Adding Nalu package. (#4428)

* Adding Nalu package.

* Fixing flake8 stuff.

* Fixing flake8 stuff.

* Reorganizing trilinos package file a little to make it less verbose.

* Reorganizing trilinos package file for more general use as well as use as a dependency of the Nalu package. Setting fpic as default for yaml-cpp and superlu.

* Explicitly stating fpic variants in dependent packages.

* Updating nalu and trilinos package files with suggested changes.

* Fixing formatting issues. Making suggested changes.

* Fixing formatting.

* Reducing amount of explicit variants in Nalu. Adding suggested changes to Trilinos package file.

* Making suggested changes to Nalu package.

* Turning off superlu-dist variant.

* Cleaning up yaml-cpp file.

* Fixing pnetcdf requirements in trilinos.

4 files changed, 315 insertions, 109 deletions

diff --git a/var/spack/repos/builtin/packages/nalu/package.py b/var/spack/repos/builtin/packages/nalu/package.py
new file mode 100644
index 0000000000..f485b5cb17
--- /dev/null
+++ b/var/spack/repos/builtin/packages/nalu/package.py
@@ -0,0 +1,64 @@
+##############################################################################
+# 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 *
+
+
+class Nalu(CMakePackage):
+    """Nalu: a generalized unstructured massively parallel low Mach flow code
+       designed to support a variety of energy applications of interest (most
+       notably Wind ECP) built on the Sierra Toolkit and Trilinos solver
+       Tpetra/Epetra stack
+    """
+
+    homepage = "https://github.com/NaluCFD/Nalu"
+    url      = "https://github.com/NaluCFD/Nalu.git"
+
+    version('master',
+            git='https://github.com/NaluCFD/Nalu.git', branch='master')
+
+    variant('debug', default=False,
+            description='Builds a debug version')
+
+    # Currently Nalu only builds static libraries; To be fixed soon
+    depends_on('yaml-cpp+fpic~shared')
+    depends_on('trilinos~shared+tpetra+muelu+belos+ifpack2+amesos2+zoltan+stk+boost~superlu-dist+superlu+hdf5+zlib+pnetcdf@master')
+
+    def build_type(self):
+        if '+debug' in self.spec:
+            return 'Debug'
+        else:
+            return 'Release'
+
+    def cmake_args(self):
+        spec = self.spec
+        options = []
+
+        options.extend([
+            '-DTrilinos_DIR:PATH=%s' % spec['trilinos'].prefix,
+            '-DYAML_DIR:PATH=%s' % spec['yaml-cpp'].prefix,
+            '-DENABLE_INSTALL:BOOL=ON'
+        ])
+
+        return options
diff --git a/var/spack/repos/builtin/packages/superlu/package.py b/var/spack/repos/builtin/packages/superlu/package.py
index 13c11b66b9..8e7303d6c8 100644
--- a/var/spack/repos/builtin/packages/superlu/package.py
+++ b/var/spack/repos/builtin/packages/superlu/package.py
@@ -38,8 +38,8 @@ class Superlu(Package):
     version('5.2.1', '3a1a9bff20cb06b7d97c46d337504447')
     version('4.3', 'b72c6309f25e9660133007b82621ba7c')
 
-    variant('fpic',    default=False,
-            description='Build with position independent code') 
+    variant('fpic',    default=True,
+            description='Build with position independent code')
 
     depends_on('cmake', when='@5.2.1:', type='build')
     depends_on('blas')
@@ -117,4 +117,4 @@ class Superlu(Package):
         headers = glob.glob(join_path('SRC', '*.h'))
         mkdir(prefix.include)
         for h in headers:
-            install(h, prefix.include) 
+            install(h, prefix.include)
diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py
index 66dc4f0e64..40929499de 100644
--- a/var/spack/repos/builtin/packages/trilinos/package.py
+++ b/var/spack/repos/builtin/packages/trilinos/package.py
@@ -46,6 +46,8 @@ class Trilinos(CMakePackage):
     homepage = "https://trilinos.org/"
     url      = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-10-1.tar.gz"
 
+    # ###################### Versions ##########################
+
     version('xsdk-0.2.0',
             git='https://github.com/trilinos/Trilinos.git', tag='xsdk-0.2.0')
     version('develop',
@@ -65,7 +67,11 @@ class Trilinos(CMakePackage):
     version('11.14.2', 'e7c3cdbbfe3279a8a68838b873ad6d51')
     version('11.14.1', 'b7760b142eef66c79ed13de7c9560f81')
 
-    variant('xsdkflags',        default=False,
+    # ###################### Variants ##########################
+
+    variant('alloptpkgs',   default=False,
+            description='Compile with all optional packages')
+    variant('xsdkflags',    default=False,
             description='Compile using the default xSDK configuration')
     variant('metis',        default=True,
             description='Compile with METIS and ParMETIS')
@@ -73,25 +79,72 @@ class Trilinos(CMakePackage):
             description='Compile with support for MUMPS solvers')
     variant('superlu-dist', default=True,
             description='Compile with SuperluDist solvers')
-    variant('superlu', default=False,
+    variant('superlu',      default=False,
             description='Compile with SuperLU solvers')
     variant('hypre',        default=True,
             description='Compile with Hypre preconditioner')
-    variant('hdf5',         default=True,  description='Compile with HDF5')
+    variant('hdf5',         default=True,
+            description='Compile with HDF5')
     variant('suite-sparse', default=True,
             description='Compile with SuiteSparse solvers')
     # not everyone has py-numpy activated, keep it disabled by default to avoid
     # configure errors
-    variant('python',       default=False, description='Build python wrappers')
+    variant('python',       default=False,
+            description='Build python wrappers')
     variant('shared',       default=True,
             description='Enables the build of shared libraries')
     variant('debug',        default=False,
             description='Builds a debug version of the libraries')
-    variant('boost',        default=True,  description='Compile with Boost')
-    variant('tpetra',       default=True,  description='Compile with Tpetra')
-    variant('exodus',       default=False, description='Compile with Exodus from SEACAS')
-
-    variant('dtk',          default=False, description='Enable DataTransferKit')
+    variant('boost',        default=True,
+            description='Compile with Boost')
+    variant('tpetra',       default=True,
+            description='Compile with Tpetra')
+    variant('epetra',       default=True,
+            description='Compile with Epetra')
+    variant('epetraext',    default=True,
+            description='Compile with EpetraExt')
+    variant('exodus',       default=True,
+            description='Compile with Exodus from SEACAS')
+    variant('pnetcdf',      default=False,
+            description='Compile with parallel-netcdf')
+    variant('zlib',         default=False,
+            description='Compile with zlib')
+    variant('stk',          default=False,
+            description='Compile with STK')
+    variant('belos',        default=True,
+            description='Compile with Belos')
+    variant('zoltan',       default=True,
+            description='Compile with Zoltan')
+    variant('zoltan2',      default=True,
+            description='Compile with Zoltan2')
+    variant('amesos',       default=True,
+            description='Compile with Amesos')
+    variant('amesos2',      default=True,
+            description='Compile with Amesos2')
+    variant('ifpack',       default=True,
+            description='Compile with Ifpack')
+    variant('ifpack2',      default=True,
+            description='Compile with Ifpack2')
+    variant('muelu',        default=True,
+            description='Compile with Muelu')
+    variant('fortran',      default=True,
+            description='Compile with Fortran support')
+    variant('ml',           default=True,
+            description='Compile with ML')
+    variant('gtest',        default=True,
+            description='Compile with Gtest')
+    variant('aztec',        default=True,
+            description='Compile with Aztec')
+    variant('sacado',       default=True,
+            description='Compile with Sacado')
+    variant('x11',          default=False,
+            description='Compile with X11')
+    variant('instantiate',  default=True,
+            description='Compile with explicit instantiation')
+    variant('instantiate_cmplx', default=False,
+            description='Compile with explicit instantiation for complex')
+    variant('dtk',          default=False,
+            description='Enable DataTransferKit')
     resource(name='dtk',
              git='https://github.com/ornl-cees/DataTransferKit',
              tag='master',
@@ -99,6 +152,8 @@ class Trilinos(CMakePackage):
              when='+dtk')
     conflicts('+dtk', when='~tpetra')
 
+    # ###################### Dependencies ##########################
+
     # Everything should be compiled with -fpic
     depends_on('blas')
     depends_on('lapack')
@@ -108,10 +163,13 @@ class Trilinos(CMakePackage):
     depends_on('glm')
     depends_on('metis@5:', when='+metis')
     depends_on('suite-sparse', when='+suite-sparse')
+    depends_on('zlib', when="+zlib")
 
     # MPI related dependencies
     depends_on('mpi')
     depends_on('netcdf+mpi')
+    depends_on('parallel-netcdf', when="+pnetcdf@master")
+    depends_on('parallel-netcdf', when="+pnetcdf@12.10.2:")
     depends_on('parmetis', when='+metis')
     # Trilinos' Tribits config system is limited which makes it very tricky to
     # link Amesos with static MUMPS, see
@@ -163,53 +221,137 @@ class Trilinos(CMakePackage):
         cxx_flags = []
         options = []
 
+        # #################### Base Settings #######################
+
         mpi_bin = spec['mpi'].prefix.bin
-        # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
-        blas = spec['blas'].libs
-        lapack = spec['lapack'].libs
         options.extend([
-            '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON',
-            '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON',
             '-DTrilinos_VERBOSE_CONFIGURE:BOOL=OFF',
             '-DTrilinos_ENABLE_TESTS:BOOL=OFF',
             '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF',
+            '-DTrilinos_ENABLE_CXX11:BOOL=ON',
             '-DCMAKE_BUILD_TYPE:STRING=%s' % (
                 'DEBUG' if '+debug' in spec else 'RELEASE'),
             '-DBUILD_SHARED_LIBS:BOOL=%s' % (
                 'ON' if '+shared' in spec else 'OFF'),
-            '-DTPL_FIND_SHARED_LIBS:BOOL=%s' % (
-                'ON' if '+shared' in spec else 'OFF'),
-            '-DTrilinos_LINK_SEARCH_START_STATIC:BOOL=%s' % (
-                'OFF' if '+shared' in spec else 'ON'),
+
+            # The following can cause problems on systems that don't have
+            # static libraries available for things like dl and pthreads
+            # for example when trying to build static libs
+            # '-DTPL_FIND_SHARED_LIBS:BOOL=%s' % (
+            #     'ON' if '+shared' in spec else 'OFF'),
+            # '-DTrilinos_LINK_SEARCH_START_STATIC:BOOL=%s' % (
+            #     'OFF' if '+shared' in spec else 'ON'),
+
+            # Force Trilinos to use the MPI wrappers instead of raw compilers
+            # this is needed on Apple systems that require full resolution of
+            # all symbols when linking shared libraries
             '-DTPL_ENABLE_MPI:BOOL=ON',
-            '-DMPI_BASE_DIR:PATH=%s' % spec['mpi'].prefix,
+            '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
+            '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
+            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc,
+            '-DMPI_BASE_DIR:PATH=%s'      % spec['mpi'].prefix
+        ])
+
+        # ################## Trilinos Packages #####################
+
+        options.extend([
+            '-DTrilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=%s' % (
+                'ON' if '+alloptpkgs' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Tpetra:BOOL=%s' % (
+                'ON' if '+tpetra' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Epetra:BOOL=%s' % (
+                'ON' if '+epetra' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_EpetraExt:BOOL=%s' % (
+                'ON' if '+epetraext' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_ML:BOOL=%s' % (
+                'ON' if '+ml' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_AztecOO:BOOL=%s' % (
+                'ON' if '+aztec' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Sacado:BOOL=%s' % (
+                'ON' if '+sacado' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Belos:BOOL=%s' % (
+                'ON' if '+belos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Zoltan:BOOL=%s' % (
+                'ON' if '+zoltan' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Zoltan2:BOOL=%s' % (
+                'ON' if '+zoltan2' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Amesos:BOOL=%s' % (
+                'ON' if '+amesos' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Amesos2:BOOL=%s' % (
+                'ON' if '+amesos2' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_MueLu:BOOL=%s' % (
+                'ON' if '+muelu' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Ifpack:BOOL=%s' % (
+                'ON' if '+ifpack' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Ifpack2:BOOL=%s' % (
+                'ON' if '+ifpack2' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_Gtest:BOOL=%s' % (
+                'ON' if '+gtest' in spec else 'OFF'),
+        ])
+
+        if '+xsdkflags' in spec:
+            options.extend(['-DUSE_XSDK_DEFAULTS=YES'])
+
+        if '+stk' in spec:
+            # Currently these are fairly specific to the Nalu package
+            # They can likely change when necessary in the future
+            options.extend([
+                '-DTrilinos_ENABLE_STKMesh:BOOL=ON',
+                '-DTrilinos_ENABLE_STKSimd:BOOL=ON',
+                '-DTrilinos_ENABLE_STKIO:BOOL=ON',
+                '-DTrilinos_ENABLE_STKTransfer:BOOL=ON',
+                '-DTrilinos_ENABLE_STKSearch:BOOL=ON',
+                '-DTrilinos_ENABLE_STKUtil:BOOL=ON',
+                '-DTrilinos_ENABLE_STKTopology:BOOL=ON',
+                '-DTrilinos_ENABLE_STKUnit_tests:BOOL=ON',
+                '-DTrilinos_ENABLE_STKUnit_test_utils:BOOL=ON',
+                '-DTrilinos_ENABLE_STKClassic:BOOL=OFF'
+            ])
+
+        if '+dtk' in spec:
+            options.extend([
+                '-DTrilinos_EXTRA_REPOSITORIES:STRING=DataTransferKit',
+                '-DTpetra_INST_INT_UNSIGNED_LONG:BOOL=ON',
+                '-DTrilinos_ENABLE_DataTransferKit:BOOL=ON'
+            ])
+
+        if '+exodus' in spec:
+            # Currently these are fairly specific to the Nalu package
+            # They can likely change when necessary in the future
+            options.extend([
+                '-DTrilinos_ENABLE_SEACAS:BOOL=ON',
+                '-DTrilinos_ENABLE_SEACASExodus:BOOL=ON',
+                '-DTrilinos_ENABLE_SEACASEpu:BOOL=ON',
+                '-DTrilinos_ENABLE_SEACASExodiff:BOOL=ON',
+                '-DTrilinos_ENABLE_SEACASNemspread:BOOL=ON',
+                '-DTrilinos_ENABLE_SEACASNemslice:BOOL=ON'
+            ])
+        else:
+            options.extend([
+                '-DTrilinos_ENABLE_SEACAS:BOOL=OFF',
+                '-DTrilinos_ENABLE_SEACASExodus:BOOL=OFF'
+            ])
+
+        # ######################### TPLs #############################
+
+        blas = spec['blas'].libs
+        lapack = spec['lapack'].libs
+        # Note: -DXYZ_LIBRARY_NAMES= needs semicolon separated list of names
+        options.extend([
             '-DTPL_ENABLE_BLAS=ON',
             '-DBLAS_LIBRARY_NAMES=%s' % ';'.join(blas.names),
             '-DBLAS_LIBRARY_DIRS=%s' % ';'.join(blas.directories),
             '-DTPL_ENABLE_LAPACK=ON',
             '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names),
             '-DLAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories),
-            '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON',
-            '-DTrilinos_ENABLE_CXX11:BOOL=ON',
             '-DTPL_ENABLE_Netcdf:BOOL=ON',
-            '-DTrilinos_ENABLE_Tpetra:BOOL=%s' % (
-                'ON' if '+tpetra' in spec else 'OFF')
+            '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix,
+            '-DTPL_ENABLE_X11:BOOL=%s' % (
+                'ON' if '+x11' in spec else 'OFF'),
+            '-DTrilinos_ENABLE_PyTrilinos:BOOL=%s' % (
+                'ON' if '+python' in spec else 'OFF'),
         ])
 
-        if '.'.join(platform.mac_ver()[0].split('.')[:2]) == '10.12':
-            # use @rpath on Sierra due to limit of dynamic loader
-            options.append('-DCMAKE_MACOSX_RPATH=ON')
-        else:
-            options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix)
-
-        # Force Trilinos to use the MPI wrappers instead of raw compilers
-        # this is needed on Apple systems that require full resolution of
-        # all symbols when linking shared libraries
-        options.extend([
-            '-DCMAKE_C_COMPILER=%s'       % spec['mpi'].mpicc,
-            '-DCMAKE_CXX_COMPILER=%s'     % spec['mpi'].mpicxx,
-            '-DCMAKE_Fortran_COMPILER=%s' % spec['mpi'].mpifc
-        ])
         if '+hypre' in spec:
             options.extend([
                 '-DTPL_ENABLE_HYPRE:BOOL=ON',
@@ -217,25 +359,6 @@ class Trilinos(CMakePackage):
                 '-DHYPRE_LIBRARY_DIRS:PATH=%s' % spec['hypre'].prefix.lib
             ])
 
-        if spec.satisfies('%intel') and spec.satisfies('@12.6.2'):
-            # Panzer uses some std:chrono that is not recognized by Intel
-            # Don't know which (maybe all) Trilinos versions this applies to
-            # Don't know which (maybe all) Intel versions this applies to
-            options.extend([
-                '-DTrilinos_ENABLE_Panzer:BOOL=OFF'
-            ])
-
-        if '+xsdkflags' in spec:
-            options.extend(['-DUSE_XSDK_DEFAULTS=YES'])
-        if '+hdf5' in spec:
-            options.extend([
-                '-DTPL_ENABLE_HDF5:BOOL=ON',
-                '-DHDF5_INCLUDE_DIRS:PATH=%s' % spec['hdf5'].prefix.include,
-                '-DHDF5_LIBRARY_DIRS:PATH=%s' % spec['hdf5'].prefix.lib
-            ])
-        else:
-            options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
-
         if '+boost' in spec:
             options.extend([
                 '-DTPL_ENABLE_Boost:BOOL=ON',
@@ -254,18 +377,6 @@ class Trilinos(CMakePackage):
         else:
             options.extend(['-DTPL_ENABLE_HDF5:BOOL=OFF'])
 
-        # Fortran lib
-        if spec.satisfies('%gcc') or spec.satisfies('%clang'):
-            libgfortran = os.path.dirname(os.popen(
-                '%s --print-file-name libgfortran.a' %
-                join_path(mpi_bin, 'mpif90')).read())
-            options.extend([
-                '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % (
-                    libgfortran),
-                '-DTrilinos_ENABLE_Fortran=ON'
-            ])
-
-        # suite-sparse related
         if '+suite-sparse' in spec:
             options.extend([
                 # FIXME: Trilinos seems to be looking for static libs only,
@@ -290,7 +401,6 @@ class Trilinos(CMakePackage):
                 '-DTPL_ENABLE_UMFPACK:BOOL=OFF',
             ])
 
-        # metis / parmetis
         if '+metis' in spec:
             options.extend([
                 '-DTPL_ENABLE_METIS:BOOL=ON',
@@ -310,7 +420,6 @@ class Trilinos(CMakePackage):
                 '-DTPL_ENABLE_ParMETIS:BOOL=OFF',
             ])
 
-        # mumps / scalapack
         if '+mumps' in spec:
             scalapack = spec['scalapack'].libs
             options.extend([
@@ -333,7 +442,6 @@ class Trilinos(CMakePackage):
                 '-DTPL_ENABLE_SCALAPACK:BOOL=OFF',
             ])
 
-        # superlu-dist:
         if '+superlu-dist' in spec:
             # Amesos, conflicting types of double and complex SLU_D
             # see
@@ -360,7 +468,6 @@ class Trilinos(CMakePackage):
                 '-DTPL_ENABLE_SuperLUDist:BOOL=OFF',
             ])
 
-        # superlu:
         if '+superlu' in spec:
             options.extend([
                 '-DTPL_ENABLE_SuperLU:BOOL=ON',
@@ -374,43 +481,55 @@ class Trilinos(CMakePackage):
                 '-DTPL_ENABLE_SuperLU:BOOL=OFF',
             ])
 
-        # python
-        if '+python' in spec:
+        if '+pnetcdf' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_PyTrilinos:BOOL=ON'
+                '-DTPL_ENABLE_Pnetcdf:BOOL=ON',
+                '-DTPL_Netcdf_Enables_Netcdf4:BOOL=ON',
+                '-DTPL_Netcdf_PARALLEL:BOOL=ON',
+                '-DPNetCDF_ROOT:PATH=%s' % spec['parallel-netcdf'].prefix
             ])
         else:
             options.extend([
-                '-DTrilinos_ENABLE_PyTrilinos:BOOL=OFF'
+                '-DTPL_ENABLE_Pnetcdf:BOOL=OFF'
             ])
 
-        # collect CXX flags:
-        options.extend([
-            '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)),
-        ])
-
-        # disable due to compiler / config errors:
-        options.extend([
-            '-DTrilinos_ENABLE_Pike=OFF',
-            '-DTrilinos_ENABLE_STK=OFF'
-        ])
-
-        if '+dtk' in spec:
+        if '+zlib' in spec:
             options.extend([
-                '-DTrilinos_EXTRA_REPOSITORIES:STRING=DataTransferKit',
-                '-DTpetra_INST_INT_UNSIGNED_LONG:BOOL=ON',
-                '-DTrilinos_ENABLE_DataTransferKit:BOOL=ON'
+                '-DTPL_ENABLE_Zlib:BOOL=ON',
+                '-DZlib_ROOT:PATH=%s' % spec['zlib'].prefix,
             ])
-
-        # exodus
-        if '+exodus' in spec:
+        else:
             options.extend([
-                '-DTrilinos_ENABLE_SEACAS:BOOL=ON'
+                '-DTPL_ENABLE_Zlib:BOOL=OFF'
             ])
-        else:
+
+        # ################# Miscellaneous Stuff ######################
+
+        # Fortran lib
+        if '+fortran' in spec:
+            if spec.satisfies('%gcc') or spec.satisfies('%clang'):
+                libgfortran = os.path.dirname(os.popen(
+                    '%s --print-file-name libgfortran.a' %
+                    join_path(mpi_bin, 'mpif90')).read())
+                options.extend([
+                    '-DTrilinos_EXTRA_LINK_FLAGS:STRING=-L%s/ -lgfortran' % (
+                        libgfortran),
+                    '-DTrilinos_ENABLE_Fortran=ON'
+                ])
+
+        # Explicit instantiation
+        if '+instantiate' in spec:
             options.extend([
-                '-DTrilinos_ENABLE_SEACAS:BOOL=OFF'
+                '-DTrilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON'
             ])
+            if '+tpetra' in spec:
+                options.extend([
+                    '-DTpetra_INST_DOUBLE:BOOL=ON',
+                    '-DTpetra_INST_INT_LONG:BOOL=ON'
+                    '-DTpetra_INST_COMPLEX_DOUBLE=%s' % (
+                        'ON' if '+instantiate_cmplx' in spec else 'OFF'
+                    )
+                ])
 
         # disable due to compiler / config errors:
         if spec.satisfies('%xl') or spec.satisfies('%xl_r'):
@@ -423,6 +542,31 @@ class Trilinos(CMakePackage):
             options.extend([
                 '-DTrilinos_ENABLE_FEI=OFF'
             ])
+
+        if '.'.join(platform.mac_ver()[0].split('.')[:2]) == '10.12':
+            # use @rpath on Sierra due to limit of dynamic loader
+            options.append('-DCMAKE_MACOSX_RPATH=ON')
+        else:
+            options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s' % prefix.lib)
+
+        if spec.satisfies('%intel') and spec.satisfies('@12.6.2'):
+            # Panzer uses some std:chrono that is not recognized by Intel
+            # Don't know which (maybe all) Trilinos versions this applies to
+            # Don't know which (maybe all) Intel versions this applies to
+            options.extend([
+                '-DTrilinos_ENABLE_Panzer:BOOL=OFF'
+            ])
+
+        # collect CXX flags:
+        options.extend([
+            '-DCMAKE_CXX_FLAGS:STRING=%s' % (' '.join(cxx_flags)),
+        ])
+
+        # disable due to compiler / config errors:
+        options.extend([
+            '-DTrilinos_ENABLE_Pike=OFF'
+        ])
+
         return options
 
     @run_after('install')
diff --git a/var/spack/repos/builtin/packages/yaml-cpp/package.py b/var/spack/repos/builtin/packages/yaml-cpp/package.py
index cc22b3420d..21400c2cfd 100644
--- a/var/spack/repos/builtin/packages/yaml-cpp/package.py
+++ b/var/spack/repos/builtin/packages/yaml-cpp/package.py
@@ -36,7 +36,7 @@ class YamlCpp(CMakePackage):
 
     variant('shared', default=True,
             description='Enable build of shared libraries')
-    variant('fpic',    default=False,
+    variant('fpic',   default=True,
             description='Build with position independent code')
 
     depends_on('boost', when='@:0.5.3')
@@ -45,13 +45,11 @@ class YamlCpp(CMakePackage):
         spec = self.spec
         options = []
 
-        if '+fpic' in spec:
-            options.extend([
-                '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true'
-            ])
-        if '+shared' in spec:
-            options.append('-DBUILD_SHARED_LIBS=ON')
-        else:
-            options.append('-DBUILD_SHARED_LIBS=OFF')
+        options.extend([
+            '-DBUILD_SHARED_LIBS:BOOL=%s' % (
+                'ON' if '+shared' in spec else 'OFF'),
+            '-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=%s' % (
+                'ON' if '+fpic' in spec else 'OFF'),
+        ])
 
         return options