openFOAM-paraview-catalyst (#10129)

* paraview: adding variants to use external packages as internal do not compile

* paraview: add latest paraview version

* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5

* catalyst: add latest catalyst version

* catalyst: added ParaView_DIR env variable to catalyst module

* add paraview, catalyst patches

- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436

* - Handle updated library paths for catalyst.

  Versions 5.4 and old places libraries under a paraview subdirectory.
  Eg, "lib/paraview-5.4", they are now placed directly under "lib"

- Minor code style cleanup

* Handle update library and python paths for ParaView-5.5

* catalyst: added ParaView_DIR path to spack_env

* BUG: applied the patch to the extracted catalyst source files

* paraview: added missing self to a member variable

* paraview: added Paraview_DIR to env

* catalyst: added osmesa variant

* of-catalyst: added new package

* add (FOAM,WM)_PROJECT_DIR  also to spack_env environment

* depends on first openfoam release supporting catalyst

* openfoam-com: added missing env variables to module generation

* openfoam: fixed flake8 errors

* of-catalyst: added full variant and openfoam version dependency

* paraview: adding variants to use external packages as internal do not compile

* catalyst: fixed libvtkexpat undefined reference linking error in Catalyst 5.5

* catalyst: added ParaView_DIR env variable to catalyst module

* add paraview, catalyst patches

- https://gitlab.kitware.com/vtk/vtk-m/merge_requests/1166
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2433
- https://gitlab.kitware.com/paraview/paraview/merge_requests/2436

* - Handle updated library paths for catalyst.

  Versions 5.4 and old places libraries under a paraview subdirectory.
  Eg, "lib/paraview-5.4", they are now placed directly under "lib"

- Minor code style cleanup

* Handle update library and python paths for ParaView-5.5

* catalyst: added ParaView_DIR path to spack_env

* BUG: applied the patch to the extracted catalyst source files

* of-catalyst: added new package

* add (FOAM,WM)_PROJECT_DIR  also to spack_env environment

* depends on first openfoam release supporting catalyst

* paraview: added missing self to a member variable

* openfoam-com: added missing env variables to module generation

* openfoam: fixed flake8 errors

* paraview: added Paraview_DIR to env

* catalyst: added osmesa variant

* of-catalyst: added full variant and openfoam version dependency

* paraview-catalyst: use always external expat and netcdf

* of-catalyst: reformatted package description

* paraview-catalyst: removed duplicated function

* catalyst: fixed flake8 error

* of-catalyst: fixed license header

* of-catalyst: minor changes

* of-catalyst: renamed gitrepo with git

* of-catalyst: removed useless gitrepo parameter

var/spack/repos/builtin/packages/catalyst/package.py

@@ -7,6 +7,7 @@
 import os
 import subprocess
 import llnl.util.tty as tty
+from spack.patch import absolute_path_for_package
 
 
 class Catalyst(CMakePackage):
@@ -33,17 +34,31 @@ class Catalyst(CMakePackage):
     variant('python', default=False, description='Enable Python support')
     variant('essentials', default=False, description='Enable Essentials support')
     variant('extras', default=False, description='Enable Extras support')
-    variant('rendering', default=False, description='Enable Vtk Rendering support')
+    variant('rendering', default=False, description='Enable VTK Rendering support')
+    variant('osmesa', default=True, description='Use offscreen rendering')
 
-    depends_on('git')
+    depends_on('git', type='build')
     depends_on('mpi')
     depends_on('python@2:2.8', when='+python', type=("build", "link", "run"))
     depends_on('python', when='~python', type=("build"))
     depends_on('mesa', when='+rendering')
-    depends_on("libx11", when='+rendering')
-    depends_on("libxt", when='+rendering')
+    depends_on('libx11', when='+rendering')
+    depends_on('libxt', when='+rendering')
     depends_on('cmake@3.3:', type='build')
 
+    @when('@5.5.0:5.5.2')
+    def patch(self):
+        """Apply the patch (it should be fixed in Paraview 5.6)
+        at the package dir to the source code in
+        root_cmakelists_dir."""
+        patch_name = 'vtkm-catalyst-pv551.patch'
+        pkg_dir = os.path.dirname(absolute_path_for_package(self))
+        patch = which("patch", required=True)
+        with working_dir(self.root_cmakelists_dir):
+            patch('-s', '-p', '1', '-i',
+                  join_path(pkg_dir, patch_name),
+                  "-d", '.')
+
     def url_for_version(self, version):
         """Handle ParaView version-based custom URLs."""
         if version < Version('5.1.0'):
@@ -53,6 +68,30 @@ def url_for_version(self, version):
         else:
             return self._urlfmt_xz.format(version.up_to(2), version, '')
 
+    @property
+    def paraview_subdir(self):
+        """The paraview subdirectory name as paraview-major.minor"""
+        return 'paraview-{0}'.format(self.spec.version.up_to(2))
+
+    @property
+    def editions(self):
+        """Transcribe spack variants into names of Catalyst Editions"""
+        selected = ['Base']  # Always required
+
+        if '+python' in self.spec:
+            selected.append('Enable-Python')
+
+        if '+essentials' in self.spec:
+            selected.append('Essentials')
+
+        if '+extras' in self.spec:
+            selected.append('Extras')
+
+        if '+rendering' in self.spec:
+            selected.append('Rendering-Base')
+
+        return selected
+
     def do_stage(self, mirror_only=False):
         """Unpacks and expands the fetched tarball.
         Then, generate the catalyst source files."""
@@ -62,38 +101,15 @@ def do_stage(self, mirror_only=False):
         paraview_dir = os.path.join(self.stage.path,
                                     'ParaView-v' + str(self.version))
         catalyst_script = os.path.join(paraview_dir, 'Catalyst', 'catalyze.py')
+        editions_dir = os.path.join(paraview_dir, 'Catalyst', 'Editions')
         catalyst_source_dir = os.path.abspath(self.root_cmakelists_dir)
 
         command = ['python', catalyst_script,
-                   '-r', paraview_dir]
+                   '-r', paraview_dir,
+                   '-o', catalyst_source_dir]
 
-        catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
-                                        'Editions', 'Base')
-        command.append('-i')
-        command.append(catalyst_edition)
-        if '+python' in self.spec:
-            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
-                                            'Editions', 'Enable-Python')
-            command.append('-i')
-            command.append(catalyst_edition)
-        if '+essentials' in self.spec:
-            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
-                                            'Editions', 'Essentials')
-            command.append('-i')
-            command.append(catalyst_edition)
-        if '+extras' in self.spec:
-            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
-                                            'Editions', 'Extras')
-            command.append('-i')
-            command.append(catalyst_edition)
-        if '+rendering' in self.spec:
-            catalyst_edition = os.path.join(paraview_dir, 'Catalyst',
-                                            'Editions', 'Rendering-Base')
-            command.append('-i')
-            command.append(catalyst_edition)
-
-        command.append('-o')
-        command.append(catalyst_source_dir)
+        for edition in self.editions:
+            command.extend(['-i', os.path.join(editions_dir, edition)])
 
         if not os.path.isdir(catalyst_source_dir):
             os.mkdir(catalyst_source_dir)
@@ -104,15 +120,29 @@ def do_stage(self, mirror_only=False):
                                                     self.stage.path))
 
     def setup_environment(self, spack_env, run_env):
+        # paraview 5.5 and later
+        # - cmake under lib/cmake/paraview-5.5
+        # - libs  under lib
+        # - python bits under lib/python2.8/site-packages
         if os.path.isdir(self.prefix.lib64):
             lib_dir = self.prefix.lib64
         else:
             lib_dir = self.prefix.lib
-        paraview_version = 'paraview-%s' % self.spec.version.up_to(2)
-        run_env.prepend_path('LIBRARY_PATH', join_path(lib_dir,
-                             paraview_version))
-        run_env.prepend_path('LD_LIBRARY_PATH', join_path(lib_dir,
-                             paraview_version))
+
+        if self.spec.version <= Version('5.4.1'):
+            lib_dir = join_path(lib_dir, paraview_subdir)
+        run_env.set('ParaView_DIR', self.prefix)
+        run_env.prepend_path('LIBRARY_PATH', lib_dir)
+        run_env.prepend_path('LD_LIBRARY_PATH', lib_dir)
+
+        if '+python' in self.spec:
+            python_version = self.spec['python'].version.up_to(2)
+            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                 'python{0}'.format(python_version),
+                                 'site-packages'))
+
+    def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
+        spack_env.set('ParaView_DIR', self.prefix)
 
     @property
     def root_cmakelists_dir(self):
@@ -136,8 +166,24 @@ def build_directory(self):
 
     def cmake_args(self):
         """Populate cmake arguments for Catalyst."""
+        spec = self.spec
+
+        def variant_bool(feature, on='ON', off='OFF'):
+            """Ternary for spec variant to ON/OFF string"""
+            if feature in spec:
+                return on
+            return off
+
+        def nvariant_bool(feature):
+            """Negated ternary for spec variant to OFF/ON string"""
+            return variant_bool(feature, on='OFF', off='ON')
+
         cmake_args = [
-            '-DPARAVIEW_GIT_DESCRIBE=v%s' % str(self.version)
+            '-DPARAVIEW_GIT_DESCRIBE=v%s' % str(self.version),
+            '-DVTK_USE_SYSTEM_EXPAT:BOOL=ON',
+            '-DVTK_USE_X:BOOL=%s' % nvariant_bool('+osmesa'),
+            '-DVTK_USE_OFFSCREEN:BOOL=%s' % variant_bool('+osmesa'),
+            '-DVTK_OPENGL_HAS_OSMESA:BOOL=%s' % variant_bool('+osmesa')
         ]
         return cmake_args
 

var/spack/repos/builtin/packages/of-catalyst/package.py

+# Copyright 2013-2018 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack import *
+
+
+class OfCatalyst(CMakePackage):
+    """Of-catalyst is a library for OpenFOAM that provides a runtime-selectable
+    function object for embedding ParaView Catalyst in-situ visualization
+    into arbitrary OpenFOAM simulations.
+    Supports in-situ conversion of the following types:
+      1) finite volume meshes and fields, single or multi-region;
+      2) finite area meshes and fields, single region;
+      3) lagrangian (clouds), single or multiple clouds.
+    This offering is part of the community repository supported by OpenCFD Ltd,
+    producer and distributor of the OpenFOAM software via www.openfoam.com,
+    and owner of the OPENFOAM trademark.
+    OpenCFD Ltd has been developing and releasing OpenFOAM since its debut
+    in 2004.
+    """
+
+    # Currently only via git
+    homepage = "https://develop.openfoam.com/Community/catalyst"
+    git = "https://develop.openfoam.com/Community/catalyst.git"
+
+    version('develop', branch='develop')
+    version('1806', tag='v1806')
+
+    variant('full', default=False, description='Build against paraview (full) or catalyst (light)')
+
+    depends_on('openfoam-com@1806', when='@1806', type=('build', 'link', 'run'))
+    depends_on('openfoam-com@develop', when='@develop', type=('build', 'link', 'run'))
+    depends_on('catalyst@5.5:', when='~full')
+    depends_on('paraview@5.5:+osmesa~qt', when='+full')
+
+    root_cmakelists_dir = 'src/catalyst'
+
+    def cmake_args(self):
+        """Populate cmake arguments for ParaView."""
+        cmake_args = [
+            '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY:PATH=%s' % join_path(
+                self.stage.source_path,
+                'spack-build')
+        ]
+
+        return cmake_args

var/spack/repos/builtin/packages/openfoam-com/package.py

@@ -405,16 +405,16 @@ def setup_environment(self, spack_env, run_env):
 
                         # Unneeded bits
                         # -------------
-                        'FOAM_SETTINGS',  # Do not use with modules
-                        'FOAM_INST_DIR',  # Old
-                        'FOAM_(APP|ETC|SRC|SOLVERS|UTILITIES)',
+                        # 'FOAM_SETTINGS',  # Do not use with modules
+                        # 'FOAM_INST_DIR',  # Old
+                        # 'FOAM_(APP|ETC|SRC|SOLVERS|UTILITIES)',
                         # 'FOAM_TUTORIALS',  # can be useful
-                        'WM_OSTYPE',      # Purely optional value
+                        # 'WM_OSTYPE',      # Purely optional value
 
                         # Third-party cruft - only used for orig compilation
                         # -----------------
                         '[A-Z].*_ARCH_PATH',
-                        '(KAHIP|METIS|SCOTCH)_VERSION',
+                        # '(KAHIP|METIS|SCOTCH)_VERSION',
 
                         # User-specific
                         # -------------
@@ -426,6 +426,7 @@ def setup_environment(self, spack_env, run_env):
                     ])
 
                 run_env.extend(mods)
+                spack_env.extend(mods)
                 minimal = False
                 tty.info('OpenFOAM bashrc env: {0}'.format(bashrc))
             except Exception:
@@ -436,8 +437,11 @@ def setup_environment(self, spack_env, run_env):
             tty.info('OpenFOAM minimal env {0}'.format(self.prefix))
             run_env.set('FOAM_PROJECT_DIR', self.projectdir)
             run_env.set('WM_PROJECT_DIR', self.projectdir)
+            spack_env.set('FOAM_PROJECT_DIR', self.projectdir)
+            spack_env.set('WM_PROJECT_DIR', self.projectdir)
             for d in ['wmake', self.archbin]:  # bin added automatically
                 run_env.prepend_path('PATH', join_path(self.projectdir, d))
+                spack_env.prepend_path('PATH', join_path(self.projectdir, d))
 
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         """Location of the OpenFOAM project directory.
@@ -445,7 +449,7 @@ def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         variable since it would mask the normal OpenFOAM cleanup of
         previous versions.
         """
-        spack_env.set('FOAM_PROJECT_DIR', self.projectdir)
+        self.setup_environment(spack_env, run_env)
 
     @property
     def projectdir(self):

var/spack/repos/builtin/packages/paraview/package.py

@@ -59,7 +59,8 @@ class Paraview(CMakePackage):
     depends_on('libpng')
     depends_on('libtiff')
     depends_on('libxml2')
-    # depends_on('netcdf')
+    depends_on('netcdf')
+    depends_on('expat')
     # depends_on('netcdf-cxx')
     # depends_on('protobuf') # version mismatches?
     # depends_on('sqlite') # external version not supported
@@ -74,6 +75,9 @@ class Paraview(CMakePackage):
     # Broken installation (ui_pqExportStateWizard.h) - fixed in 5.2.0
     patch('ui_pqExportStateWizard.patch', when='@:5.1.2')
 
+    # Broken vtk-m config. Upstream catalyst changes
+    patch('vtkm-catalyst-pv551.patch', when='@5.5.0:5.5.2')
+
     def url_for_version(self, version):
         """Handle ParaView version-based custom URLs."""
         if version < Version('5.1.0'):
@@ -81,34 +85,50 @@ def url_for_version(self, version):
         else:
             return self._urlfmt.format(version.up_to(2), version, '')
 
+    @property
+    def paraview_subdir(self):
+        """The paraview subdirectory name as paraview-major.minor"""
+        return 'paraview-{0}'.format(self.spec.version.up_to(2))
+
     def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
         if os.path.isdir(self.prefix.lib64):
             lib_dir = self.prefix.lib64
         else:
             lib_dir = self.prefix.lib
-        paraview_version = 'paraview-%s' % self.spec.version.up_to(2)
+        spack_env.set('ParaView_DIR', self.prefix)
         spack_env.set('PARAVIEW_VTK_DIR',
-                      join_path(lib_dir, 'cmake', paraview_version))
+                      join_path(lib_dir, 'cmake', self.paraview_subdir))
 
     def setup_environment(self, spack_env, run_env):
+        # paraview 5.5 and later
+        # - cmake under lib/cmake/paraview-5.5
+        # - libs  under lib
+        # - python bits under lib/python2.8/site-packages
         if os.path.isdir(self.prefix.lib64):
             lib_dir = self.prefix.lib64
         else:
             lib_dir = self.prefix.lib
-        paraview_version = 'paraview-%s' % self.spec.version.up_to(2)
-        run_env.prepend_path('LIBRARY_PATH', join_path(lib_dir,
-                             paraview_version))
-        run_env.prepend_path('LD_LIBRARY_PATH', join_path(lib_dir,
-                             paraview_version))
+
+        run_env.set('ParaView_DIR', self.prefix)
         run_env.set('PARAVIEW_VTK_DIR',
-                    join_path(lib_dir, 'cmake', paraview_version))
+                    join_path(lib_dir, 'cmake', self.paraview_subdir))
+
+        if self.spec.version <= Version('5.4.1'):
+            lib_dir = join_path(lib_dir, self.paraview_subdir)
+
+        run_env.prepend_path('LIBRARY_PATH', lib_dir)
+        run_env.prepend_path('LD_LIBRARY_PATH', lib_dir)
+
         if '+python' in self.spec:
-            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
-                                 paraview_version))
-            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
-                                 paraview_version, 'site-packages'))
-            run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
-                                 paraview_version, 'site-packages', 'vtk'))
+            if self.spec.version <= Version('5.4.1'):
+                pv_pydir = join_path(lib_dir, 'site-packages')
+                run_env.prepend_path('PYTHONPATH', pv_pydir)
+                run_env.prepend_path('PYTHONPATH', join_path(pv_pydir, 'vtk'))
+            else:
+                python_version = self.spec['python'].version.up_to(2)
+                run_env.prepend_path('PYTHONPATH', join_path(lib_dir,
+                                     'python{0}'.format(python_version),
+                                     'site-packages'))
 
     def cmake_args(self):
         """Populate cmake arguments for ParaView."""
@@ -139,7 +159,8 @@ def nvariant_bool(feature):
             '-DVTK_USE_SYSTEM_HDF5:BOOL=%s' % variant_bool('+hdf5'),
             '-DVTK_USE_SYSTEM_JPEG:BOOL=ON',
             '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON',
-            '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF',
+            '-DVTK_USE_SYSTEM_NETCDF:BOOL=ON',
+            '-DVTK_USE_SYSTEM_EXPAT:BOOL=ON',
             '-DVTK_USE_SYSTEM_TIFF:BOOL=ON',
             '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON',
         ]