Installing multiple versions of Chaste's dependencies for testing compatibility
As part of Chaste's automated testing, we build and run our main test packs with a range of different library versions, to ensure we do not inadvertently break support. This page describes the steps used to set up the machine that runs these tests, and hence needs many different versions of the dependencies installed. Note that using different dependency versions also requires support in the hostconfig configuration, a snippet of which is included below (the definitive version is at source:trunk/python/hostconfig/machines/chaste64.py, and is not publicly accessible).
A pre-requisite to the instructions below is that a 'bob' account has been set up as a normal automated build account, and the .bashrc file of the account running the instructions contains the following (at the top):
export PATH=$HOME/mpi/bin:$HOME/hdf5/bin:$HOME/bin:$PATH source /opt/intel/bin/compilervars.sh intel64 export INTEL_LICENSE_FILE="28519@flexlm.nsms.ox.ac.uk"
The following bash script was used to install the dependencies.
# Link to the existing bob account for some dependencies # Either link to bob for MPICH / ParMetis or see below #ln -s ~bob/mpi #ln -s /home/bob/ParMetis-3.1 ln -s /home/bob/petsc-3.1-p8 mkdir -p ~/bin # The folder where automated builds will take place mkdir -p ~/eclipse/workspace # Dependency sources go in ~/src mkdir -p ~/src cd ~/src wget https://chaste.cs.ox.ac.uk/trac/raw-attachment/wiki/InstallGuides/NonRootDeveloper/mpich-1.2.7p1.tar.gz wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD/ParMetis-3.1.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-2.3.2-p4.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-2.3.3-p15.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.0.0-p12.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.1-p8.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.2-p7.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.3-p5.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.4.2.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.5.2.tar.gz wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.6.1.tar.gz wget http://downloads.sourceforge.net/project/boost/boost/1.37.0/boost_1_37_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.40.0/boost_1_40_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.42.0/boost_1_42_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.46.1/boost_1_46_1.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.48.0/boost_1_48_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.49.0/boost_1_49_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.51.0/boost_1_51_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.53.0/boost_1_53_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.54.0/boost_1_54_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.56.0/boost_1_56_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.57.0/boost_1_57_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.58.0/boost_1_58_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.59.0/boost_1_59_0.tar.bz2 wget http://downloads.sourceforge.net/project/boost/boost/1.60.0/boost_1_60_0.tar.bz2 wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.6.10/src/hdf5-1.6.10.tar.bz2 wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.9/src/hdf5-1.8.9.tar.bz2 wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.bz2 wget http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.tar.bz2 wget http://mirror.ox.ac.uk/sites/rsync.apache.org/xerces/c/2/sources/xerces-c-src_2_8_0.tar.gz wget http://mirror.ox.ac.uk/sites/rsync.apache.org/xerces/c/3/sources/xerces-c-3.1.1.tar.gz wget http://www.codesynthesis.com/download/xsd/2.3/linux-gnu/x86_64/xsd-2.3.1-x86_64-linux-gnu.tar.bz2 wget http://www.codesynthesis.com/download/xsd/3.1/linux-gnu/x86_64/xsd-3.1.0-x86_64-linux-gnu.tar.bz2 wget http://www.codesynthesis.com/download/xsd/3.2/linux-gnu/x86_64/xsd-3.2.0-x86_64-linux-gnu.tar.bz2 wget http://www.codesynthesis.com/download/xsd/3.3/linux-gnu/x86_64/xsd-3.3.0-x86_64-linux-gnu.tar.bz2 wget http://www.codesynthesis.com/download/xsd/4.0/linux-gnu/x86_64/xsd-4.0.0-x86_64-linux-gnu.tar.bz2 wget https://chaste.cs.ox.ac.uk/public/deps/xsd-setg.patch wget https://chaste.cs.ox.ac.uk/public/deps/cvode-2.5.0.tar.gz wget https://chaste.cs.ox.ac.uk/public/deps/cvode-2.6.0.tar.gz wget https://chaste.cs.ox.ac.uk/public/deps/cvode-2.7.0.tar.gz wget https://chaste.cs.ox.ac.uk/public/deps/cvode-2.8.1.tar.gz wget http://www.cmake.org/files/v2.8/cmake-2.8.12.2.tar.gz wget http://www.vtk.org/files/release/5.10/vtk-5.10.1.tar.gz wget http://www.vtk.org/files/release/6.0/vtk-6.0.0.tar.gz wget http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz wget http://prdownloads.sourceforge.net/scons/scons-2.4.0.tar.gz for f in *gz; do tar -zxf $f; done for f in *bz2; do tar -jxf $f; done # Texttest, for acceptance testing cd wget http://downloads.sourceforge.net/project/texttest/texttest/3.19/texttest-3.19.zip unzip texttest-3.19.zip mv texttest-3.19.zip src/ # CodeSynthesis XSD cd ~/src mv xsd-*-linux-gnu .. for ver in ~/xsd-3*; do cd $ver patch -p0 <~/src/xsd-setg.patch done # CVODE cd ~/src wget --no-check-certificate https://chaste.cs.ox.ac.uk/cgi-bin/trac.cgi/raw-attachment/wiki/InstallCvode/cvode.patch cd ~/src/cvode-2.5.0/ patch -p0 < ../cvode.patch ./configure --prefix=$HOME/cvode --with-cflags=-O3 --with-fflags=-O3 --disable-mpi --enable-shared && make && make install cd ~/src/cvode-2.6.0/ patch -p0 < ../cvode.patch ./configure --prefix=$HOME/cvode_2_6 --with-cflags=-O3 --with-fflags=-O3 --disable-mpi --enable-shared && make && make install cd ~/src/cvode-2.7.0/ patch -p0 < ../cvode.patch ./configure --prefix=$HOME/cvode_2_7 --with-cflags=-O3 --with-fflags=-O3 --disable-mpi --enable-shared && make && make install # Note that CVODE 2.8 moved to a CMake build cd ~/src/cvode-2.8.1/ mkdir build cd build cmake -DCMAKE_INSTALL_PREFIX=/home/robert/cvode_2_8 -DBUILD_SHARED_LIBS=ON -DCMAKE_BUILD_TYPE=Release -DEXAMPLES_ENABLE=OFF .. make && make install # MPI - option # Note that on userpc58 this is a symbolic link to the bob MPI - see top of script cd ~/src/mpich-1.2.7p1 CCFLAGS=-fPIC CFLAGS=-fPIC ./configure --prefix=${HOME}/mpi --with-comm=shared --with-device=ch_shmem --enable-sharedlib --disable-f77 make cd examples/test/ make testing cd ../.. make install # ParMETIS - option # Note that on userpc59 this is a symbolic link to the bob ParMETIS - see top of script cd ~/src/ParMetis-3.1/ export PATH=${HOME}/mpi/bin:${PATH} cp Makefile.in Makefile.in.orig sed 's/mpicc/\/home\/robert\/mpi\/bin\/mpicc/' Makefile.in.orig > Makefile.in make cd mv src/ParMetis-3.1 . chmod -R a+rX ParMetis-3.1 # Boost cd ~/src/boost_1_37_0/ ./configure --prefix=$HOME/boost_1_37 && make && make install cd ~/src/boost_1_40_0/ ./bootstrap.sh --prefix=$HOME/boost_1_40 && ./bjam -j 10 install cd ~/src/boost_1_42_0/ ./bootstrap.sh --prefix=$HOME/boost_1_42 && ./bjam -j 10 install cd ~/src/boost_1_46_1/ ./bootstrap.sh --prefix=$HOME/boost_1_46_1 && ./bjam -j 10 install cd ~/src/boost_1_48_0/ ./bootstrap.sh --prefix=$HOME/boost_1_48 && ./b2 -j 10 install cd ~/src/boost_1_49_0/ ./bootstrap.sh --prefix=$HOME/boost_1_49 && ./b2 -j 10 install cd ~/src/boost_1_51_0/ ./bootstrap.sh --prefix=$HOME/boost_1_51 && ./b2 -j 10 install cd ~/src/boost_1_53_0/ ./bootstrap.sh --prefix=$HOME/boost_1_53 && ./b2 -j 10 install cd ~/src/boost_1_54_0/ ./bootstrap.sh --prefix=$HOME/boost_1_54 && ./b2 -j 10 install cd ~/src/boost_1_55_0/ ./bootstrap.sh --prefix=$HOME/boost_1_55 && ./b2 -j 10 install cd ~/src/boost_1_56_0/ ./bootstrap.sh --prefix=$HOME/boost_1_56 && ./b2 -j 10 install cd ~/src/boost_1_57_0/ ./bootstrap.sh --prefix=$HOME/boost_1_57 && ./b2 -j 10 install cd ~/src/boost_1_58_0/ ./bootstrap.sh --prefix=$HOME/boost_1_58 && ./b2 -j 10 install cd ~/src/boost_1_59_0/ ./bootstrap.sh --prefix=$HOME/boost_1_59 && ./b2 -j 10 install cd ~/src/boost_1_60_0/ ./bootstrap.sh --prefix=$HOME/boost_1_60 && ./b2 -j 10 install # HDF5 export OLD_PATH=$PATH export PATH=${HOME}/mpi/bin:${PATH} cd ~/src/hdf5-1.6.10/ export CC=mpicc ./configure --enable-shared --enable-parallel --prefix=${HOME}/hdf5 && make -j10 && make install cd ~/src/hdf5-1.8.9/ ./configure --enable-shared --enable-parallel --prefix=${HOME}/hdf5_1_8_9 && make -j10 && make install # Note: HDF5 1.8.13 doesn't like MPICH 1 #cd ~/src/hdf5-1.8.13 #./configure --enable-parallel --prefix=${HOME}/hdf5_1_8_13 && make -j10 && make install export PATH=$OLD_PATH unset CC # Xerces cd ~/src/xerces-c-src_2_8_0 export XERCESCROOT=`pwd` cd $XERCESCROOT/src/xercesc ./runConfigure -plinux -cgcc -xg++ -P${HOME}/xercesc_2_8 && make && make install cd ~/src/xerces-c-3.1.1 ./configure --enable-netaccessor-socket --prefix=${HOME}/xercesc_3_1 && make && make install # PETSc cd ~/src mv petsc-[0-9]* ../ cd ~/petsc-2.3.2-p4/ export PETSC_DIR=`pwd` unset PETSC_ARCH # Just in case! ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false -PETSC_ARCH=linux-gnu --with-clanguage=cxx --with-shared --with-fortran=0 && make all ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false -PETSC_ARCH=linux-gnu-opt --with-clanguage=cxx --with-shared --with-fortran=0 --with-debugging=0 && make all ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false -PETSC_ARCH=linux-gnu-profile --with-clanguage=cxx --with-shared --with-fortran=0 --CFLAGS=-pg -CXXFLAGS=-pg -LDFLAGS=-pg && make all ./config/configure.py --with-cxx=icpc --with-cc=icc --with-vendor-compiler=intel --with-mpi-dir=${HOME}/mpi --with-x=false --with-debugging=0 -PETSC_ARCH=linux-intel-opt-mkl --with-clanguage=cxx --with-blas-lapack-dir=/opt/intel/composerxe/mkl/lib/intel64/ --with-fortran=0 && make all cd ~/petsc-2.3.3-p15/ export PETSC_DIR=`pwd` unset PETSC_ARCH # Just in case! ./config/configure.py --with-make-np=10 --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false -PETSC_ARCH=linux-gnu --with-clanguage=cxx --with-shared --with-fortran=0 && make all ./config/configure.py --with-make-np=10 --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false --with-debugging=0 -PETSC_ARCH=linux-gnu-opt --with-clanguage=cxx --with-shared --with-fortran=0 && make all ./config/configure.py --with-make-np=10 --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false -PETSC_ARCH=linux-gnu-profile --with-clanguage=cxx --with-shared --with-fortran=0 --CFLAGS=-pg -CXXFLAGS=-pg -LDFLAGS=-pg && make all cd ~/petsc-3.0.0-p12/ export PETSC_DIR=`pwd` export PETSC_ARCH=linux-gnu ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false --with-clanguage=cxx --with-shared --with-fortran=0 && make all export PETSC_ARCH=linux-gnu-opt ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false --with-debugging=0 --with-clanguage=cxx --with-shared --with-fortran=0 && make all export PETSC_ARCH=linux-gnu-profile ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false --with-clanguage=cxx --with-shared --with-fortran=0 --CFLAGS=-pg -CXXFLAGS=-pg -LDFLAGS=-pg && make all cd ~/petsc-3.1-p8/ export PETSC_DIR=`pwd` export PETSC_ARCH=linux-gnu ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false --with-clanguage=cxx --with-shared --with-fortran=0 && make all export PETSC_ARCH=linux-gnu-opt ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false --with-debugging=0 --with-clanguage=cxx --with-shared --with-fortran=0 && make all export PETSC_ARCH=linux-gnu-profile ./config/configure.py --download-c-blas-lapack=1 --with-mpi-dir=${HOME}/mpi --with-x=false --with-clanguage=cxx --with-shared --with-fortran=0 --CFLAGS=-pg -CXXFLAGS=-pg -LDFLAGS=-pg && make all # Note: this is dangerous! Since PETSc has its own MPICH it needs its own HDF5, which will be used in preference to any lofty/_hostconfig specification # See e.g. https://chaste.cs.ox.ac.uk/tests.py/testsuite?buildType=_hostconfig,petsc=3-2,hdf5=1-8,boost=1-40,xsd=4-0,cvode=2-7&machine=userpc59.cs.ox.ac.uk&revision=23319&runtime=0&status=OK&testsuite=global-test-TestChasteBuildInfo×tamp=1420204242.7705&type=nightly which reports using HDF5 1.8.6 (despite 1.8.9 being installed above), # and https://chaste.cs.ox.ac.uk/tests.py/testsuite?buildType=_hostconfig,petsc=3-3,hdf5=1-6,boost=1-54,xsd=3-1,cvode=2-7,parmetis=4&machine=userpc59.cs.ox.ac.uk&revision=23315&runtime=0&status=OK&testsuite=global-test-TestChasteBuildInfo×tamp=1419722101.4278&type=nightly which reports using HDF5 1.8.8. cd ~/petsc-3.2-p7/ export PETSC_DIR=`pwd` export PETSC_ARCH=linux-gnu ./config/configure.py --download-f2cblaslapack=1 --download-mpich=1 --download-parmetis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 && ./config/builder.py export PETSC_ARCH=linux-gnu-opt ./config/configure.py --download-f2cblaslapack=1 --download-mpich=1 --download-parmetis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --with-debugging=0 && ./config/builder.py export PETSC_ARCH=linux-gnu-profile ./config/configure.py --download-f2cblaslapack=1 --download-mpich=1 --download-parmetis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --CFLAGS="-fno-omit-frame-pointer -pg" -CXXFLAGS="-fno-omit-frame-pointer -pg" -LDFLAGS=-pg && ./config/builder.py # Build HDF5 1.8.13 as a replacement for the HDF5 1.8.6 that PETSc 3.2 would install itself export PETSC_DIR=$HOME/petsc-3.2-p7 cd ~/src/hdf5-1.8.13 OLD_PATH=$PATH for build in linux-gnu linux-gnu-opt linux-gnu-profile ; do export PATH=$PETSC_DIR/$build/bin:$OLD_PATH export CC=$PETSC_DIR/$build/bin/mpicc if [ $build == "linux-gnu-profile" ] ; then export CFLAGS="-fno-omit-frame-pointer -pg" else unset CFLAGS fi make clean && ./configure --enable-parallel --prefix=$PETSC_DIR/$build && make -j10 && make install done unset CFLAGS export PATH=$OLD_PATH # "ParMetis updated to 4.0.2 and split from Metis 5.0.2 which is now separate." on http://www.mcs.anl.gov/petsc/documentation/changes/33.html # ParMETIS now requires METIS --download-parmetis=1 # METIS requires cmake # As previous (3.2): this is dangerous! cd ~/petsc-3.3-p5/ export PETSC_DIR=`pwd` export PETSC_ARCH=linux-gnu ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 && ./config/builder.py export PETSC_ARCH=linux-gnu-opt ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --with-debugging=0 && ./config/builder.py export PETSC_ARCH=linux-gnu-profile ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --CFLAGS="-fno-omit-frame-pointer -pg" -CXXFLAGS="-fno-omit-frame-pointer -pg" -LDFLAGS=-pg && ./config/builder.py ## PETSc 3.4 is used in multiple versions of Ubuntu including 14.04 LTS. We therefore use this version for optional compilation with HYPRE. ## NOTE: Compilation with Hypre requires a Fortran compiler. For Intel compilation it also specifically requires {{{ifort}}} since {{{icpc/gfortran}}} compilation of HDF5 dependency is buggy. # As previous (3.2): this is dangerous! cd ~/petsc-3.4.2/ export PETSC_DIR=`pwd` export PETSC_ARCH=linux-gnu ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --download-hypre=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=1 && ./config/builder.py export PETSC_ARCH=linux-gnu-opt ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --download-hypre=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=1 --with-debugging=0 && ./config/builder.py export PETSC_ARCH=linux-gnu-profile ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --download-hypre=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=1 --CFLAGS="-fno-omit-frame-pointer -pg" -CXXFLAGS="-fno-omit-frame-pointer -pg" -LDFLAGS=-pg && ./config/builder.py # (See above) Remember that Intel compilers require # source /opt/intel/bin/compilervars.sh intel64 ; export INTEL_LICENSE_FILE="28519@flexlm.nsms.ox.ac.uk" export PETSC_ARCH=linux-intel ./config/configure.py --with-cxx=icpc --with-cc=icc --with-fc=ifort --with-vendor-compiler=intel --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --download-hypre=1 --with-x=false --with-clanguage=cxx --with-fortran=1 && make all export PETSC_ARCH=linux-intel-opt-mkl ./config/configure.py --with-cxx=icpc --with-cc=icc --with-fc=ifort --with-vendor-compiler=intel --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --download-hypre=1 --with-x=false --with-debugging=0 -PETSC_ARCH=linux-intel-opt-mkl --with-clanguage=cxx --with-blas-lapack-dir=/opt/intel/composerxe/mkl/lib/intel64/ --with-fortran=1 && ./config/builder.py cd ~/petsc-3.5.2/ export PETSC_DIR=`pwd` export PETSC_ARCH=linux-gnu ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 && make all export PETSC_ARCH=linux-gnu-opt ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --with-debugging=0 && make all export PETSC_ARCH=linux-gnu-profile ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --CFLAGS="-fno-omit-frame-pointer -pg" -CXXFLAGS="-fno-omit-frame-pointer -pg" -LDFLAGS=-pg && make all cd ~/petsc-3.6.1/ export PETSC_DIR=`pwd` export PETSC_ARCH=linux-gnu ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 && make all export PETSC_ARCH=linux-gnu-opt ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --with-debugging=0 && make all export PETSC_ARCH=linux-gnu-profile ./config/configure.py --with-make-np=10 --download-f2cblaslapack=1 --download-mpich=1 --download-hdf5=1 --download-parmetis=1 --download-metis=1 --with-x=false --with-clanguage=cxx --with-shared-libraries --with-fortran=0 --CFLAGS="-fno-omit-frame-pointer -pg" -CXXFLAGS="-fno-omit-frame-pointer -pg" -LDFLAGS=-pg && make all # VTK; needs recent CMake to build! cd ~/src/cmake-2.8.12.2/ ./bootstrap --prefix=$HOME/cmake --parallel=4 && make -j10 && make install cd ~/bin for f in ~/cmake/bin/*; do ln -s $f; done # Note cmake calls below rely on defaults VTK_BUILD_ALL_MODULES=OFF, BUILD_SHARED_LIBS=ON # 5.10 mkdir ~/src/vtk-build-5.10 cd ~/src/vtk-build-5.10 cmake -DCMAKE_INSTALL_PREFIX=$HOME/vtk-5.10 ../VTK5.10.1 && make -j10 && make install # 6.0 mkdir ~/src/vtk-build-6.0 cd ~/src/vtk-build-6.0 cmake -DCMAKE_INSTALL_PREFIX=$HOME/vtk-6.0 ../VTK6.0.0 && make -j10 && make install # 6.1 mkdir ~/src/vtk-build-6.1 cd ~/src/vtk-build-6.1 cmake -DCMAKE_INSTALL_PREFIX=$HOME/vtk-6.1 ../VTK-6.1.0 && make -j10 && make install # SCons cd ~/src/scons-2.4.0 python setup.py install --prefix=$HOME --no-scons-script # Run it with scons-2.4.0, not scons
Hostconfig configuration
import glob import os petsc_2_2_path = '../../../petsc-2.2.1/' petsc_2_3_path = '../../../petsc-2.3.2-p4/' petsc_3_0_path = '../../../petsc-3.0.0-p12/' petsc_build_name = 'linux-gnu' petsc_build_name_profile = 'linux-gnu-profile' petsc_build_name_optimized = 'linux-gnu-opt' petsc_build_name_production = 'linux-intel-opt-mkl' parmetis_path = '../../../ParMetis-3.1/' intel_path='/opt/intel/composerxe' icpc = 'icpc' other_includepaths = ['../../../xsd-3.2.0-x86_64-linux-gnu/libxsd', '../../../hdf5/include', parmetis_path] other_libpaths = [os.path.join(petsc_2_3_path, 'externalpackages/f2cblaslapack/linux-gnu/'), '../../../hdf5/lib', parmetis_path] blas_lapack = ['f2clapack', 'f2cblas'] blas_lapack_production = ['mkl_lapack', 'mkl', 'svml'] other_libraries = ['boost_serialization', 'boost_filesystem', 'xerces-c', 'hdf5', 'z', 'parmetis', 'metis'] ccflags = '' ldflags = '' tools = {'texttest': '../../../texttest-3.19/source/bin/texttest.py', 'xsd': '../../../xsd-3.2.0-x86_64-linux-gnu/bin/xsd', 'mpicxx': 'mpicxx', 'mpirun': 'mpirun'} def Configure(prefs, build): """Allow the user to specify which version of various libraries we're using.""" # PETSc global petsc_path global petsc_2_3_path external_packages = 'externalpackages' # We default to PETSc 3 (see hostconfig.py) if present for this user if os.path.isdir(petsc_3_0_path): prefs['petsc'] = prefs.get('petsc', '3.0') else: prefs['petsc'] = prefs.get('petsc', '2.3') if prefs['petsc'] == '3.4': petsc_path = '/home/lofty/petsc-3.4.2' elif prefs['petsc'] == '3.3': petsc_path = '/home/lofty/petsc-3.3-p5' elif prefs['petsc'] == '3.2': petsc_path = '/home/lofty/petsc-3.2-p7' elif prefs['petsc'] == '3.1': petsc_path = '/home/lofty/petsc-3.1-p8' elif prefs['petsc'] == '3.0': petsc_path = petsc_3_0_path elif prefs['petsc'] == '2.3.3': petsc_2_3_path = '/home/lofty/petsc-2.3.3-p15/' #For testing SUBMINOR=3 petsc_path = petsc_2_3_path elif prefs['petsc'] == '2.3': petsc_path = petsc_2_3_path elif prefs['petsc'] == '2.2': petsc_path = petsc_2_2_path external_packages = 'packages' else: raise ValueError('Unsupported PETSc version "%s" requested' % prefs['petsc']) if build.is_optimised: build_name = petsc_build_name_optimized else: build_name = petsc_build_name other_libpaths[0] = os.path.join(petsc_path, external_packages, 'f2cblaslapack', build_name) # Boost prefs['boost'] = prefs.get('boost', '1.40') # 1.40 is installed system-wide for ver in ['1.37', '1.42', '1.46.1', '1.48', '1.49', '1.51', '1.53', '1.54', '1.55']: if prefs['boost'] == ver: AddBoost('/home/lofty/boost_' + ver.replace('.', '_'), prefs['boost']) break else: if prefs['boost'] != '1.40': raise ValueError('Unsupported Boost version "%s" requested' % prefs['boost']) # HDF5 prefs['hdf5'] = prefs.get('hdf5', '1.6') if prefs['hdf5'] == '1.8': AddHdf5('/home/lofty/hdf5_1_8_9/') elif prefs['hdf5'] == '1.6': AddHdf5('../../../hdf5/') else: raise ValueError('Unsupported HDF5 version "%s" requested' % prefs['hdf5']) # Xerces prefs['xerces'] = prefs.get('xerces', '3.1') if prefs['xerces'] == '2.8': AddXerces('/home/lofty/xercesc_2_8') # XSD prefs['xsd'] = prefs.get('xsd', '3.2') if prefs['xsd'] == '4.0': AddXsd('../../../xsd-4.0.0-x86_64-linux-gnu') elif prefs['xsd'] == '3.3': AddXsd('../../../xsd-3.3.0-x86_64-linux-gnu') elif prefs['xsd'] == '3.2': AddXsd('../../../xsd-3.2.0-x86_64-linux-gnu') elif prefs['xsd'] == '3.1': AddXsd('../../../xsd-3.1.0-x86_64-linux-gnu') elif prefs['xsd'] == '2.3': AddXsd('../../../xsd-2.3.1-x86_64-linux-gnu') else: raise ValueError('Unsupported XSD version "%s" requested' % prefs['xsd']) # Parmetis. We don't switch the libraries explicitly for this, since Parmetis 4 is obtained via PETSc 3.3. # Instead we remove the version 3 includes if version 4 is requested. if 'parmetis' in prefs: global ccflags parmetis = prefs['parmetis'] ccflags += ' -DCHASTE_PARMETIS_REQUIRED=' + str(parmetis) petsc_ver = map(int, prefs['petsc'].split('.')[:2]) if parmetis == '3' and petsc_ver >= [3, 3]: raise ValueError('You cannot use both ParMETIS 3 and PETSc >= 3.3') if parmetis == '4': if petsc_ver < [3, 3]: raise ValueError('To use ParMETIS 4 you must install it using a recent PETSc (>= 3.3)') RemoveFromPath(other_includepaths, parmetis_path) RemoveFromPath(other_libpaths, parmetis_path) # Optional libraries global use_cvode global use_vtk global use_adaptivity use_cvode = int(prefs.get('use-cvode', 1)) if use_cvode: prefs['cvode'] = prefs.get('cvode', '2.5') if prefs['cvode'] == '2.5': cvode_path = '../../../cvode' elif prefs['cvode'] == '2.6': cvode_path = '/home/lofty/cvode_2_6' elif prefs['cvode'] == '2.7': cvode_path = '/home/lofty/cvode_2_7' else: raise ValueError('Unsupported CVODE version "%s" requested' % prefs['cvode']) other_includepaths.append(os.path.join(cvode_path, 'include')) DetermineCvodeVersion(other_includepaths[-1]) other_libpaths.append(os.path.join(cvode_path, 'lib')) other_libraries.extend(['sundials_cvode', 'sundials_nvecserial']) use_vtk = int(prefs.get('use-vtk', 1)) # VTK is required for adaptivity to work, so if vtk was explicitly # turned off, turn off adaptivity too. use_adaptivity = int(prefs.get('use-adaptivity', 1)) and use_vtk # Todo #2367 - give a warning if adaptivity is requested, because it is no longer supported. # This has to come after the 'if use_adaptivity' block, because the libraries there depend on these if use_vtk: prefs['vtk'] = prefs.get('vtk', '5') if prefs['vtk'] == '6.1': other_includepaths.append('/home/lofty/vtk-6.1/include/vtk-6.1') other_libpaths.append('/home/lofty/vtk-6.1/lib') other_libraries.extend(['vtkCommonCore-6.1','vtkCommonDataModel-6.1','vtkIOXML-6.1','vtkCommonExecutionModel-6.1','vtkFiltersCore-6.1','libvtkFiltersGeometry-6.1']) elif prefs['vtk'] == '6.0': other_includepaths.append('/home/lofty/vtk-6.0/include/vtk-6.0') other_libpaths.append('/home/lofty/vtk-6.0/lib') other_libraries.extend(['vtkCommonCore-6.0','vtkCommonDataModel-6.0','vtkIOXML-6.0','vtkCommonExecutionModel-6.0','vtkFiltersCore-6.0','libvtkFiltersGeometry-6.0']) elif prefs['vtk'] == '5.10': other_includepaths.append('/home/lofty/vtk-5.10/include/vtk-5.10') other_libpaths.append('/home/lofty/vtk-5.10/lib/vtk-5.10') other_libraries.extend(['vtkGraphics','vtkFiltering','vtkIO','vtkCommon', 'vtksys', 'vtkexpat', 'vtkzlib']) else: vtk_include_path = filter(os.path.isdir, glob.glob('/usr/include/vtk-5*')) if len(vtk_include_path) != 1: raise ValueError("No or multiple system headers for VTK 5 found") vtk_version = float(vtk_include_path[0].split('-')[1]) other_includepaths.append(vtk_include_path[0]) other_libraries.extend(['vtkIO','vtkGraphics','vtkCommon', 'z']) if vtk_version >= 5.6: other_libraries.append('vtkFiltering')