Merge branch 'mac_fixes' into stable/proteus

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:
+  pytest-xdist:
+  boost:
+    toolset: darwin

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/")

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

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'

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

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'

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']
 

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

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

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

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"

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']

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}',
   ]
-

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']

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:

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/*'