From 3cd7609a09a16b85b398fc24139a3dc3a40bffe2 Mon Sep 17 00:00:00 2001
From: Romain Boman <romain.boman@gmail.com>
Date: Fri, 4 Mar 2022 15:32:10 +0100
Subject: [PATCH] update CUPyDO script
---
build_CUPyDO.sh | 576 ++++++++++++++++++++++++++++++++++++++----------
1 file changed, 459 insertions(+), 117 deletions(-)
diff --git a/build_CUPyDO.sh b/build_CUPyDO.sh
index a7f53de..a30d5ba 100755
--- a/build_CUPyDO.sh
+++ b/build_CUPyDO.sh
@@ -1,94 +1,354 @@
#!/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
--
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