CEED 1.0 (#7423)

* ceed bundle package including OCCA, MAGMA, Nek5000, mfem, and PETSc

Very preliminary, a lot of ad hoc decisions, fragile, missing functionality
All packages do build on my MacOS laptop with Cuda

Funded-by: ECP
Project: CEED
Time: 4 hours
Reported-by: Tzanio Kolev <kolev1@llnl.gov>

* Some adjustments in a few CEED-related packages.

This is still very preliminary, but with these changes I'm able to build from
scratch on a Mac laptop and a Linux desktop (RHEL7).

Note that there doesn't seem to be a good way to support CUDA in Spack, so
you'll have to install that manually yourself. You will also need a Fortran
compiler, in particular on a Mac where you also have to make sure that it
is being picked up in ~/.spack/darwin/compilers.yaml.

* ceed bundle package including OCCA, MAGMA, Nek5000, mfem, and PETSc

Very preliminary, a lot of ad hoc decisions, fragile, missing functionality
All packages do build on my MacOS laptop with Cuda

Funded-by: ECP
Project: CEED
Time: 4 hours
Reported-by: Tzanio Kolev <kolev1@llnl.gov>

* Reverting Mac-related CUDA checks in the OCCA and MAGMA packages.

A much better solution is to install CUDA manually and add it to
~/.spack/darwin/packages.yaml:

packages:
    cuda:
        paths:
            cuda@8.0.54: /usr/local/cuda

* Fix flake8 warnings

Funded-by: CEED
Project: CEED/Spack

* remove unneeded commented out code

Funded-by: CEED
Project: CEED/Spack

* Don't have PETSc use MUMPS to speedup install time, try parallel installs for Magma

Funded-by: CEED
Project: CEED/Spack

* Added libceed package and made changes to get the ceed metapackage up and running.

* Get the ceed package up and running and added installing the .h file in the libceed package.

* All packages are now pointed at specific versions (either tagged or git hashed.

* Changed some of the specific versions in the CEED metapackage.

* Some version updates.

* Applied Cameron Smith's patch for the latest pumi.

* Merge

* Nek5000: Use tarball instead of git tag

* Major update of the mfem package - needs more testing. Add a testing
shell script for mfem, test_builds.sh, in the mfem directory. It builds
a number of mfem configurations to ensure they all work.

Add 'suite-sparse' variant to petsc.

Add 'develop' version of libceed.

Add 'metis' variant of laghos.

Update the dependencies of ceed.

* Changes in petsc's handling of zlib to make the latest build work on Mac.

* [MFEM] When using '+libunwind', mfem needs '-ldl'.

* [OCCA] Remove debug print statements.

* [PETSc] Replace the check ('zlib' in spec) with ('+zlib' in spec) - the
latter checks if 'zlib' variant of petsc is enabled which is incorrect;
the former checks if petsc is configured to depend on 'zlib'.

* [MFEM] Add conduit variant.

* [libCEED] Enable testing using 'make prove'.

* [MFEM] Tweak test_builds.sh - all builds pass on fedora 27.

* Add a post install test

* Add a post installation check for NekCEM

* pumi: bump git hash, remove unused patch

* Fixed testing of Laghos package

* Adding variants in CEED package

* Empty file for URL didn't work on LLNL/LC. Replacing with bundle-package.txt -> README.md.

* [MFEM] If the spec defines the 'cxxflags' compiler flags, use that value
to set the CXXFLAGS value in the mfem build system.

* Disabling HDF5 by default.

You can still build it with "spack install ceed+hdf5".

* libceed: fix use of prefix versus DESTDIR

* Added cuda variant for libCEED (off by default)

* [libCEED] When building v0.1, fix ceed.pc before installing it.

* [CEED] Add variants for OCCA and PUMI. Replace the hdf5 variant with
a variant called quickbuild that disables variants in packages to
speedup the build - currently hdf5, boost, and superlu-dist in PETSc.

* [libCEED] Remove unused 'import os'.

* [MAGMA] Add version 2.3.0.

* [OCCA] Major update of occa/package.py.

* [libCEED] Several improvements.

* [CEED] Use fixed versions for occa and libceed.

* [OCCA] Fix a bug in CUDA setup.

* NekCEM doesn't need depends_on('python')

* [OCCA,libCEED,MFEM,CEED] Update occa and libceed versions plus a few
tweaks in occa and mfem.

* Switching to gslib-1.0.2 to fix summitdev bug.

* [Nek5000] Use the Fortran 77 compiler instead of the 'fc' compiler.
Propagate any 'fflags' and 'cflags' specifications to the Nek tools.

* [MFEM] Tweak for 'ppc64le'.

* attempt to override fips compatibility error for md5

* Compiler option changes in libCEED to fix summitdev build.

* Disable the nekcem install test until it can be fixed.

* [NekCEM] Major update of the package to fix various issues.

* [NekCEM] Fix formatting

* zoltan: remove non-portable -g0 flag

the pgi compiler does not accept it

* pumi: specify dependency on cmake > 3

* [Nek5000] Add dependency on libx11 when needed. Various hacks to
support IBM XL compilers.

* [NekCEM] Link with the pthreads library - it is required.

* [MAGMA] Add a patch for magma v2.3.0 when building with gcc <= 4.8.
Add dependency on BLAS.

* [CEED] Update to magma 2.3.0. When building with gcc < 4.9 constrain
the used suite-sparse version to <= 5.1.0 - starting with v5.2.0,
suite-sparse requires gcc >= 4.9.

* Small updates

* [libceed, gslib] Fix style

* [Nek5000] Need 'libxt' as a dependency as well.

* [MUMPS] Temporary workaround for ray.

* Updating occa and libceed to laters pre-1.0.0 and pre-0.2 hashes

* petsc: add pkg-config patch for variable quoting

Variable definitions in pkg-config are processed more like make than a
shell, so don't need quoting.  Older versions of pkg-config (<= 0.28)
did not remove the quotes when printing the value.

Freedesktop #67904 (https://bugs.freedesktop.org/show_bug.cgi?id=67904)

Reported-by: Tzanio Kolev <kolev1@llnl.gov>

* petsc: add 3.8.4 and myself as co-maintainer

* Updating libceed to latest pre-0.2 hash.

* [PETSc] Add the 'headers' and 'libs' properties.

* [MFEM] Explicitly add rpaths to link flags for external packages.
This is necessary when MFEM's exported options (in config.mk) are
used outside of Spack for linking against MFEM.

* Unset MFEM_DIR before building MFEM

* [PETSc] As observed by @jedbrown, there is no need to define the 'libs'
property explicitly - the default handler works fine too.

* Build MAGMA shared by default, install a few additional headers

* Forgot a self

* Switching to OCCA tag v1.0.0-alpha.4.

Adding urls for OCCA and libCEED ('spack uninstall' complains otherwise).

* Removed FIXMEs for OCCA tag

* [occa] Cleaned up tagged versions

* [libceed] Updated occa to v1.0.0-alpha.5

* [ceed] Updated occa to v1.0.0-alpha.5

* [libCEED] Always define the 'NDEBUG' makefile option based on the
'debug' variant setting - this should always work regardless of the
default setting inside the libceed makefile.

* [MUMPS] Revert a temporary workaround.

* [CEED, libCEED] Minor tweaks.

* libCEED v0.2 release

* [CEED] Use version 0.2 of libCEED.

* [HPGMG] Remove duplicate version.

* [CEED] Update the hpgmg version

* hpgmg: use tarball for 0.3

The Git repository contains somewhat heavy documentation so the tarballs
are much faster.

* hpgmg: +fe was default for the 0.3 release

* hpgmg: explicitly name build directory to avoid use of ambient PETSC_ARCH

* [HPGMG] Fix flake8 formatting

* libceed@0.2: work around occaFree issue

2 files changed, 114 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/ceed/README.md b/var/spack/repos/builtin/packages/ceed/README.md
new file mode 100644
index 0000000000..74bcae1d17
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceed/README.md
@@ -0,0 +1,3 @@
+This is a bundle for the CEED software suite.
+
+See https://ceed.exascaleproject.org for details.
diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py
new file mode 100644
index 0000000000..f6569a324c
--- /dev/null
+++ b/var/spack/repos/builtin/packages/ceed/package.py
@@ -0,0 +1,111 @@
+##############################################################################
+# 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 *
+import os
+
+
+class Ceed(Package):
+    """Ceed is a collection of benchmarks, miniapps, software libraries and
+       APIs for efficient high-order finite element and spectral element
+       discretizations for exascale applications developed in the Department of
+       Energy (DOE) and partially supported by the Exascale Computing Project
+       (ECP). This is a Spack bundle package that installs the CEED software
+       components."""
+
+    homepage = "https://ceed.exascaleproject.org"
+
+    url  = 'file://' + os.path.dirname(__file__) + '/README.md'
+    sha1 = 'b2eefd95c09ba573f663a761b84811a2d7e39788'
+
+    version('1.0.0', sha1, expand=False)
+
+    variant('cuda', default=False,
+            description='Build MAGMA; enable CUDA support in libCEED and OCCA')
+    variant('mfem', default=True, description='Build MFEM and Laghos')
+    variant('nek', default=True,
+            description='Build Nek5000, GSLIB, Nekbone, and NekCEM')
+    variant('occa', default=True,
+            description='Build OCCA; enable OCCA support in libCEED')
+    variant('petsc', default=True,
+            description='Build PETSc and HPGMG')
+    variant('pumi', default=True,
+            description='Build PUMI')
+    variant('quickbuild', default=True,
+            description='Speed-up the build by disabling variants in packages')
+    # TODO: Add 'int64' variant?
+
+    # LibCEED
+    depends_on('libceed@0.2~cuda', when='@1.0.0~cuda')
+    depends_on('libceed@0.2+cuda', when='@1.0.0+cuda')
+    depends_on('libceed@0.2+occa', when='@1.0.0+occa')
+    depends_on('libceed@0.2~occa', when='@1.0.0~occa')
+
+    # OCCA
+    depends_on('occa@v1.0.0-alpha.5~cuda', when='@1.0.0+occa~cuda')
+    depends_on('occa@v1.0.0-alpha.5+cuda', when='@1.0.0+occa+cuda')
+
+    # Nek5000, GSLIB, Nekbone, and NekCEM
+    depends_on('nek5000@17.0', when='@1.0.0+nek')
+    depends_on('gslib@1.0.2', when='@1.0.0+nek')
+    depends_on('nekbone@17.0', when='@1.0.0+nek')
+    depends_on('nekcem@0b8bedd', when='@1.0.0+nek')
+
+    # PETSc, HPGMG
+    # For a +quickbuild we disable boost, hdf5, and superlu-dist in PETSc.
+    # Ideally, these can be turned into recommendations to Spack for
+    # concretizing the PETSc spec, if Spack ever supports recommendations.
+    depends_on('petsc@3.8.3~boost~hdf5~superlu-dist',
+               when='@1.0.0+petsc+quickbuild')
+    depends_on('petsc@3.8.3+mpi+double~int64', when='@1.0.0+petsc~mfem')
+    # The mfem petsc examples need the petsc variants +hypre, +suite-sparse,
+    # and +mumps:
+    depends_on('petsc@3.8.3+mpi+hypre+suite-sparse+mumps+double~int64',
+               when='@1.0.0+petsc+mfem')
+    depends_on('hpgmg@a0a5510df23b+fe', when='@1.0.0+petsc')
+
+    # MAGMA
+    depends_on('magma@2.3.0', when='@1.0.0+cuda')
+
+    # PUMI
+    depends_on('pumi@2.1.0', when='@1.0.0+pumi')
+
+    # MFEM, Laghos
+    depends_on('mfem@3.3.2+mpi+examples+miniapps', when='@1.0.0+mfem~petsc')
+    depends_on('mfem@3.3.2+mpi+petsc+examples+miniapps',
+               when='@1.0.0+mfem+petsc')
+    depends_on('laghos@1.0', when='@1.0.0+mfem')
+    # The next line seems to be necessary because the concretizer somehow
+    # decides that mfem requires 'hypre+internal-superlu' even though the mfem
+    # package lists simply 'hypre' as dependency. This is only an issue because
+    # petsc explicitly requires 'hypre~internal-superlu' which for the
+    # concretizer is a conflict.
+    depends_on('hypre~internal-superlu', when='@1.0.0+mfem')
+
+    # If using gcc version <= 4.8 build suite-sparse version <= 5.1.0
+    depends_on('suite-sparse@:5.1.0', when='@1.0.0%gcc@:4.8+mfem+petsc')
+
+    # Dummy install
+    def install(self, spec, prefix):
+        install('README.md', prefix)