime: needs slpp (lua parser for python) 
+#   https://github.com/SirAnthony/slpp
+#   https://pypi.org/project/SLPP/
+#   => sudo pip3 install slpp
+
+function build_PFEM3D()
+{
+    if [ ! -d PFEM3D ] ; then
+        echo "PFEM3D: cloning PFEM3D ${PFEM3D_VERSION}"
+        git -c advice.detachedHead=false \
+            clone --quiet \
+            --branch ${PFEM3D_VERSION} \
+            git@github.com:ImperatorS79/PFEM3D.git
+    else
+        echo "PFEM3D: already cloned"     
+    fi
+
+    if [ ! -f PFEM3D/build/bin/pfem ] ; then
+        echo "PFEM3D: building"
+        BASE=`pwd`
+        export GMSH=${BASE}/Gmsh
+        export Sol2_DIR=${BASE}/sol2/lib/cmake/sol2/
+        export PATH=${GMSH}/bin:${GMSH}/lib:${PATH}
+        export INCLUDE=${GMSH}/include:${INCLUDE}
+        export LIB=${GMSH}/lib:${LIB}
+        cd PFEM3D
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        cd build
+        cmake -Wno-dev -DCMAKE_BUILD_TYPE=Release \
+            -DUSE_SWIG=1 -DBUILD_TESTING=1 ..
+        make -j ${NCORES}
+        cp ${BASE}/Gmsh/lib/libgmsh.so bin/
+        cd ../..
+    else
+        echo "PFEM3D: already built"     
+    fi
+}
+
+# Waves
+#   https://gitlab.uliege.be/am-dept/waves
+
+function build_waves()
+{
+    if [ ! -d waves ] ; then
+        echo "waves: cloning waves ${WAVES_VERSION}"
+        git -c advice.detachedHead=false \
+            clone --quiet \
+            --branch ${WAVES_VERSION} \
+            git@gitlab.uliege.be:am-dept/waves.git
+    else
+        echo "waves: already cloned" 
+    fi
+
+    if [ ! -f waves/build/bin/libwaves.so ] ; then
+        echo "waves: building"
+        cd waves
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        cd build
+        cmake -Wno-dev -C../CMake/disable-trilinos.cmake ..
+        make -j ${NCORES}
+        cd ../..
+    else
+        echo "waves: already built"
+    fi
+}
+
+# PFEM:
+#   https://gitlab.uliege.be/am-dept/PFEM
+
+function build_PFEM()
+{
+    if [ ! -d PFEM ] ; then
+        echo "PFEM: cloning PFEM ${PFEM_VERSION}"
+        git -c advice.detachedHead=false \
+            clone --quiet \
+            --branch ${PFEM_VERSION} \
+            git@gitlab.uliege.be:am-dept/PFEM.git
+    else
+        echo "PFEM: already cloned" 
+    fi
+
+    if [ ! -f PFEM/build/bin/libpfem.so ] ; then
+        echo "PFEM: building"
+        cd PFEM
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        cd build
+        cmake -Wno-dev ..
+        make -j ${NCORES}
+        cd ../..
+    else
+        echo "PFEM: already built"
+    fi
+}
+
+# Metafor
+
 function build_Metafor()
 {
     if [ ! -d Metafor ] ; then
@@ -98,86 +358,168 @@ function build_Metafor()
     
     # clone 
     if [ ! -d linuxbin ] ; then
+        echo "Metafor/linuxbin: cloning linuxbin"
         git clone git@gitlab.uliege.be:am-dept/linuxbin.git
-    fi
+    else
+        echo "Metafor/linuxbin: already cloned" 
+    fi        
+
     if [ ! -d oo_meta ] ; then
-        git clone --depth=10 git@gitlab.uliege.be:am-dept/MN2L/oo_meta.git
+        echo "Metafor/oo_meta: cloning oo_meta ${METAFOR_VERSION}" 
+        git -c advice.detachedHead=false \
+            clone --recursive --depth=1 \
+            --branch ${METAFOR_VERSION} \
+            git@gitlab.uliege.be:am-dept/MN2L/oo_meta.git
+    else
+        echo "Metafor/oo_meta: already cloned" 
     fi
 
     # build
-    if [ -d oo_metaB ] ; then
-        rm -rf oo_metaB
+    if [ ! -f oo_metaB/bin/Metafor ] ; then
+        echo "Metafor/oo_meta: building"
+        if [ -d oo_metaB ] ; then
+            rm -rf oo_metaB
+        fi
+        mkdir oo_metaB
+        cd oo_metaB
+        cmake -Wno-dev -C ../oo_meta/CMake/ubuntu-CUPyDO.cmake ../oo_meta
+        make -j ${NCORES}
+        cd ..
+    else
+        echo "Metafor/oo_meta: already built"
     fi
-    mkdir oo_metaB
-    cd oo_metaB
-    cmake -C ../oo_meta/CMake/ubuntu-CUPyDO.cmake ../oo_meta
-    make -j 12
-    cd ../..
+    
+    cd ..
 }
 
-function build_SU2()
+function build_CUPyDO()
 {
-    # clone/build SU2
-    if [ ! -d SU2.src ] ; then
-	mkdir SU2.src
+    if [ ! -d CUPyDO ] ; then
+        echo "CUPyDO: cloning CUPyDO ${CUPYDO_VERSION}"
+        git clone --branch ${CUPYDO_VERSION} \
+            git@github.com:ulgltas/CUPyDO.git 
+    else
+        echo "CUPyDO: already cloned" 
     fi
-    cd SU2.src
 
-    if [ ! -d SU2 ] ; then
-        git clone git@github.com:su2code/SU2.git
+    if [ ! -f CUPyDO/ccupydo/_CCupydo.so ] ; then
+        echo "CUPyDO: building"
+        cd CUPyDO
+        if [ -d build ] ; then
+            rm -rf build
+        fi
+        mkdir build
+        cd build
+        cmake -Wno-dev -DWITH_MPI=OFF ..
+        make -j ${NCORES}
+        make install
+        cd ../..
+    else
+        echo "CUPyDO: already built"
     fi
-    cd SU2
-    git checkout tags/v6.2.0
-    unset MKLROOT   # <= MKL should be disabled
-    ./bootstrap
-    ./configure --prefix=`readlink -f ../../SU2` \
-		CXXFLAGS="-O3" \
-                --enable-PY_WRAPPER
-    make -j 12
-    make install
-    cd ../..
 }
 
-function build_VLM()
+function do_build()
 {
-    # clone/build VLM
-    if [ ! -d VLM ] ; then
-        git clone git@github.com:ulgltas/VLM.git
+    # create CUPyDO main folder
+    if [ ! -d CUPyDO ] ; then
+        mkdir CUPyDO
     fi
-    cd VLM
+    cd CUPyDO
 
-    if [ -d build ] ; then
-	rm -rf build
-    fi
-    mkdir build
-    cd build
-    cmake ..
-    make -j 6
+    # build codes
+    get_last_Gmsh
+    get_geoGen
+    build_sol2
+    build_modali
+    build_NativeSolid
+    build_pyBeam
+    build_VLM
+    build_SU2
+    build_PFEM3D
+    build_waves
+    build_PFEM
+    build_Metafor
+    build_CUPyDO
 
-    make install # is it required?
-    
-    cd ../..
+    # leave CUPyDO main folder
+    cd ..
 }
 
+function do_tests()
+{
+    echo "do_tests()..."
+    cd CUPyDO
+    cd CUPyDO/build
+    ctest -j ${NCORES} #2>&1 > ctest_stdout.txt
+    # output the last lines to stdout (useful for shortening mails)
+    #tail -n 50 ctest_stdout.txt
+    cd ../../..
+    echo "done."
+}
 
- 
-# create CUPyDO main folder
-if [ ! -d CUPyDO ] ; then
-    mkdir CUPyDO
-fi
-cd CUPyDO
+function usage()
+{
+    echo "usage: $0 -b -j 2  : build (using 2 cores)"
+    echo "       $0 -b -t    : build and test"
+    echo "       $0 -b -t -q : build and test (batch mode)"
+    exit 1
+}
 
-# build codes
+function go_batch()
+{
+    CMD_TXT="$0 -j ${NCORES}"
+    if [ "$DO_BUILD" = true ] ; then
+        CMD_TXT="$CMD_TXT -b"
+    fi 
+    if [ "$DO_TESTS" = true ] ; then
+        CMD_TXT="$CMD_TXT -t"
+    fi
+    echo "starting script in batch mode:"
+    echo "    $CMD_TXT"
+    echo $CMD_TXT | at now -m
+    exit 0
+}
+
+NCORES=`nproc --all`
+RUNBATCH=false
+DO_BUILD=false
+DO_TESTS=false
+DISPLAY_USAGE=true
 
-build_CUPyDO
-build_waves
-build_PFEM
-build_Metafor
-build_SU2
-build_modali
-build_NativeSolid
-build_VLM
+# -- args
 
+while getopts "j:hbtq" option
+do
+  case $option in
+    j ) 
+        NCORES=$OPTARG ;;
+    h ) 
+        usage ;;
+    q ) 
+        RUNBATCH=true ;;
+    b ) 
+        DO_BUILD=true ;
+        DISPLAY_USAGE=false ;;
+    t ) 
+        DO_TESTS=true ;
+        DISPLAY_USAGE=false ;;
+    * ) 
+        echo "[getopts] Bad option: $option" ; exit 1 ;;
+  esac
+done
+shift $(($OPTIND - 1))
 
-# leave CUPyDO main folder
-cd ..
+if [ "$RUNBATCH" = true ] ; then
+    go_batch
+else
+    if [ "$DISPLAY_USAGE" = true ] ; then
+        usage
+    fi
+    if [ "$DO_BUILD" = true ] ; then
+        do_build
+    fi
+    if [ "$DO_TESTS" = true ] ; then
+        do_tests
+    fi  
+fi