Merge branch 'issue/build_scripts' into 'master'

Issue/build scripts

- build scripts and install scripts with automatic boost and petsc builds
- configure scipt for an easy installation of amdis

See merge request !6

.gitlab-ci.yml

@@ -6,7 +6,6 @@ cache:
 
 before_script:
   - tools/install_boost.sh
-  - tools/install_petsc.sh
 
 build:9-debug-gcc:
   stage: build
@@ -28,6 +27,7 @@ build:9-parallel-debug-gcc:
   stage: build
   image: duneci/base:9
   script:
+  - tools/install_petsc.sh
   - tools/build_parallel_amdis.sh Debug
   only:
   - master
@@ -36,6 +36,7 @@ build:9-parallel-release-gcc:
   stage: build
   image: duneci/base:9
   script:
+  - tools/install_petsc.sh
   - tools/build_parallel_amdis.sh Release
   only:
   - master

configure.sh

+#!/bin/bash
+
+AMDIS_VERSION="1.1"
+
+BUILD_DIR=$( pwd )
+SRC_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
+
+# default parameters
+INSTALL_PREFIX="/usr/local"
+DEBUG="0"
+VERBOSE="OFF"
+ENABLE_EXTENSIONS="OFF"
+ENABLE_UMFPACK="OFF"
+ENABLE_COMPRESSION="OFF"
+ENABLE_PARALLEL="OFF"
+BOOST_PREFIX="${BOOST_ROOT}"
+DOWNLOAD_BOOST="0"
+BOOST_VERSION="1.62.0"
+PETSC_PREFIX="${PETSC_DIR}"
+DOWNLOAD_PETSC="0"
+PETSC_VERSION="3.5.4"
+PARMETIS_PREFIX=""
+ZOLTAN_PREFIX=""
+DOWNLOAD_ZOLTAN="0"
+ZOLTAN_VERSION="3.83"
+
+
+# a help message
+help() {
+cat << EOF
+$(basename "$0") configures AMDiS, by calling the corresponding cmake commands.
+
+Usage: $(basename "$0") [OPTION]... [VAR=VALUE]...
+
+Defaults for the options are specified in brackets.
+
+Configuration:
+  -h, --help             Display this help and exit.
+  -V, --version          Display version information of AMDiS and exit.
+
+Installation directories:
+  --prefix=PREFIX        Install files in PREFIX [${INSTALL_PREFIX}]
+
+By default, 'make install' will install all the files in
+'${INSTALL_PREFIX}/lib', '${INSTALL_PREFIX}/include' and '${INSTALL_PREFIX}/share'.
+You can specify an installation prefix other than '${INSTALL_PREFIX}' using '--prefix',
+for instance '--prefix=${HOME}/amdis'.
+
+Compile parameters:
+  --debug                Compile without optimization and with debug information.
+  -v, --verbose          Show additional information during the compile process.
+
+Optional Features:
+  --enable-extensions    Compile and install sources from the extensions folder.
+  --enable-compression   Compile with support for output compression. This
+                         requires boost-iostreams with enabled ZLib and libbz2
+                         support.
+  --enable-parallel      Compile the parallel version of AMDiS. Needs PETSc and
+                         Parmetis. (see --with-petsc-dir, --with-parmetis-dir)
+
+Optional Packages:
+  --with-umfpack         Adds support for the direct solver UMFPACK.
+  --with-suitesparse     (see --with-umfpack)
+
+  --with-boost-dir=DIR   Sets the boost root directory. [${BOOST_PREFIX}]
+  --download-boost       Download and install boost to '${SRC_DIR}/packages/boost'.
+
+  --with-petsc-dir=DIR   Sets the PETSc root directory, i.e. a directory
+                         containing the folders 'lib/', 'include/' with e.g.
+                         'lib/libpetsc.so' [${PETSC_DIR}].
+  --download-petsc       Download and install petsc, version ${PETSC_VERSION},
+                         to '${SRC_DIR}/packages/petsc'.
+  --with-parmetis-dir=DIR  Sets the PARMETIS root directory, i.e. a directory
+                         containing the folders 'lib/', 'include/' with e.g.
+                         'include/parmetis.h' [=PETSC_DIR].
+
+  --with-zoltan          Add support for the Parallel Partitioning suite Zoltan.
+  --with-zoltan-dir=DIR  Sets the Zoltan root directory, i.e. a directory
+                         containing the folders 'lib/', 'include/' with e.g.
+                         'include/zoltan_cpp.h' [${ZOLTAN_PREFIX}].
+  --download-zoltan      Download and install Zoltan, version ${ZOLTAN_VERSION},
+                         to '${SRC_DIR}/packages/zoltan'.
+
+Report bugs to <amdis.fem@gmail.com>.
+EOF
+}
+
+# parse command line
+if [ $# -gt 0 ]; then
+  while [[ $1 = -* ]]; do
+  case "$1" in
+    -h|-\?|--help)
+        help
+        exit ;;
+    -V|--version)
+        echo "AMDiS v${AMDIS_VERSION}"
+        exit ;;
+    --prefix)
+        INSTALL_PREFIX="$2"
+        shift 2 ;;
+    --prefix=?*)
+        INSTALL_PREFIX="${1#*=}"
+        shift ;;
+    --prefix=)
+        printf 'ERROR: "--prefix" requires a non-empty option argument.\n' >&2
+        exit 1 ;;
+    --debug)
+        DEBUG="1"
+        shift ;;
+    -v|--verbose)
+        VERBOSE="ON"
+        shift ;;
+    --enable-extensions)
+        ENABLE_EXTENSIONS="ON"
+        shift ;;
+    --enable-compression)
+        ENABLE_COMPRESSION="ON"
+        shift ;;
+    --enable-parallel)
+        ENABLE_PARALLEL="ON"
+        shift ;;
+    --with-umfpack|--with-suitesparse)
+        ENABLE_UMFPACK="ON"
+        shift ;;
+    --with-boost-dir)
+        BOOST_PREFIX="$2"
+        shift 2 ;;
+    --with-boost-dir=?*)
+        BOOST_PREFIX="${1#*=}"
+        shift ;;
+    --with-boost-dir=)
+        printf 'ERROR: "--with-boost-dir" requires a non-empty option argument.\n' >&2
+        exit 1 ;;
+    --download-boost)
+        DOWNLOAD_BOOST="1"
+        shift ;;
+    --with-petsc-dir)
+        PETSC_PREFIX="$2"
+        shift 2 ;;
+    --with-petsc-dir=?*)
+        PETSC_PREFIX="${1#*=}"
+        shift ;;
+    --with-petsc-dir=)
+        printf 'ERROR: "--with-petsc-dir" requires a non-empty option argument.\n' >&2
+        exit 1 ;;
+    --download-petsc)
+        DOWNLOAD_PETSC="1"
+        shift ;;
+    --with-parmetis-dir)
+        PARMETIS_PREFIX="$2"
+        shift 2 ;;
+    --with-parmetis-dir=?*)
+        PARMETIS_PREFIX="${1#*=}"
+        shift ;;
+    --with-parmetis-dir=)
+        printf 'ERROR: "--with-parmetis-dir" requires a non-empty option argument.\n' >&2
+        exit 1 ;;
+    --with-zoltan)
+        ENABLE_ZOLTAN="ON"
+        shift ;;
+    --with-zoltan-dir)
+        ZOLTAN_PREFIX="$2"
+        shift 2 ;;
+    --with-zoltan-dir=?*)
+        ZOLTAN_PREFIX="${1#*=}"
+        shift ;;
+    --with-zoltan-dir=)
+        printf 'ERROR: "--with-zoltan-dir" requires a non-empty option argument.\n' >&2
+        exit 1 ;;
+    --download-zoltan)
+        DOWNLOAD_ZOLTAN="1"
+        shift ;;
+    --)
+        shift
+        break ;;
+    -?*)
+        printf 'WARNING: Unknown option (ignored): %s\n' "$1" >&2
+        shift ;;
+    *)
+        break
+  esac
+
+  done
+fi
+
+# Download and install boost
+if [ "${DOWNLOAD_BOOST}" -eq "1" ]; then
+  BOOST_FILENAME="boost_${BOOST_VERSION//[.]/_}.tar.gz"
+  if [ ! -d /tmp/src/boost ]; then
+    mkdir -p /tmp/src/boost
+    curl -SL "http://netcologne.dl.sourceforge.net/project/boost/boost/${BOOST_VERSION}/${BOOST_FILENAME}" \
+      | tar --strip-components=1 -xzC /tmp/src/boost
+  fi
+
+  BOOST_PREFIX=${SRC_DIR}/packages/boost/${BOOST_VERSION}
+
+  cd /tmp/src/boost
+  ./bootstrap.sh --prefix=${BOOST_PREFIX} --with-libraries=system,iostreams,filesystem,program_options,date_time,unit_test_framework
+  if [ "${ENABLE_COMPRESSION}" = "ON" ]; then
+    ./b2 -s cxxflags="-std=c++11" --build-type=minimal variant=release install
+  else
+    ./b2 -s NO_BZIP2=1 -s NO_ZLIB=1 cxxflags="-std=c++11" --build-type=minimal variant=release install
+  fi
+  rm -rf /tmp/src/boost
+fi
+
+
+# Download and install PETSc
+if [ "${DOWNLOAD_PETSC}" -eq "1" ]; then
+  if [ ! -d /tmp/src/petsc ]; then
+    mkdir -p /tmp/src/petsc
+    curl -SL "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-${PETSC_VERSION}.tar.gz" \
+      | tar --strip-components=1 -xzC /tmp/src/petsc
+  fi
+
+  PETSC_PREFIX=${SRC_DIR}/packages/petsc/${PETSC_VERSION}
+
+  if [ -n "${PARMETIS_PREFIX}" ]; then
+    PARMETIS_CONFIG="--with-parmetis-dir=${PARMETIS_PREFIX}"
+  else
+    PARMETIS_CONFIG="--download-parmetis=1"
+  fi
+
+  # Install PETSc
+  cd /tmp/src/petsc
+  ./configure --prefix=${PETSC_PREFIX} --with-pic=1 \
+              --with-debugging=${DEBUG}   --with-clanguage=c++ \
+              --with-metis=1       --download-metis=yes \
+              --with-parmetis=1      ${PARMETIS_CONFIG} \
+              --with-scalapack=1   --download-scalapack=yes \
+              --with-hypre=1       --download-hypre=yes \
+              --with-mumps=1       --download-mumps=yes \
+              --with-fblaslapack=1 --download-fblaslapack=yes
+  make && make install
+  rm -rf /tmp/src/petsc
+fi
+
+
+# set parmetis dir, if not already set
+if [ -z "${PARMETIS_PREFIX}" ]; then
+  PARMETIS_PREFIX="${PETSC_PREFIX}"
+fi
+
+
+if [ "${DEBUG}" -eq "0" ]; then
+  BUILD_TYPE="Release"
+  CXX_FLAGS="-O3"
+else
+  BUILD_TYPE="Debug"
+  CXX_FLAGS="-g"
+fi
+
+
+# Download and install Zoltan
+if [ "${DOWNLOAD_ZOLTAN}" -eq "1" ]; then
+  if [ ! -d /tmp/src/zoltan ]; then
+    mkdir -p /tmp/src/zoltan
+    curl -SL "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions/zoltan_distrib_v${ZOLTAN_VERSION}.tar.gz" \
+      | tar --strip-components=1 -xC /tmp/src/zoltan
+  fi
+
+  ZOLTAN_PREFIX=${SRC_DIR}/packages/zoltan
+
+  # Install Zoltan
+  cd /tmp/src/zoltan
+  mkdir build && cd build
+  ../configure --prefix=${ZOLTAN_PREFIX} --enable-mpi \
+              --enable-zoltan-cppdriver \
+              --with-cxxflags="-std=c++11 -fpic" \
+              --with-cflags="-fpic" --with-fcflags="-fpic" \
+              --with-parmetis=yes  --with-parmetis-libdir=${PARMETIS_PREFIX}/lib \
+              --with-parmetis-incdir=${PARMETIS_PREFIX}/include
+  make && make install
+  rm -rf /tmp/src/zoltan
+fi
+
+
+if [ -n "${BOOST_PREFIX}" ]; then
+  BOOST_CONFIG="-DBOOST_ROOT:PATH=${BOOST_PREFIX}"
+else
+  BOOST_CONFIG=""
+fi
+
+# Install AMDiS
+cd ${BUILD_DIR}
+if [ "${ENABLE_PARALLEL}" = "OFF" ]; then
+  cmake -DENABLE_UMFPACK:BOOL=${ENABLE_UMFPACK} \
+        -DCMAKE_BUILD_TYPE:String=${BUILD_TYPE} \
+        -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_PREFIX} \
+        -DCMAKE_CXX_FLAGS:STRING="${CXX_FLAGS}" \
+        -DCMAKE_VERBOSE_MAKEFILE:BOOL=${VERBOSE} \
+        -DENABLE_EXTENSIONS:BOOL=${ENABLE_EXTENSIONS} \
+        -DENABLE_COMPRESSION:BOOL=${ENABLE_COMPRESSION} ${BOOST_CONFIG} \
+        ${SRC_DIR}/AMDiS/
+else
+  cmake -DCMAKE_CXX_COMPILER=mpic++ \
+        -DCMAKE_C_COMPILER=mpicc \
+        -DCMAKE_BUILD_TYPE:String=${BUILD_TYPE} \
+        -DCMAKE_INSTALL_PREFIX:PATH=${INSTALL_PREFIX} \
+        -DCMAKE_CXX_FLAGS:STRING="${CXX_FLAGS}" \
+        -DENABLE_EXTENSIONS:BOOL=${ENABLE_EXTENSIONS} \
+        -DENABLE_COMPRESSION:BOOL=${ENABLE_COMPRESSION} \
+        -DENABLE_UMFPACK:BOOL=${ENABLE_UMFPACK} \
+        -DCMAKE_VERBOSE_MAKEFILE:BOOL=${VERBOSE} \
+        -DENABLE_PARALLEL_DOMAIN:BOOL=ON \
+        -DPETSC_DIR:PATH=${PETSC_PREFIX} \
+        -DENABLE_ZOLTAN:BOOL=${ENABLE_ZOLTAN} \
+        -DZOLTAN_DIR:PATH=${ZOLTAN_PREFIX} \
+        -DPARMETIS_DIR:PATH=${PARMETIS_PREFIX} ${BOOST_CONFIG} \
+        ${SRC_DIR}/AMDiS/
+fi
+
+if [ "$?" -eq "0" ]; then
+  echo "Compile and install the code with...
+make && make install"
+fi

tools/build_amdis.sh

@@ -10,9 +10,9 @@ if [ "$1" == "Debug" ]; then
 fi
 
 # at first build AMDiS
+cmake -E remove_directory ${ROOT}/build_${POSTFIX}
 cmake -E make_directory ${ROOT}/build_${POSTFIX}
 cmake -E chdir ${ROOT}/build_${POSTFIX} cmake \
-      -DUSE_NEW_CMAKE:BOOL=ON \
       -DCMAKE_INSTALL_PREFIX=${ROOT}/install_${POSTFIX} \
       -DCMAKE_BUILD_TYPE=${CONFIURATION} \
       -DENABLE_CXX11:BOOL=ON \
@@ -20,10 +20,11 @@ cmake -E chdir ${ROOT}/build_${POSTFIX} cmake \
       -DENABLE_UMFPACK:BOOL=OFF \
       -DBOOST_ROOT:PATH=${ROOT}/install/boost \
        ${ROOT}/AMDiS
-cmake --build ${ROOT}/build_${POSTFIX} --target install
+cmake --build ${ROOT}/build_${POSTFIX} --target install -- -j2
 
 # now build the demos
 BASEDIR=${ROOT}/demo
+cmake -E remove_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E make_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E chdir ${BASEDIR}/build_${POSTFIX} cmake \
       -DAMDIS_DIR=${ROOT}/install_${POSTFIX}/share/amdis \
@@ -33,7 +34,8 @@ cmake -E chdir ${BASEDIR}/build_${POSTFIX} cmake \
 cmake --build ${BASEDIR}/build_${POSTFIX}
 
 # now build and run the test_suite
-BASEDIR=${ROOT}/tools/test_suite
+BASEDIR=${ROOT}/test
+cmake -E remove_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E make_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E chdir ${BASEDIR}/build_${POSTFIX} cmake \
       -DAMDIS_DIR=${ROOT}/install_${POSTFIX}/share/amdis \

tools/build_parallel_amdis.sh

@@ -13,9 +13,9 @@ if [ "$1" == "Debug" ]; then
 fi
 
 # at first build AMDiS
+cmake -E remove_directory ${ROOT}/build_${POSTFIX}
 cmake -E make_directory ${ROOT}/build_${POSTFIX}
 cmake -E chdir ${ROOT}/build_${POSTFIX} cmake \
-      -DUSE_NEW_CMAKE:BOOL=ON \
       -DCMAKE_INSTALL_PREFIX=${ROOT}/install_${POSTFIX} \
       -DCMAKE_BUILD_TYPE=${CONFIURATION} \
       -DENABLE_CXX11:BOOL=ON \
@@ -25,10 +25,11 @@ cmake -E chdir ${ROOT}/build_${POSTFIX} cmake \
       -DBOOST_ROOT:PATH=${ROOT}/install/boost \
       -DPETSC_DIR:PATH=${ROOT}/install/petsc \
        ${ROOT}/AMDiS
-cmake --build ${ROOT}/build_${POSTFIX} --target install
+cmake --build ${ROOT}/build_${POSTFIX} --target install -- -j2
 
 # now build the demos
 BASEDIR=${ROOT}/demo
+cmake -E remove_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E make_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E chdir ${BASEDIR}/build_${POSTFIX} cmake \
       -DAMDIS_DIR=${ROOT}/install_${POSTFIX}/share/amdis \
@@ -39,7 +40,8 @@ cmake -E chdir ${BASEDIR}/build_${POSTFIX} cmake \
 cmake --build ${BASEDIR}/build_${POSTFIX}
 
 # now build and run the test_suite
-BASEDIR=${ROOT}/tools/test_suite
+BASEDIR=${ROOT}/tests
+cmake -E remove_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E make_directory ${BASEDIR}/build_${POSTFIX}
 cmake -E chdir ${BASEDIR}/build_${POSTFIX} cmake \
       -DAMDIS_DIR=${ROOT}/install_${POSTFIX}/share/amdis \

tools/install_boost.sh

@@ -5,20 +5,22 @@ set -x
 
 ROOT=${PWD}
 
-if [ ! -d install/ ]; then
-   mkdir -p install
-fi
-cd install
+BOOST_VERSION="1.62.0"
+BOOST_FILENAME="boost_${BOOST_VERSION//[.]/_}.tar.gz"
+
+INSTALL_PREFIX=${ROOT}/install
+mkdir -p ${INSTALL_PREFIX}
 
-#install current boost version
-if [ ! -d boost ]; then
-   curl -o boost.tar.gz "http://netcologne.dl.sourceforge.net/project/boost/boost/1.60.0/boost_1_60_0.tar.gz"
-   mkdir boost_tmp
-   tar --strip-components=1 -xf boost.tar.gz -C boost_tmp
-   rm boost.tar.gz
-   cd boost_tmp
-   ./bootstrap.sh --prefix=${ROOT}/install/boost --with-libraries=system,iostreams,filesystem,program_options,date_time
-   ./b2 -s NO_BZIP2=1 cxxflags="-std=c++11" --build-type=minimal install
-   cd ${ROOT}/install
-   rm -rf boost_tmp
-fi
\ No newline at end of file
+BUILD_DIR=/tmp/$USER/boost_build
+mkdir -p ${BUILD_DIR}
+
+# install boost
+if [ ! -d ${INSTALL_PREFIX}/boost ]; then
+  curl -SL "http://netcologne.dl.sourceforge.net/project/boost/boost/${BOOST_VERSION}/${BOOST_FILENAME}" \
+    | tar --strip-components=1 -xzC ${BUILD_DIR}
+  cd ${BUILD_DIR}
+  ./bootstrap.sh --prefix=${INSTALL_PREFIX}/boost/${BOOST_VERSION}/ \
+                 --with-libraries=system,iostreams,filesystem,program_options,date_time,unit_test_framework
+  ./b2 -s NO_BZIP2=1 cxxflags="-std=c++11" --build-type=minimal variant=release -j 4 install
+  rm -rf ${BUILD_DIR}
+fi

tools/install_petsc.sh

@@ -5,25 +5,26 @@ set -x
 
 ROOT=${PWD}
 
-if [ ! -d install/ ]; then
-   mkdir -p install
-fi
-cd install
+PETSC_VERSION="3.5.4"
+PETSC_FILENAME="petsc-lite-${PETSC_VERSION}.tar.gz"
+
+INSTALL_PREFIX=${ROOT}/install
+mkdir -p ${INSTALL_PREFIX}
+
+BUILD_DIR=/tmp/$USER/petsc_build
+mkdir -p ${BUILD_DIR}
 
 # install petsc
-if [ ! -d petsc ]; then
-   curl -o petsc.tar.gz "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.5.4.tar.gz"
-   mkdir petsc_tmp
-   tar --strip-components=1 -xf petsc.tar.gz -C petsc_tmp
-   rm petsc.tar.gz
-   cd petsc_tmp
+if [ ! -d ${INSTALL_PREFIX}/petsc ]; then
+  curl -SL "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/${PETSC_FILENAME}" \
+    | tar --strip-components=1 -xzC ${BUILD_DIR}
+   cd ${BUILD_DIR}
    # minimal petsc configuration, just for test purposes
-   ./configure --prefix=${ROOT}/install/petsc --with-pic=1 --with-debugging=0 \
-               --with-clanguage=c++ --with-cxx-dialect=c++11 \
-               --with-metis=1 --download-metis=yes \
-               --with-parmetis=1 --download-parmetis=yes \
+   ./configure --prefix=${INSTALL_PREFIX}/petsc/${PETSC_VERSION}/ --with-pic=1 \
+               --with-clanguage=c++ --with-debugging=0 \
+               --with-metis=1       --download-metis=yes \
+               --with-parmetis=1    --download-parmetis=yes \
                --with-fblaslapack=1 --download-fblaslapack=yes
    make && make install
-   cd ${ROOT}/install
-   rm -rf petsc_tmp
+   rm -rf ${BUILD_DIR}
 fi