I need to install dune for one of my PDE-lectures and we were given this file as installation:
install.sh:
# here you may manually define command names
# comment out these definitions to overwrite the default from your system
#export F77=gfortran-mp-7
#export CC=gcc-mp-7
#export CXX=g++-mp-7
#export CXXFLAGS='-I/opt/local/include -L/opt/local/lib -O3 -DNDEBUG'
#export MPICC=mpicc-mpich-gcc7
#export MPICXX=mpicxx-mpich-gcc7
#export CMAKE=/opt/bin/cmake #im pool
# print requirements
print_requirements_message ()
{
echo "Run this installer with "
echo ""
echo " installer <directory>"
echo ""
echo "where <directory> is the name of a directory where to install to."
echo "This directory is created if it does not exist."
echo ""
echo "In order to run this script you need the following software installed on your machine."
echo "Use your package manager (or on the Mac macports or homebrew) to do this."
echo ""
echo "C++ Compiler. With pdelab gcc>=5.1 should be fine"
echo "MPI-2 (including support for MPI IO)"
echo "cmake>=3.0"
echo "git"
echo "wget"
echo ""
echo "Optionally you should consider to get:"
echo "Paraview for visualization (http://www.paraview.org)"
echo "Gmsh for mesh generation (http://gmsh.info)"
}
#
if [ $# -eq 0 ]
then
print_requirements_message
exit 1
fi
# usage: installer <directory>
# directory: new directory in current directory where software is installed
# bash setup
set -x
set -e
# first we create a new directory, step into it and remember where we are
mkdir -p $1
cd $1
ROOT=$(pwd)
# make directory where to put external software
if [ ! "$EXTERNAL_HOME" ]; then
EXTERNAL_HOME=$ROOT/external
mkdir -p $EXTERNAL_HOME
fi
# extract default settings for the command names
if [ ! "$F77" ]; then
F77=gfortran
fi
if [ ! "$CC" ]; then
CC=gcc
fi
if [ ! "$MPICC" ]; then
MPICC=mpicc
fi
if [ ! "$MPICXX" ]; then
MPICXX=mpicxx
fi
if [ ! "$CXX" ]; then
CXX=g++
fi
if [ ! "$CXXFLAGS" ]; then
CXXFLAGS="-O3 -DNDEBUG"
fi
CFLAGS="$CXXFLAGS"
if [ ! "$MAKE_FLAGS" ]; then
MAKE_FLAGS="-j2"
fi
# now lets define some functions
# install vector class library
install_vcl ()
{
curl -O http://www.agner.org/optimize/vectorclass.zip
unzip vectorclass.zip -d $EXTERNAL_HOME/vcl
}
# build fftw3
install_fftw3 ()
{
FFTWVERSION=3.3.4
pushd $EXTERNAL_HOME
mkdir -p tarballs
pushd tarballs
wget http://www.fftw.org/fftw-$FFTWVERSION.tar.gz
tar zxvf fftw-$FFTWVERSION.tar.gz
pushd fftw-$FFTWVERSION
( ./configure CC=$CC MPICC=$MPICC CFLAGS="$CXXFLAGS" --enable-mpi --prefix=$EXTERNAL_HOME/fftw3 && make && make install) || exit $?
popd
rm -rf fftw-$FFTWVERSION
popd
popd
}
# build hdf5 with mpi support
install_hdf5 ()
{
pushd $EXTERNAL_HOME
mkdir -p tarballs
pushd tarballs
# HDF5VERSION=1.8.17
# curl -O http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-$HDF5VERSION.tar.gz
MAJOR=1.8
MINOR=14
HDF5VERSION=$MAJOR.$MINOR
wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-$MAJOR/hdf5-$HDF5VERSION/src/hdf5-$HDF5VERSION.tar.gz
tar zxvf hdf5-$HDF5VERSION.tar.gz
pushd hdf5-$HDF5VERSION
( ./configure CC=$MPICC --enable-parallel --enable-static --prefix=$EXTERNAL_HOME/hdf5 && make && make install) || exit $?
popd
# rm -rf hdf5-$HDF5VERSION
popd
popd
}
# check out all the required dune modules
checkout_dune_core ()
{
# dune core modules
for i in common geometry grid istl localfunctions; do
git clone https://gitlab.dune-project.org/core/dune-$i.git
cd dune-$i
git checkout releases/2.6
cd ..
done
# modules in staging
for i in functions uggrid typetree; do
git clone https://gitlab.dune-project.org/staging/dune-$i.git
cd dune-$i
git checkout releases/2.6
cd ..
done
# dune-alugrid
git clone https://gitlab.dune-project.org/extensions/dune-alugrid.git
cd dune-alugrid
git checkout releases/2.6
cd ..
# install whitespace hook
./dune-common/bin/dunecontrol vcsetup
}
checkout_dune_pdelab ()
{
# dune pdelab modules
git clone https://gitlab.dune-project.org/pdelab/dune-pdelab.git
cd dune-pdelab
git checkout releases/2.6
# There is a typo in the 2.6 release of the following file.
git checkout master dune/pdelab/finiteelement/pk1d.hh
cd ..
# install whitespace hook
./dune-common/bin/dunecontrol vcsetup
}
checkout_dune_pdelab_applications ()
{
# applications
# git clone https://gitlab.dune-project.org/pdelab/dune-pdelab-tutorials.git
#git clone https://gitlab.dune-project.org/oklein/dune-randomfield.git
# git clone https://parcomp-git.iwr.uni-heidelberg.de/Teaching/dune-funcep.git
#git clone https://parcomp-git.iwr.uni-heidelberg.de/Teaching/dune-npde.git
git clone https://alecgilbert@bitbucket.org/alecgilbert/dune-npde-student-ws-2019.git
# git clone https://parcomp-git.iwr.uni-heidelberg.de/Teaching/dune-parsolve.git
# git clone https://parcomp-git.iwr.uni-heidelberg.de/peter/dune-padua.git
#git clone https://parcomp-git.iwr.uni-heidelberg.de/peter/dune-dr.git
# install whitespace hook
./dune-common/bin/dunecontrol vcsetup
}
# generate options file for Dune build system
# generate options file for Dune build system
generate_optsfile ()
{
CC=$(which $CC)
CXX=$(which $CXX)
F77=$(which $F77)
echo "CMAKE_FLAGS=\"
-DCMAKE_C_COMPILER='$CC'
-DCMAKE_CXX_COMPILER='$CXX'
-DCMAKE_Fortran_COMPILER='$F77'
-DCMAKE_CXX_FLAGS_RELEASE='-O3 -DNDEBUG -g0 -funroll-loops -ftemplate-depth=5120 -march=native -Wa,-q'
-DHDF5_ROOT=$EXTERNAL_HOME/hdf5
-DFFTW3_ROOT_DIR=$EXTERNAL_HOME/fftw3
-DCMAKE_BUILD_TYPE=Release
-DDUNE_SYMLINK_TO_SOURCE_TREE=1
\""> release.opts
}
extra_flags ()
{
# These are just more flags that you may put in generate_optsfile ()
echo "CMAKE_FLAGS=\"
-DUG_ROOT=$EXTERNAL_HOME/ug
-DVCL_ROOT=$EXTERNAL_HOME/vcl
-DHDF5_ROOT=$EXTERNAL_HOME/hdf5
-DFFTW3_ROOT_DIR=$EXTERNAL_HOME/fftw3
-DCMAKE_DISABLE_FIND_PACKAGE_ParMETIS=1
-DCMAKE_DISABLE_FIND_PACKAGE_SuperLU=1
\""
}
# create build script
generate_buildscript ()
{
echo '#!/bin/bash
ROOT=$(pwd)
BUILDDIR=$ROOT/release-build
OPTSFILE=release.opts
MODULES="common geometry uggrid grid alugrid istl localfunctions typetree functions pdelab npde"
for i in $MODULES; do
echo build $i
./dune-common/bin/dunecontrol --builddir=$BUILDDIR --opts=$OPTSFILE --only=dune-$i all
done
'> buildmodules.sh
chmod 755 buildmodules.sh
}
# now run your selection of commands
#install_vcl
#install_fftw3
#install_hdf5
checkout_dune_core
checkout_dune_pdelab
checkout_dune_pdelab_applications
generate_optsfile
generate_buildscript
But I receive multiple warning, when executing this script. This is the output of install.sh:
+ set -e
+ mkdir -p dune
+ cd dune
++ pwd
+ ROOT=/Users/matthias/Documents/studium_matthias/semester_7/num_2/dune
+ '[''!'''']'
+ EXTERNAL_HOME=/Users/matthias/Documents/studium_matthias/semester_7/num_2/dune/external
+ mkdir -p /Users/matthias/Documents/studium_matthias/semester_7/num_2/dune/external
+ '[''!'''']'
+ F77=gfortran
+ '[''!'''']'
+ CC=gcc
+ '[''!'''']'
+ MPICC=mpicc
+ '[''!'''']'
+ MPICXX=mpicxx
+ '[''!'''']'
+ CXX=g++
+ '[''!'''']'
+ CXXFLAGS='-O3 -DNDEBUG'
+ CFLAGS='-O3 -DNDEBUG'
+ '[''!'''']'
+ MAKE_FLAGS=-j2
+ checkout_dune_core
+ for i in common geometry grid istl localfunctions
+ git clone https://gitlab.dune-project.org/core/dune-common.git
Cloning into 'dune-common'...
remote: Enumerating objects: 58950, done.
remote: Counting objects: 100% (58950/58950), done.
remote: Compressing objects: 100% (14945/14945), done.
remote: Total 58950 (delta 43852), reused 58924 (delta 43839)
Receiving objects: 100% (58950/58950), 13.57 MiB | 2.64 MiB/s, done.
Resolving deltas: 100% (43852/43852), done.
+ cd dune-common
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ for i in common geometry grid istl localfunctions
+ git clone https://gitlab.dune-project.org/core/dune-geometry.git
Cloning into 'dune-geometry'...
remote: Enumerating objects: 6213, done.
remote: Counting objects: 100% (6213/6213), done.
remote: Compressing objects: 100% (1605/1605), done.
remote: Total 6213 (delta 4583), reused 6205 (delta 4578)
Receiving objects: 100% (6213/6213), 1.93 MiB | 7.79 MiB/s, done.
Resolving deltas: 100% (4583/4583), done.
+ cd dune-geometry
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ for i in common geometry grid istl localfunctions
+ git clone https://gitlab.dune-project.org/core/dune-grid.git
Cloning into 'dune-grid'...
remote: Enumerating objects: 75949, done.
remote: Counting objects: 100% (75949/75949), done.
remote: Compressing objects: 100% (17282/17282), done.
remote: Total 75949 (delta 58559), reused 75863 (delta 58493)s
Receiving objects: 100% (75949/75949), 22.53 MiB | 13.58 MiB/s, done.
Resolving deltas: 100% (58559/58559), done.
+ cd dune-grid
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ for i in common geometry grid istl localfunctions
+ git clone https://gitlab.dune-project.org/core/dune-istl.git
Cloning into 'dune-istl'...
remote: Enumerating objects: 18832, done.
remote: Counting objects: 100% (18832/18832), done.
remote: Compressing objects: 100% (4651/4651), done.
remote: Total 18832 (delta 14128), reused 18786 (delta 14094)
Receiving objects: 100% (18832/18832), 2.92 MiB | 10.58 MiB/s, done.
Resolving deltas: 100% (14128/14128), done.
+ cd dune-istl
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ for i in common geometry grid istl localfunctions
+ git clone https://gitlab.dune-project.org/core/dune-localfunctions.git
Cloning into 'dune-localfunctions'...
remote: Enumerating objects: 15165, done.
remote: Counting objects: 100% (15165/15165), done.
remote: Compressing objects: 100% (3033/3033), done.
remote: Total 15165 (delta 11812), reused 15109 (delta 11763)
Receiving objects: 100% (15165/15165), 1.97 MiB | 7.66 MiB/s, done.
Resolving deltas: 100% (11812/11812), done.
+ cd dune-localfunctions
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ for i in functions uggrid typetree
+ git clone https://gitlab.dune-project.org/staging/dune-functions.git
Cloning into 'dune-functions'...
remote: Enumerating objects: 9728, done.
remote: Counting objects: 100% (9728/9728), done.
remote: Compressing objects: 100% (3195/3195), done.
remote: Total 9728 (delta 6721), reused 9440 (delta 6521)
Receiving objects: 100% (9728/9728), 1.86 MiB | 8.61 MiB/s, done.
Resolving deltas: 100% (6721/6721), done.
+ cd dune-functions
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ for i in functions uggrid typetree
+ git clone https://gitlab.dune-project.org/staging/dune-uggrid.git
Cloning into 'dune-uggrid'...
remote: Enumerating objects: 46990, done.
remote: Counting objects: 100% (46990/46990), done.
remote: Compressing objects: 100% (10520/10520), done.
remote: Total 46990 (delta 36237), reused 46847 (delta 36105)
Receiving objects: 100% (46990/46990), 16.85 MiB | 9.79 MiB/s, done.
Resolving deltas: 100% (36237/36237), done.
+ cd dune-uggrid
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ for i in functions uggrid typetree
+ git clone https://gitlab.dune-project.org/staging/dune-typetree.git
Cloning into 'dune-typetree'...
remote: Enumerating objects: 2892, done.
remote: Counting objects: 100% (2892/2892), done.
remote: Compressing objects: 100% (856/856), done.
remote: Total 2892 (delta 1784), reused 2863 (delta 1764)
Receiving objects: 100% (2892/2892), 528.23 KiB | 4.26 MiB/s, done.
Resolving deltas: 100% (1784/1784), done.
+ cd dune-typetree
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ git clone https://gitlab.dune-project.org/extensions/dune-alugrid.git
Cloning into 'dune-alugrid'...
remote: Enumerating objects: 29009, done.
remote: Counting objects: 100% (29009/29009), done.
remote: Compressing objects: 100% (6171/6171), done.
remote: Total 29009 (delta 22930), reused 28748 (delta 22700)
Receiving objects: 100% (29009/29009), 34.33 MiB | 9.98 MiB/s, done.
Resolving deltas: 100% (22930/22930), done.
+ cd dune-alugrid
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ cd ..
+ ./dune-common/bin/dunecontrol vcsetup
WARNING: could not find module 'dune-python',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-python' is suggested by dune-alugrid
Skipping 'dune-python'!
WARNING: could not find module 'dune-corepy',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-corepy' is suggested by dune-alugrid
Skipping 'dune-corepy'!
--- going to build dune-common dune-geometry dune-uggrid dune-grid dune-alugrid dune-istl dune-localfunctions dune-typetree dune-functions ---
--- calling vcsetup for dune-common ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-common done ---
--- calling vcsetup for dune-geometry ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-geometry done ---
--- calling vcsetup for dune-uggrid ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-uggrid done ---
--- calling vcsetup for dune-grid ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-grid done ---
--- calling vcsetup for dune-alugrid ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-alugrid done ---
--- calling vcsetup for dune-istl ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-istl done ---
--- calling vcsetup for dune-localfunctions ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-localfunctions done ---
--- calling vcsetup for dune-typetree ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-typetree done ---
--- calling vcsetup for dune-functions ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-functions done ---
--- done ---
+ checkout_dune_pdelab
+ git clone https://gitlab.dune-project.org/pdelab/dune-pdelab.git
Cloning into 'dune-pdelab'...
remote: Enumerating objects: 39389, done.
remote: Counting objects: 100% (39389/39389), done.
remote: Compressing objects: 100% (10028/10028), done.
remote: Total 39389 (delta 28721), reused 39308 (delta 28661)
Receiving objects: 100% (39389/39389), 6.41 MiB | 10.27 MiB/s, done.
Resolving deltas: 100% (28721/28721), done.
+ cd dune-pdelab
+ git checkout releases/2.6
Branch 'releases/2.6' set up to track remote branch 'releases/2.6' from 'origin'.
Switched to a new branch 'releases/2.6'
+ git checkout master dune/pdelab/finiteelement/pk1d.hh
Updated 1 path from 0dbcbb9e
+ cd ..
+ ./dune-common/bin/dunecontrol vcsetup
WARNING: could not find module 'dune-python',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-python' is suggested by dune-alugrid
Skipping 'dune-python'!
WARNING: could not find module 'dune-corepy',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-corepy' is suggested by dune-alugrid
Skipping 'dune-corepy'!
WARNING: could not find module 'dune-python',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-python' is suggested by dune-alugrid
Skipping 'dune-python'!
WARNING: could not find module 'dune-corepy',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-corepy' is suggested by dune-alugrid
Skipping 'dune-corepy'!
--- going to build dune-common dune-geometry dune-uggrid dune-grid dune-alugrid dune-istl dune-localfunctions dune-typetree dune-functions dune-pdelab ---
--- calling vcsetup for dune-common ---
--- dune-common done ---
--- calling vcsetup for dune-geometry ---
--- dune-geometry done ---
--- calling vcsetup for dune-uggrid ---
--- dune-uggrid done ---
--- calling vcsetup for dune-grid ---
--- dune-grid done ---
--- calling vcsetup for dune-alugrid ---
--- dune-alugrid done ---
--- calling vcsetup for dune-istl ---
--- dune-istl done ---
--- calling vcsetup for dune-localfunctions ---
--- dune-localfunctions done ---
--- calling vcsetup for dune-typetree ---
--- dune-typetree done ---
--- calling vcsetup for dune-functions ---
--- dune-functions done ---
--- calling vcsetup for dune-pdelab ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-pdelab done ---
--- done ---
+ checkout_dune_pdelab_applications
+ git clone https://alecgilbert@bitbucket.org/alecgilbert/dune-npde-student-ws-2019.git
Cloning into 'dune-npde-student-ws-2019'...
remote: Counting objects: 165, done.
remote: Compressing objects: 100% (118/118), done.
remote: Total 165 (delta 44), reused 159 (delta 41)
Receiving objects: 100% (165/165), 4.09 MiB | 3.38 MiB/s, done.
Resolving deltas: 100% (44/44), done.
+ ./dune-common/bin/dunecontrol vcsetup
WARNING: could not find module 'dune-python',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-python' is suggested by dune-alugrid
Skipping 'dune-python'!
WARNING: could not find module 'dune-corepy',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-corepy' is suggested by dune-alugrid
Skipping 'dune-corepy'!
WARNING: could not find module 'dune-python',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-python' is suggested by dune-alugrid
Skipping 'dune-python'!
WARNING: could not find module 'dune-corepy',
module is also unknown to pkg-config.
Maybe you need to adjust PKG_CONFIG_PATH!
'dune-corepy' is suggested by dune-alugrid
Skipping 'dune-corepy'!
--- going to build dune-common dune-geometry dune-uggrid dune-grid dune-alugrid dune-istl dune-localfunctions dune-typetree dune-functions dune-pdelab dune-npde ---
--- calling vcsetup for dune-common ---
--- dune-common done ---
--- calling vcsetup for dune-geometry ---
--- dune-geometry done ---
--- calling vcsetup for dune-uggrid ---
--- dune-uggrid done ---
--- calling vcsetup for dune-grid ---
--- dune-grid done ---
--- calling vcsetup for dune-alugrid ---
--- dune-alugrid done ---
--- calling vcsetup for dune-istl ---
--- dune-istl done ---
--- calling vcsetup for dune-localfunctions ---
--- dune-localfunctions done ---
--- calling vcsetup for dune-typetree ---
--- dune-typetree done ---
--- calling vcsetup for dune-functions ---
--- dune-functions done ---
--- calling vcsetup for dune-pdelab ---
--- dune-pdelab done ---
--- calling vcsetup for dune-npde ---
--> Installing Git pre-commit hook to enforce whitespace policy
--- dune-npde done ---
--- done ---
+ generate_optsfile
++ which gcc
+ CC=/usr/bin/gcc
++ which g++
+ CXX=/usr/bin/g++
++ which gfortran
+ F77=/usr/local/bin/gfortran
+ echo 'CMAKE_FLAGS="
-DCMAKE_C_COMPILER='\''/usr/bin/gcc'\''
-DCMAKE_CXX_COMPILER='\''/usr/bin/g++'\''
-DCMAKE_Fortran_COMPILER='\''/usr/local/bin/gfortran'\''
-DCMAKE_CXX_FLAGS_RELEASE='\''-O3 -DNDEBUG -g0 -funroll-loops -ftemplate-depth=5120 -march=native -Wa,-q'\''
-DHDF5_ROOT=/Users/matthias/Documents/studium_matthias/semester_7/num_2/dune/external/hdf5
-DFFTW3_ROOT_DIR=/Users/matthias/Documents/studium_matthias/semester_7/num_2/dune/external/fftw3
-DCMAKE_BUILD_TYPE=Release
-DDUNE_SYMLINK_TO_SOURCE_TREE=1
"'
+ generate_buildscript
+ echo '#!/bin/bash
ROOT=$(pwd)
BUILDDIR=$ROOT/release-build
OPTSFILE=release.opts
MODULES="common geometry uggrid grid alugrid istl localfunctions typetree functions pdelab npde"
for i in $MODULES; do
echo build $i
./dune-common/bin/dunecontrol --builddir=$BUILDDIR --opts=$OPTSFILE --only=dune-$i all
done
'
+ chmod 755 buildmodules.sh
I'm on a MacBook and have the following software installed:
- Apple clang version 11.0.0 (clang-1100.0.33.8)
- cmake version 3.15.5
- git
- GNU Wget 1.20.3 built on darwin19.0.0.
How can I approach this problem? Why is dunecontrol vcsetup failing?