update conduit for 0.5.0 release (#13455)

* add support for static (via ~shared) and use vtk-m 1.2

* updating vtkh package to output cmake configure file and pinning it to vtkm 1.2

* trying a different cmake for vtkh

* removing problematic b

* making conduit respect ~python

* fixing ascent python logic

* update ascent package

* consistant cmake usage

* conditionally add tbb in ascent if vtkh

* applying becker fix

* adding vtkh tag

* fixing vtkh tagged version

* updating ascent and conduit for static builds

* enabling openmp

* reverting files that should not have been changed

* ascent updates

* more robust handling of variants

* fixing ascent package typo

* ascent: add optional support for mfem

* enable mfem conduit support for ascent

* add optional adios dep to conduit

* remove ver req from conduit

* ascent: remove confusing comment

* tweaks to conduit and ascent pkg recipes

* fix typo in conduit package

* pref conduit master

* fixing mfem typo for ascent

* reverting files

* adding mirror for bzip

* changing mfem to depend on conduit@master to get updated relay

* restore use of conduit 0.3.1 or greater for mfem

* set master as prefered conduit version

* allow mfem to use conduit master

* adding rover package and editing ascent

* updating vtkm cmake dep

* updates from axom

* guard ascent python support on +shared

* removing rover to simply ascent package

* add fortran variant to conduit, to allow us to turn off conduit support even when a fortran compiler is specified

* fix fortran compiler check so it can work on cray systems

* working towards cuda fix for vtkm lagrange filter

* update ascent package with more variants, and patch to avoid nvcc issue

* hdf5 flags fix for BGQ

* flake8

* extra guards for cuda patch

* conduit and ascent fortran fix

* fix patch for non cuda case

* add test variant to conduit, tweak ascent pkg

* change min ver of cmake used for ascent

* h5z-zfp package: unset FC when ~fortran

* conform to expected upstream solution

* pinning vtkm

* going back to vtkm master

* add back vtk-m variant for shared libs

* update ascent and vtkh packages

* wire up option to run tests during install

* add post install test

* add testing to ascent

* tweak for blueos xl

* add ctest output on error for run_tests

* enable ctest output on error for run_tests

* add testing of the using-with-make example

* update using-with-make examples

* typo in ascent using-with-cmake test

* fix ascent using test exe names

* more fixes, less sleep

* more fixes, less sleep ...

* remove unwired up version

* improvments suggested on review

* adding new cmake

* Update package.py

* Update package.py

* changes post cori os update

* fix cray hack

* Update package.py

Fixing 'fix'. Inconsistent variable names in conduit package

* type in spack recipes

* add zfp support to conduit

* fix indent error in conduit pkg

* move to use build phases, add sphinx rtd as dep, fix ex names in tests

* add conduit 0.5.0 release

* flake8

* remove old cray hack

* incorp feedback from review

* fix to use proper build env sig

2 files changed, 92 insertions, 25 deletions

diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py
index d837e51010..8d8210edd1 100644
--- a/var/spack/repos/builtin/packages/ascent/package.py
+++ b/var/spack/repos/builtin/packages/ascent/package.py
@@ -72,7 +72,7 @@ class Ascent(Package):
     # package dependencies
     ###########################################################################
 
-    depends_on("cmake@3.9.2:3.9.999", type='build')
+    depends_on("cmake@3.14:", type='build')
     depends_on("conduit~python", when="~python")
     depends_on("conduit+python", when="+python+shared")
     depends_on("conduit~shared~python", when="~shared")
@@ -120,8 +120,8 @@ class Ascent(Package):
     #######################
     depends_on("py-sphinx", when="+python+doc", type='build')
 
-    def setup_environment(self, spack_env, run_env):
-        spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1')
+    def setup_build_environment(self, env):
+        env.set('CTEST_OUTPUT_ON_FAILURE', '1')
 
     def install(self, spec, prefix):
         """
@@ -353,12 +353,21 @@ class Ascent(Package):
         cfg.write("# MPI Support\n")
 
         if "+mpi" in spec:
+            mpicc_path = spec['mpi'].mpicc
+            mpicxx_path = spec['mpi'].mpicxx
+            mpifc_path = spec['mpi'].mpifc
+            # if we are using compiler wrappers on cray systems
+            # use those for mpi wrappers, b/c  spec['mpi'].mpicxx
+            # etc make return the spack compiler wrappers
+            # which can trip up mpi detection in CMake 3.14
+            if cpp_compiler == "CC":
+                mpicc_path = "cc"
+                mpicxx_path = "CC"
+                mpifc_path = "ftn"
             cfg.write(cmake_cache_entry("ENABLE_MPI", "ON"))
-            cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc))
-            cfg.write(cmake_cache_entry("MPI_CXX_COMPILER",
-                                        spec['mpi'].mpicxx))
-            cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
-                                        spec['mpi'].mpifc))
+            cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path))
+            cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path))
+            cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path))
             mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
             if os.path.isfile(mpiexe_bin):
                 # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index af1cc70c85..acc1498b70 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -38,6 +38,7 @@ class Conduit(Package):
     git      = "https://github.com/LLNL/conduit.git"
 
     version('master', branch='master', submodules=True, preferred=True)
+    version('0.5.0', sha256='7efac668763d02bd0a2c0c1b134d9f5ee27e99008183905bb0512e5502b8b4fe')
     version('0.4.0', sha256='c228e6f0ce5a9c0ffb98e0b3d886f2758ace1a4b40d00f3f118542c0747c1f52')
     version('0.3.1', sha256='7b358ca03bb179876291d4a55d6a1c944b7407a80a588795b9e47940b1990521')
     version('0.3.0', sha256='52e9cf5720560e5f7492876c39ef2ea20ae73187338361d2744bdf67567da155')
@@ -66,6 +67,9 @@ class Conduit(Package):
     variant("silo", default=False, description="Build Conduit Silo support")
     variant("adios", default=False, description="Build Conduit ADIOS support")
 
+    # zfp compression
+    variant("zfp", default=True, description="Build Conduit ZFP support")
+
     # variants for dev-tools (docs, etc)
     variant("doc", default=False, description="Build Conduit's documentation")
     # doxygen support is wip, since doxygen has several dependencies
@@ -94,6 +98,10 @@ class Conduit(Package):
     #######################
     # I/O Packages
     #######################
+
+    ###############
+    # HDF5
+    ###############
     # TODO: cxx variant is disabled due to build issue Cyrus
     # experienced on BGQ. When on, the static build tries
     # to link against shared libs.
@@ -105,16 +113,27 @@ class Conduit(Package):
     depends_on("hdf5~cxx~mpi~fortran", when="+hdf5~hdf5_compat+shared")
     depends_on("hdf5~shared~cxx~mpi~fortran", when="+hdf5~hdf5_compat~shared")
 
+    ###############
+    # Silo
+    ###############
     # we are not using silo's fortran features
     depends_on("silo~fortran", when="+silo+shared")
     depends_on("silo~shared~fortran", when="+silo~shared")
 
+    ###############
+    # ADIOS
+    ###############
     depends_on("adios+mpi~hdf5+shared",       when="+adios+mpi+shared")
     depends_on("adios+mpi~hdf5~shared~blosc", when="+adios+mpi~shared")
     depends_on("adios~mpi~hdf5+shared",       when="+adios~mpi+shared")
     depends_on("adios~mpi~hdf5~shared~blosc", when="+adios~mpi~shared")
 
     #######################
+    # ZFP
+    #######################
+    depends_on("zfp", when="+zfp")
+
+    #######################
     # MPI
     #######################
     depends_on("mpi", when="+mpi")
@@ -123,10 +142,14 @@ class Conduit(Package):
     # Documentation related
     #######################
     depends_on("py-sphinx", when="+python+doc", type='build')
+    depends_on("py-sphinx-rtd-theme", when="+python+doc", type='build')
     depends_on("doxygen", when="+doc+doxygen")
 
-    def setup_environment(self, spack_env, run_env):
-        spack_env.set('CTEST_OUTPUT_ON_FAILURE', '1')
+    # build phases used by this package
+    phases = ["configure", "build", "install"]
+
+    def setup_build_environment(self, env):
+        env.set('CTEST_OUTPUT_ON_FAILURE', '1')
 
     def url_for_version(self, version):
         """
@@ -145,9 +168,9 @@ class Conduit(Package):
             return "https://github.com/LLNL/conduit/releases/download/v{0}/conduit-v{1}-src-with-blt.tar.gz".format(v, v)
         return url
 
-    def install(self, spec, prefix):
+    def configure(self, spec, prefix):
         """
-        Build and install Conduit.
+        Configure Conduit.
         """
         with working_dir('spack-build', create=True):
             py_site_pkgs_dir = None
@@ -157,6 +180,9 @@ class Conduit(Package):
             host_cfg_fname = self.create_host_config(spec,
                                                      prefix,
                                                      py_site_pkgs_dir)
+            # save this filename for
+            # other package recipe steps to access
+            self.host_cfg_fname = host_cfg_fname
             cmake_args = []
             # if we have a static build, we need to avoid any of
             # spack's default cmake settings related to rpaths
@@ -170,17 +196,31 @@ class Conduit(Package):
             cmake_args.extend(["-C", host_cfg_fname, "../src"])
             print("Configuring Conduit...")
             cmake(*cmake_args)
+
+    def build(self, spec, prefix):
+        """
+        Build Conduit.
+        """
+        with working_dir('spack-build'):
             print("Building Conduit...")
             make()
-            # run unit tests if requested
-            if "+test" in spec and self.run_tests:
-                print("Running Conduit Unit Tests...")
-                make("test")
-            print("Installing Conduit...")
+
+    @run_after('build')
+    @on_package_attributes(run_tests=True)
+    def test(self):
+        with working_dir('spack-build'):
+            print("Running Conduit Unit Tests...")
+            make("test")
+
+    def install(self, spec, prefix):
+        """
+        Install Conduit.
+        """
+        with working_dir('spack-build'):
             make("install")
             # install copy of host config for provenance
             print("Installing Conduit CMake Host Config File...")
-            install(host_cfg_fname, prefix)
+            install(self.host_cfg_fname, prefix)
 
     @run_after('install')
     @on_package_attributes(run_tests=True)
@@ -203,7 +243,7 @@ class Conduit(Package):
                           example_src_dir]
             cmake(*cmake_args)
             make()
-            example = Executable('./example')
+            example = Executable('./conduit_example')
             example()
         print("Checking using-with-make example...")
         example_src_dir = join_path(install_prefix,
@@ -216,7 +256,7 @@ class Conduit(Package):
             for example_file in example_files:
                 shutil.copy(example_file, ".")
             make("CONDUIT_DIR={0}".format(install_prefix))
-            example = Executable('./example')
+            example = Executable('./conduit_example')
             example()
 
     def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
@@ -366,12 +406,21 @@ class Conduit(Package):
         cfg.write("# MPI Support\n")
 
         if "+mpi" in spec:
+            mpicc_path = spec['mpi'].mpicc
+            mpicxx_path = spec['mpi'].mpicxx
+            mpifc_path = spec['mpi'].mpifc
+            # if we are using compiler wrappers on cray systems
+            # use those for mpi wrappers, b/c  spec['mpi'].mpicxx
+            # etc make return the spack compiler wrappers
+            # which can trip up mpi detection in CMake 3.14
+            if cpp_compiler == "CC":
+                mpicc_path = "cc"
+                mpicxx_path = "CC"
+                mpifc_path = "ftn"
             cfg.write(cmake_cache_entry("ENABLE_MPI", "ON"))
-            cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc))
-            cfg.write(cmake_cache_entry("MPI_CXX_COMPILER",
-                                        spec['mpi'].mpicxx))
-            cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
-                                        spec['mpi'].mpifc))
+            cfg.write(cmake_cache_entry("MPI_C_COMPILER", mpicc_path))
+            cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", mpicxx_path))
+            cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER", mpifc_path))
             mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
             if os.path.isfile(mpiexe_bin):
                 # starting with cmake 3.10, FindMPI expects MPIEXEC_EXECUTABLE
@@ -385,6 +434,15 @@ class Conduit(Package):
         else:
             cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
 
+        #######################
+        # ZFP
+        #######################
+        cfg.write("# zfp from spack \n")
+        if "+zfp" in spec:
+            cfg.write(cmake_cache_entry("ZFP_DIR", spec['zfp'].prefix))
+        else:
+            cfg.write("# zfp not built by spack \n")
+
         #######################################################################
         # I/O Packages
         #######################################################################