diff --git a/examples/proteus.darwin.yaml b/examples/proteus.darwin.yaml index ba7713af2..43646f429 100644 --- a/examples/proteus.darwin.yaml +++ b/examples/proteus.darwin.yaml @@ -12,7 +12,7 @@ extends: - file: osx_clt.yaml -# The packages list specifies all the packages that you +# The packages list specifies all the packages that you # require installed. <#> will ensure that all packages # and their dependencies are installed when you build this # profile. @@ -25,6 +25,7 @@ packages: version: '2.1' python: host: false + link: shared build_with: | blas: @@ -33,7 +34,7 @@ packages: use: host-osx-framework-accelerate daetk: mpi: - use: mpich + use: openmpi mpi4py: nose: hdf5: @@ -44,22 +45,23 @@ packages: ipython: matplotlib: petsc: - version: 3.6.1 + version: 3.7.5 build_with: | - parmetis + parmetis, cmake, suitesparse download: | - superlu + superlu, superlu_dist coptflags: -O2 link: shared debug: false disable_fortran: true petsc4py: - version: 3.6.0 + version: 3.7.0 with_conf: true pillow: pytables: + scorec: sphinx: - superlu: + #superlu: sympy: tetgen: triangle: @@ -73,9 +75,12 @@ packages: python-netcdf4: h5py: ode: + openblas: jupyter: functools: use: host-functools yaml: pytest: - pytest-xdist: \ No newline at end of file + pytest-xdist: + boost: + toolset: darwin diff --git a/osx_clt.yaml b/osx_clt.yaml index 8a6c84c05..87989a871 100644 --- a/osx_clt.yaml +++ b/osx_clt.yaml @@ -5,3 +5,5 @@ parameters: platform: Darwin fortran: false PATH: /usr/bin:/bin:/usr/sbin:/sbin + PROLOGUE: | + export MACOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion | sed -E "s/([0-9]+\.[0-9]+).*/\1/") diff --git a/pkgs/boost/boost.yaml b/pkgs/boost/boost.yaml index 544a8d0c6..42ffa94ca 100644 --- a/pkgs/boost/boost.yaml +++ b/pkgs/boost/boost.yaml @@ -7,8 +7,8 @@ dependencies: build: [bzip2, mpi, zlib, {{build_with}}] sources: -- key: tar.bz2:oj5jgizc3fbipnrkxmn5fvaxepxminlk - url: http://downloads.sourceforge.net/boost/boost_1_59_0.tar.bz2 +- key: tar.bz2:nbvp774ytlberd3zvf5zi6ppxhzkxlqd + url: http://downloads.sourceforge.net/boost/boost_1_60_0.tar.bz2 build_stages: - name: bootstrap @@ -17,14 +17,6 @@ build_stages: bash: | ./bootstrap.sh --with-toolset={{toolset}} --prefix=${ARTIFACT} -- name: boost_1_55_fix_warnings - before: bjam - after: bootstrap - handler: bash - files: [boost_1_55_fix_warnings.patch] - bash: | - patch -p2 < _hashdist/boost_1_55_fix_warnings.patch - - name: set-address_model before: bjam handler: bash diff --git a/pkgs/cmake.yaml b/pkgs/cmake.yaml index a3d7d922c..40af41b73 100644 --- a/pkgs/cmake.yaml +++ b/pkgs/cmake.yaml @@ -4,8 +4,8 @@ dependencies: build: [zlib, bzip2, curl, openssl, libidn, expat, ncurses] sources: -- key: tar.gz:3j6mgtq44hmc4z5dfkyidqbmfbcvgtgy - url: https://cmake.org/files/v3.4/cmake-3.4.2.tar.gz +- key: tar.gz:zzozcyjznydfagya4uutg6brkcuhymyi + url: https://cmake.org/files/v3.8/cmake-3.8.1.tar.gz build_stages: - when: platform == 'Darwin' diff --git a/pkgs/doxygen/doxygen.yaml b/pkgs/doxygen/doxygen.yaml index aa79e5f47..ee058e5d3 100644 --- a/pkgs/doxygen/doxygen.yaml +++ b/pkgs/doxygen/doxygen.yaml @@ -7,11 +7,11 @@ sources: - key: tar.gz:chw522awd5akqmsoig2jnhncxz67neew url: https://github.com/doxygen/doxygen/archive/Release_1_8_13.tar.gz -build_stages: - - when: platform == 'Darwin' - name: patch - before: configure - files: [libiconv_plug.patch] - handler: bash - bash: | - patch -up1 < _hashdist/libiconv_plug.patch +#build_stages: +# - when: platform == 'Darwin' +# name: patch +# before: configure +# files: [libiconv_plug.patch] +# handler: bash +# bash: | +# patch -up1 < _hashdist/libiconv_plug.patch diff --git a/pkgs/h5py.yaml b/pkgs/h5py.yaml index 9d03edb5c..80f3b3374 100644 --- a/pkgs/h5py.yaml +++ b/pkgs/h5py.yaml @@ -14,6 +14,7 @@ build_stages: before: install handler: bash bash: | - export HDF5_VERSION='1.8.16' + export HDF5_VERSION='1.8.13' export CC=${MPICC} export SETUPTOOLS_PACKAGE_EXTRA_OPTIONS="configure --mpi" + #export HDF5_VERSION='1.8.16' diff --git a/pkgs/hdf5/hdf5.yaml b/pkgs/hdf5/hdf5.yaml index 49c386626..ad1db1af8 100644 --- a/pkgs/hdf5/hdf5.yaml +++ b/pkgs/hdf5/hdf5.yaml @@ -3,9 +3,8 @@ dependencies: build: [mpi, zlib, szip] sources: -- key: tar.bz2:covk4w5bbnyhjhxbogebnjfux7vnrf6c - url: http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.16/src/hdf5-1.8.16.tar.bz2 - +- key: tar.bz2:yl22ieqqpk5g7gp5pjfj3nwol5p4qfy6 + url: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.bz2 defaults: # /bin/h5pcc contains hard-coded path relocatable: false @@ -24,8 +23,8 @@ build_stages: after: configure before: make bash: | - for f in {test,testpar,tools/*,perform,hl/*,hl/*/*}/Makefile - do + for f in {test,testpar,tools/*,perform,hl/*,hl/*/*}/Makefile + do sed -i 's/CCLD = $(CC)/CCLD = $(CC) -static/g' $f done @@ -37,6 +36,7 @@ build_stages: '--enable-shared', '--enable-production=yes', '--enable-parallel=yes', + '--enable-largefile=yes', '--with-default-api-version=v18'] - when: machine == 'CrayXE6' @@ -49,6 +49,7 @@ build_stages: '--enable-shared', '--enable-production=yes', '--enable-parallel=yes', + '--enable-largefile=yes', '--with-default-api-version=v18', '--with-pic'] diff --git a/pkgs/mpich.yaml b/pkgs/mpich.yaml index 387f549b5..de2990f3b 100644 --- a/pkgs/mpich.yaml +++ b/pkgs/mpich.yaml @@ -10,7 +10,7 @@ build_stages: - when: not fortran name: configure mode: update - extra: ['--disable-f77', '--disable-fc'] + extra: ['--disable-f77', '--disable-fc', '--disable-fortran'] sources: - key: tar.gz:a54gpgtlne6xw7fp6n77tuufnxbl7rit diff --git a/pkgs/openmpi.yaml b/pkgs/openmpi.yaml index 423c88b02..d0f2f8610 100644 --- a/pkgs/openmpi.yaml +++ b/pkgs/openmpi.yaml @@ -1,8 +1,8 @@ extends: [autotools_package] sources: -- url: http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.5.tar.bz2 - key: tar.bz2:7y33voe3l3zdjyfmqlohtaucykvqreal +- url: https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.6.tar.bz2 + key: tar.bz2:mvqgdbfaqsqo3jqqfma6li3kr4bnggk5 defaults: # lib/openmpi/mca_carto_auto_detect.la contains hard-coded path diff --git a/pkgs/parmetis/parmetis.yaml b/pkgs/parmetis/parmetis.yaml index 05fc58db5..15d74a959 100644 --- a/pkgs/parmetis/parmetis.yaml +++ b/pkgs/parmetis/parmetis.yaml @@ -11,7 +11,7 @@ defaults: # lib/libmetis.so contains hard-coded path relocatable: false # Skip build-time tests (not recommended) - without_check: false + without_check: platform != "Darwin" build_stages: - name: setup_builddir diff --git a/pkgs/readline.yaml b/pkgs/readline.yaml index b60e5b403..a8ef2b735 100644 --- a/pkgs/readline.yaml +++ b/pkgs/readline.yaml @@ -11,8 +11,16 @@ build_stages: mode: override extra: ['--enable-shared', '--with-curses'] - - name: make + - when: platform != 'Darwin' + name: make mode: replace handler: bash bash: | make SHOBJ_CFLAGS="-fPIC -D_REENTRANT" SHOBJ_LDFLAGS="-shared -Wl,-rpath=$NCURSES_DIR/lib" SHLIB_LIBS="-ltinfo" + + - when: platform == 'Darwin' + name: make + mode: replace + handler: bash + bash: | + make SHOBJ_CFLAGS="-fPIC -D_REENTRANT" SHOBJ_LDFLAGS="-shared -Wl,-rpath,$NCURSES_DIR/lib" SHLIB_LIBS="-ltinfo" diff --git a/pkgs/remus.yaml b/pkgs/remus.yaml new file mode 100644 index 000000000..4d7c801a9 --- /dev/null +++ b/pkgs/remus.yaml @@ -0,0 +1,14 @@ +extends: [cmake_package] +dependencies: + build: [boost, zmq] + +sources: +- url: https://gitlab.kitware.com/cmb/remus.git + key: git:1148df5bb86a2dc9bd61d19edbe6f77c582a5641 + +defaults: + relocatable: true + +build_stages: +- name: configure + extra: ['-D BUILD_SHARED_LIBS:BOOL=ON'] diff --git a/pkgs/scorec.yaml b/pkgs/scorec.yaml index 87a3cf3a4..7000c119a 100644 --- a/pkgs/scorec.yaml +++ b/pkgs/scorec.yaml @@ -3,9 +3,9 @@ dependencies: build: [mpi, parmetis, zoltan] sources: - - url: https://github.com/SCOREC/core.git - key: git:e219777edd875d35096dfedd7197300b8e2f3837 - + - url: https://github.com/tjcorona/core.git + key: git:374c1f0640d2a96242e7a5fd01fd27bd5a935b11 + defaults: relocatable: true @@ -29,4 +29,3 @@ build_stages: '-DZOLTAN_PREFIX:PATH=${ZOLTAN_DIR}', '-DPARMETIS_PREFIX:PATH=${PARMETIS_DIR}', ] - diff --git a/pkgs/smtk.yaml b/pkgs/smtk.yaml new file mode 100644 index 000000000..8b53bc060 --- /dev/null +++ b/pkgs/smtk.yaml @@ -0,0 +1,31 @@ +extends: [cmake_package] +dependencies: + build: [boost, gdal, hdf5, netcdf4, mpi, python, remus, vtk, zmq] + +sources: +- url: https://gitlab.kitware.com/tjcorona/smtk.git + key: git:9c18b1d7207d17995ce260e095e7a5e9ae5f63cb + +defaults: + relocatable: true + +build_stages: +- name: configure + extra: ['-D SMTK_ENABLE_VTK_SUPPORT:BOOL=ON', + '-D SMTK_ENABLE_DISCRETE_SESSION:BOOL=ON', + '-D SMTK_ENABLE_EXODUS_SESSION:BOOL=ON', + '-D SMTK_ENABLE_MESH_SESSION:BOOL=ON', + '-D SMTK_ENABLE_POLYGON_SESSION:BOOL=ON', + '-D SMTK_ENABLE_REMOTE_SESSION:BOOL=ON', + '-D SMTK_ENABLE_REMUS_SUPPORT:BOOL=ON', + '-D SMTK_ENABLE_PYTHON_WRAPPING:BOOL=ON', + '-D SMTK_USE_PYBIND11:BOOL=ON', + '-D SMTK_USE_SYSTEM_MOAB:BOOL=OFF', + '-D ENABLE_HDF5:BOOL=ON', + '-D ENABLE_NETCDF:BOOL=ON', + '-D NETCDF_ROOT:STRING=${NETCDF4_DIR}', + '-D VTK_DIR:STRING=${VTK_DIR}', + '-D PYTHON_LIBRARY:FILEPATH=${PYTHON_DIR}/lib/libpython2.7.dylib', + '-D PYTHON_EXECUTABLE:FILEPATH=${PYTHON_DIR}/bin/python2.7', + '-D PYTHON_INCLUDE_DIR:PATH=${PYTHON_DIR}/include/python2.7', + '-D NETCDF_C_LIBRARY=${NETCDF4_DIR}/lib/libnetcdf.dylib'] diff --git a/pkgs/szip.yaml b/pkgs/szip.yaml index 89409a14f..544d577f7 100755 --- a/pkgs/szip.yaml +++ b/pkgs/szip.yaml @@ -1,7 +1,7 @@ extends: [cmake_package] sources: -- url: http://www.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz +- url: https://support.hdfgroup.org/ftp/lib-external/szip/2.1/src/szip-2.1.tar.gz key: tar.gz:valnsxkwmlucpfrfvpn6u7iomikx27i7 build_stages: diff --git a/pkgs/vtk/vtk.yaml b/pkgs/vtk/vtk.yaml index 3ae611637..fb9fabafb 100644 --- a/pkgs/vtk/vtk.yaml +++ b/pkgs/vtk/vtk.yaml @@ -2,6 +2,7 @@ extends: [cmake_package] dependencies: build: - python + - gdal - setuptools - libtiff - when platform == 'linux': @@ -14,7 +15,7 @@ sources: url: http://www.vtk.org/files/release/7.1/VTK-7.1.1.tar.gz defaults: - # lib/vtk-5.10/libvtkHybrid.so.5.10.1 contains hard-coded path + # lib/vtk-7.1/libvtkHybrid.so.7.1.0 contains hard-coded path relocatable: false vtk_use_tk: false @@ -28,37 +29,27 @@ build_stages: export PYTHONPATH=${ARTIFACT}/{{python_site_packages_rel}}:$PYTHONPATH mkdir -p ${ARTIFACT}/{{python_site_packages_rel}} -- when: platform == 'Cygwin' - files: [vtk-5.10.1-cygwin.patch] - name: vtk_cygwin_patch - handler: bash - before: setup_builddir - bash: | - patch -p1 < _hashdist/vtk-5.10.1-cygwin.patch - -- when: platform == 'Darwin' - files: [vtk-disable-gc.patch] - name: vtk_disable_gc_patch - handler: bash - before: setup_builddir - bash: | - patch -p1 < _hashdist/vtk-disable-gc.patch - - name: configure - extra: + extra: - '-D BUILD_TESTING:BOOL=OFF' - '-D BUILD_EXAMPLES:BOOL=OFF' - '-D BUILD_SHARED_LIBS:BOOL=ON' - '-D VTK_WRAP_PYTHON:BOOL=ON' - '-D VTK_WRAP_TCL:BOOL=OFF' - - '-D PYTHON_EXECUTABLE:FILEPATH="${PYTHON}"' + - '-D VTK_USE_GL2PS:BOOL=ON' + - '-D VTK_PYTHON_SETUP_ARGS:STRING="--prefix=. --root=${ARTIFACT} --single-version-externally-managed"' + - '-D PYTHON_EXECUTABLE:FILEPATH=${PYTHON_DIR}/bin/python2.7' + - '-D PYTHON_INCLUDE_DIR:PATH=${PYTHON_DIR}/include/python2.7' + - '-D PYTHON_LIBRARY:FILEPATH=${PYTHON_DIR}/lib/libpython2.7.dylib' - '-D VTK_USE_SYSTEM_TIFF:BOOL=ON' - - '-D VTK_Group_Imaging:BOOL=ON' - - '-D VTK_Group_MPI:BOOL=ON' - - '-D VTK_Group_Rendering:BOOL=ON' - - '-D VTK_Group_StandAlone:BOOL=ON' - - '-D VTK_Group_Views:BOOL=ON' - - '-D VTK_Group_Web:BOOL=ON' + - '-D Module_vtkGeovisCore:BOOL=ON' + - '-D Module_vtkIOGDAL:BOOL=ON' + - '-D Module_vtkViewsInfovis:BOOL=ON' + - '-D Module_vtkRenderingMatplotlib:BOOL=ON' + - '-D Module_vtkRenderingGL2PSOpenGL2:BOOL=ON' + - '-D Module_vtkTestingRendering:BOOL=ON' + - '-D Module_vtkIOParallelExodus:BOOL=ON' + - '-D GDAL_DIR:PATH=${GDAL_DIR}' - when: vtk_use_tk name: configure @@ -70,25 +61,6 @@ build_stages: mode: update extra: ['-D VTK_USE_TK:BOOL=OFF'] -- when: platform == 'Darwin' - name: rpath_fix - after: install - handler: bash - bash: | - for vtklib in ${ARTIFACT}/lib/vtk-5.10/*.dylib; do - if [ ! -L ${vtklib} ]; then - install_name_tool -id @rpath/$(basename ${vtklib}) ${vtklib} - otool -L ${vtklib} | while read line; do - set +e - lib=$(echo $line | sed 's/\(lib.*\.dylib\).*/\1/' | grep ^lib) - set -e - if [ ! -z ${lib} ]; then - install_name_tool -change ${lib} @rpath/${lib} ${vtklib} - fi - done - fi - done - profile_links: - name: python_packages link: 'lib/python{{pyver}}/site-packages/*'