Adding FASTMath uber package and missing FASTMath packages (#4120)

* adding 0.5.1 and variant for uint8 bit stream word type

* Revisions as per davydden

* fixing style (flake8) issues

* - switched to derive from MakefilePackage
- fixed typo in variant check
- Confirmed installs correctly with bswtuint8 variant

* added build method; changed zfp_incdir to incdir

* * Adding uber fastmath package to support 'spack install fastmath'
* Adding dims variant boxlib to control compile-time spatial dimension count
* Explicitly disabling many parts of moab to get lib to build. Don't need tools yet.
* Add logic to spack/setup-env to not refer to $SYS_TYPE if its not defined.

* adding mesquite package

* * Added Chombo (still working on Fortran name mangling)
* Made mesquite depend on mpi
* Fixed use of boxlib's dims numerical variant

* adding PUMI

* flake8 compliance

* adding phasta

* fixing flake8 issues

* undue $SYS_TYPE protection change

* fixing install step for fastmath uber package; resolve issues requested by adamjstewart in PR

* revisions as per adamjstewart

* re-enabling trilinos and phasta dependencies

* all changes requested modulu values= and assert statement

* fixing cmake_args usage in pumi; fixing lib installs for chombo

* first pass at numerical variant

* fixing dims variant as per @adamjstewart

* fixing func/var name collision

* fixing means of disabling -Werror

* fix name collision for cmake_args var/func

* fixing chombo homepage/url; make FASTMath use chombo#3.2; remove extraneous comment about boxlib dim

* remove dummy fastmath package; switch to @BarrySmith soln for install of dummy bundle

* fix flake8 import os issue

* remove extraneous comment

* adding url for fastmath scidac site

* final fixes as per @adamjstewart

* adding 1 dims option for boxlib

* switching make(all) to gmake(all)

3 files changed, 175 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/chombo/Make.defs.local.template.patch b/var/spack/repos/builtin/packages/chombo/Make.defs.local.template.patch
new file mode 100644
index 0000000000..cc72659445
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chombo/Make.defs.local.template.patch
@@ -0,0 +1,23 @@
+*** lib/mk/Make.defs.local.template	2017-05-02 16:00:16.000000000 -0700
+--- lib/mk/Make.defs.local.template.patched	2017-05-02 18:50:36.000000000 -0700
+***************
+*** 129,135 ****
+--- 129,137 ----
+  #HDFMPILIBFLAGS= -L<hdf_parallel_dir>/lib -lhdf5 -lz
+  #USE_MF        =
+  #USE_MT        =
++ #USE_LAPACK    =
+  #USE_SETVAL    =
++ #USE_TIMER     =
+  #CH_AR         =
+  #CH_CPP        =
+  #DOXYGEN       =
+***************
+*** 151,155 ****
+--- 153,158 ----
+  #ldoptflags    =
+  #ldprofflags   =
+  #syslibflags   =
++ #lapackincflags =
+  
+  #end  -- dont change this line
diff --git a/var/spack/repos/builtin/packages/chombo/hdf5-16api.patch b/var/spack/repos/builtin/packages/chombo/hdf5-16api.patch
new file mode 100644
index 0000000000..6525061886
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chombo/hdf5-16api.patch
@@ -0,0 +1,12 @@
+*** lib/src/BoxTools/HDF5Portable.H	2017-05-02 13:57:57.000000000 -0700
+--- lib/src/BoxTools/HDF5Portable.H.patched	2017-05-02 13:55:30.000000000 -0700
+***************
+*** 15,20 ****
+--- 15,21 ----
+  extern "C"
+  {
+  #ifdef CH_USE_HDF5
++ #define H5_USE_16_API
+  #include <hdf5.h>
+  #else
+    typedef long hid_t;
diff --git a/var/spack/repos/builtin/packages/chombo/package.py b/var/spack/repos/builtin/packages/chombo/package.py
new file mode 100644
index 0000000000..1ae50e6bc0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/chombo/package.py
@@ -0,0 +1,140 @@
+##############################################################################
+# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC.
+# Produced at the Lawrence Livermore National Laboratory.
+#
+# This file is part of Spack.
+# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
+# LLNL-CODE-647188
+#
+# For details, see https://github.com/llnl/spack
+# Please also see the LICENSE file for our notice and the LGPL.
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU Lesser General Public License (as
+# published by the Free Software Foundation) version 2.1, February 1999.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and
+# conditions of the GNU Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+##############################################################################
+from spack import *
+from shutil import copyfile
+import glob
+
+
+class Chombo(MakefilePackage):
+    """The Chombo package provides a set of tools for implementing finite
+       difference and finite-volume methods for the solution of partial
+       differential equations on block-structured adaptively refined
+       logically rectangular (i.e. Cartesian) grids."""
+
+    homepage = "https://commons.lbl.gov/display/chombo"
+    url      = "http://bitbucket.org/drhansj/chombo-xsdk.git"
+
+    # Use whatever path Brian V. and Terry L. agreed upon, but preserve version
+    version('3.2', git='http://bitbucket.org/drhansj/chombo-xsdk.git', commit='71d856c')
+    version('develop', git='http://bitbucket.org/drhansj/chombo-xsdk.git', tag='master')
+#    version('3.2', svn='https://anag-repo.lbl.gov/svn/Chombo/release/3.2')
+
+    variant('mpi', default=True, description='Enable MPI parallel support')
+    variant('hdf5', default=True, description='Enable HDF5 support')
+    variant('dims',
+        default='3',
+        values=('1', '2', '3', '4', '5', '6'),
+        multi=False,
+        description='Number of PDE dimensions [1-6]'
+    )
+
+    patch('hdf5-16api.patch', when='@3.2', level=0)
+    patch('Make.defs.local.template.patch', when='@3.2', level=0)
+
+    depends_on('blas')
+    depends_on('lapack')
+    depends_on('gmake', type='build')
+    depends_on('mpi', when='+mpi')
+    depends_on('hdf5', when='+hdf5')
+    depends_on('hdf5+mpi', when='+mpi+hdf5')
+
+    def edit(self, spec, prefix):
+
+        # Set fortran name mangling in Make.defs
+        defs_file = FileFilter('./lib/mk/Make.defs')
+        defs_file.filter('^\s*#\s*cppcallsfort\s*=\s*',
+                         'cppcallsfort = -DCH_FORT_UNDERSCORE')
+
+        # Set remaining variables in Make.defs.local
+        # Make.defs.local.template.patch ensures lines for USE_TIMER,
+        # USE_LAPACK and lapackincflags are present
+        copyfile('./lib/mk/Make.defs.local.template',
+                 './lib/mk/Make.defs.local')
+
+        defs_file = FileFilter('./lib/mk/Make.defs.local')
+
+        # Unconditional settings
+        defs_file.filter('^\s*#\s*DEBUG\s*=\s*', 'DEBUG = FALSE')
+        defs_file.filter('^\s*#\s*OPT\s*=\s*', 'OPT = TRUE')
+        defs_file.filter('^\s*#\s*PIC\s*=\s*', 'PIC = TRUE')
+        # timer code frequently fails compiles. So disable it.
+        defs_file.filter('^\s*#\s*USE_TIMER\s*=\s*', 'USE_TIMER = FALSE')
+
+        # LAPACK setup
+        lapack_blas = spec['lapack'].libs + spec['blas'].libs
+        defs_file.filter('^\s*#\s*USE_LAPACK\s*=\s*', 'USE_LAPACK = TRUE')
+        defs_file.filter(
+            '^\s*#\s*lapackincflags\s*=\s*',
+            'lapackincflags = -I%s' % spec['lapack'].prefix.include)
+        defs_file.filter(
+            '^\s*#\s*syslibflags\s*=\s*',
+            'syslibflags = %s' % lapack_blas.ld_flags)
+
+        # Compilers and Compiler flags
+        defs_file.filter('^\s*#\s*CXX\s*=\s*', 'CXX = %s' % spack_cxx)
+        defs_file.filter('^\s*#\s*FC\s*=\s*', 'FC = %s' % spack_fc)
+        if '+mpi' in spec:
+            defs_file.filter(
+                '^\s*#\s*MPICXX\s*=\s*',
+                'MPICXX = %s' % self.spec['mpi'].mpicxx)
+
+        # Conditionally determined settings
+        defs_file.filter(
+            '^\s*#\s*MPI\s*=\s*',
+            'MPI = %s' % ('TRUE' if '+mpi' in spec else 'FALSE'))
+        defs_file.filter(
+            '^\s*#\s*DIM\s*=\s*',
+            'DIM = %s' % spec.variants['dims'].value)
+
+        # HDF5 settings
+        if '+hdf5' in spec:
+            defs_file.filter('^\s*#\s*USE_HDF5\s*=\s*', 'USE_HDF5 = TRUE')
+            defs_file.filter(
+                '^\s*#\s*HDFINCFLAGS\s*=.*',
+                'HDFINCFLAGS = -I%s' % spec['hdf5'].prefix.include)
+            defs_file.filter(
+                '^\s*#\s*HDFLIBFLAGS\s*=.*',
+                'HDFLIBFLAGS = %s' % spec['hdf5'].libs.ld_flags)
+            if '+mpi' in spec:
+                defs_file.filter(
+                    '^\s*#\s*HDFMPIINCFLAGS\s*=.*',
+                    'HDFMPIINCFLAGS = -I%s' % spec['hdf5'].prefix.include)
+                defs_file.filter(
+                    '^\s*#\s*HDFMPILIBFLAGS\s*=.*',
+                    'HDFMPILIBFLAGS = %s' % spec['hdf5'].libs.ld_flags)
+
+    def build(self, spec, prefix):
+        with working_dir('lib'):
+            gmake('all')
+
+    def install(self, spec, prefix):
+        with working_dir('lib'):
+            install_tree('include', prefix.include)
+            libfiles = glob.glob('lib*.a')
+            libfiles += glob.glob('lib*.so')
+            libfiles += glob.glob('lib*.dylib')
+            mkdirp(prefix.lib)
+            for lib in libfiles:
+                install(lib, prefix.lib)