Update Package : ExodusII (#1504)

* Added support for the 'maxdims' and 'maxvars' flags for 'NetCDF'.

* Added the '+mpi' variant and improved dependencies for 'exodusii'.
Improved the 'exodusii' package so that it's less reliant on patches.

* Added better type checking to variant values in the 'netcdf' package.

* Corrected the required CMake version for the 'exodusii' package.

* Fixed the dependencies of the '+mpi' variant of the 'exodusii' package.

var/spack/repos/builtin/packages/exodusii/cmake-exodus.patch

@@ -0,0 +1,9 @@
+diff --git a/cmake-exodus b/cmake-exodus
+index 67ccd34..9b749e3 100755
+--- a/cmake-exodus
++++ b/cmake-exodus
+@@ -1,3 +1,4 @@
++#!/bin/bash
+ EXTRA_ARGS=$@
+ 
+ ### The following assumes you are building in a subdirectory of ACCESS Root

var/spack/repos/builtin/packages/exodusii/exodus-cmake.patch

@@ -1,12 +0,0 @@
-diff --git a/cmake-exodus b/cmake-exodus
-index 787fd9d..ed073a2 100755
---- a/cmake-exodus
-+++ b/cmake-exodus
-@@ -1,4 +1,6 @@
--EXTRA_ARGS=$@
-+#!/bin/bash
-+
-+EXTRA_ARGS=-DSEACASProj_ENABLE_CXX11=OFF
- 
- ### Change this to point to the compilers you want to use
- CC=gcc

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

@@ -27,10 +27,8 @@
 # TODO: Add support for a C++11 enabled installation that filters out the
 # TODO: "C++11-Disabled" flag (but only if the spec compiler supports C++11).
 
-# TODO: Add support for parallel installation that uses MPI.
+# TODO: Use variant forwarding to forward the 'mpi' variant to the direct
-
+# TODO: dependencies 'hdf5' and 'netcdf'.
-# TODO: Create installation options for NetCDF that support larger page size
-# TODO: suggested by Exodus (see the repository "README" file).
 
 
 class Exodusii(Package):
@@ -46,34 +44,43 @@ class Exodusii(Package):
     homepage = "https://github.com/gsjaardema/seacas"
     url      = "https://github.com/gsjaardema/seacas/archive/master.zip"
 
-    version('2016-02-08',
+    version('2016-08-09', git='https://github.com/gsjaardema/seacas.git', commit='2ffeb1b')
-            git='https://github.com/gsjaardema/seacas.git', commit='dcf3529')
 
-    depends_on('cmake@2.8.7:', type='build')
+    variant('mpi', default=True, description='Enables MPI parallelism.')
-    depends_on('hdf5~shared~mpi')
-    depends_on('netcdf~mpi')
 
-    patch('exodus-cmake.patch')
+    depends_on('cmake@2.8.11:', type='build')
+    depends_on('mpi', when='+mpi')
 
-    def patch(self):
+    # https://github.com/gsjaardema/seacas/blob/master/NetCDF-Mapping.md
-        ff = FileFilter('cmake-exodus')
+    depends_on('netcdf maxdims=65536 maxvars=524288')
+    depends_on('hdf5+shared')
 
-        ff.filter('CMAKE_INSTALL_PREFIX:PATH=${ACCESS}',
+    patch('cmake-exodus.patch')
-                  'CMAKE_INSTALL_PREFIX:PATH=%s' % self.spec.prefix,
-                  string=True)
-        ff.filter('NetCDF_DIR:PATH=${TPL}',
-                  'NetCDF_DIR:PATH=%s' % self.spec['netcdf'].prefix,
-                  string=True)
-        ff.filter('HDF5_ROOT:PATH=${TPL}',
-                  'HDF5_ROOT:PATH=%s' % self.spec['hdf5'].prefix,
-                  string=True)
 
     def install(self, spec, prefix):
-        mkdirp('build')
+        cc_path = spec['mpi'].mpicc if '+mpi' in spec else self.compiler.cc
-        cd('build')
+        cxx_path = spec['mpi'].mpicxx if '+mpi' in spec else self.compiler.cxx
 
-        cmake_exodus = Executable('../cmake-exodus')
+        config_args = std_cmake_args[:]
-        cmake_exodus()
+        config_args.extend([
+            # General Flags #
+            '-DSEACASProj_ENABLE_CXX11:BOOL=OFF',
+            '-DSEACASProj_ENABLE_Zoltan:BOOL=OFF',
+            '-DHDF5_ROOT:PATH={0}'.format(spec['hdf5'].prefix),
+            '-DNetCDF_DIR:PATH={0}'.format(spec['netcdf'].prefix),
 
-        make()
+            # MPI Flags #
-        make('install')
+            '-DTPL_ENABLE_MPI={0}'.format('ON' if '+mpi' in spec else 'OFF'),
+            '-DCMAKE_C_COMPILER={0}'.format(cc_path),
+            '-DCMAKE_CXX_COMPILER={0}'.format(cxx_path),
+        ])
+
+        build_directory = join_path(self.stage.source_path, 'spack-build')
+        source_directory = self.stage.source_path
+
+        with working_dir(build_directory, create=True):
+            mcmake = Executable(join_path(source_directory, 'cmake-exodus'))
+            mcmake(*config_args)
+
+            make()
+            make('install')

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

@@ -27,8 +27,8 @@
 
 class Netcdf(Package):
     """NetCDF is a set of software libraries and self-describing,
-    machine-independent data formats that support the creation, access,
+       machine-independent data formats that support the creation, access,
-    and sharing of array-oriented scientific data.
+       and sharing of array-oriented scientific data.
 
     """
 
@@ -41,6 +41,13 @@ class Netcdf(Package):
 
     variant('mpi',  default=True,  description='Enables MPI parallelism')
     variant('hdf4', default=False, description='Enable HDF4 support')
+    # These variants control the number of dimensions (i.e. coordinates and
+    # attributes) and variables (e.g. time, entity ID, number of coordinates)
+    # that can be used in any particular NetCDF file.
+    variant('maxdims', default=1024,
+            description='Defines the maximum dimensions of NetCDF files.')
+    variant('maxvars', default=8192,
+            description='Defines the maximum variables of NetCDF files.')
 
     depends_on("m4", type='build')
     depends_on("hdf", when='+hdf4')
@@ -56,6 +63,20 @@ class Netcdf(Package):
     # https://github.com/Unidata/netcdf-c/issues/250
     depends_on('hdf5@:1.8', when='@:4.4.0')
 
+    def patch(self):
+        try:
+            max_dims = int(self.spec.variants['maxdims'].value)
+            max_vars = int(self.spec.variants['maxvars'].value)
+        except (ValueError, TypeError):
+            raise TypeError('NetCDF variant values max[dims|vars] must be '
+                            'integer values.')
+
+        ff = FileFilter(join_path('include', 'netcdf.h'))
+        ff.filter(r'^(#define\s+NC_MAX_DIMS\s+)\d+(.*)$',
+                  r'\1{0}\2'.format(max_dims))
+        ff.filter(r'^(#define\s+NC_MAX_VARS\s+)\d+(.*)$',
+                  r'\1{0}\2'.format(max_vars))
+
     def install(self, spec, prefix):
         # Workaround until variant forwarding works properly
         if '+mpi' in spec and spec.satisfies('^hdf5~mpi'):