updates to conduit and ascent packages (new PR) (#6584)

* optional path to use spacks py-site-pkgs, install host-cfg for provenance

* add more comments and address review requests

* only use st-pkgs-dir when +python

* ascent does not need doxygen

* capture mpiexec if it exists

* added missing import

* flake8 fix

* default adios variant to False

* ascent develop now reqs conduit master

* optional path to use spacks py-site-pkgs, install host-cfg for provenance

* add more comments and address review requests

* only use st-pkgs-dir when +python

* ascent does not need doxygen

* capture mpiexec if it exists

* added missing import

* flake8 fix

* default adios variant to False

* ascent develop now reqs conduit master

* conduit: use hdf5 1.8 for wider output compat

3 files changed, 76 insertions, 30 deletions

diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py
index 854bf1e909..eda0f93c1c 100644
--- a/var/spack/repos/builtin/packages/ascent/package.py
+++ b/var/spack/repos/builtin/packages/ascent/package.py
@@ -78,7 +78,7 @@ class Ascent(Package):
     variant("tbb", default=True, description="Build tbb support")
     variant("cuda", default=False, description="Build cuda support")
 
-    variant("adios", default=True, description="Build Adios filter support")
+    variant("adios", default=False, description="Build Adios filter support")
 
     # variants for dev-tools (docs, etc)
     variant("doc", default=False, description="Build Conduit's documentation")
@@ -88,7 +88,7 @@ class Ascent(Package):
     ###########################################################################
 
     depends_on("cmake", when="+cmake")
-    depends_on("conduit")
+    depends_on("conduit@master")
 
     #######################
     # Python
@@ -125,7 +125,13 @@ class Ascent(Package):
         Build and install Conduit.
         """
         with working_dir('spack-build', create=True):
-            host_cfg_fname = self.create_host_config(spec, prefix)
+            py_site_pkgs_dir = None
+            if "+python" in spec:
+                py_site_pkgs_dir = site_packages_dir
+
+            host_cfg_fname = self.create_host_config(spec,
+                                                     prefix,
+                                                     py_site_pkgs_dir)
             cmake_args = []
             # if we have a static build, we need to avoid any of
             # spack's default cmake settings related to rpaths
@@ -140,12 +146,26 @@ class Ascent(Package):
             cmake(*cmake_args)
             make()
             make("install")
-            # TODO also copy host_cfg_fname into install
+            # install copy of host config for provenance
+            install(host_cfg_fname, prefix)
 
-    def create_host_config(self, spec, prefix):
+    def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         """
         This method creates a 'host-config' file that specifies
         all of the options used to configure and build ascent.
+
+        For more details about 'host-config' files see:
+            http://ascent.readthedocs.io/en/latest/BuildingAscent.html
+
+        Note:
+          The `py_site_pkgs_dir` arg exists to allow a package that
+          subclasses this package provide a specific site packages
+          dir when calling this function. `py_site_pkgs_dir` should
+          be an absolute path or `None`.
+
+          This is necessary because the spack `site_packages_dir`
+          var will not exist in the base class. For more details
+          on this issue see: https://github.com/spack/spack/issues/6261
         """
 
         #######################
@@ -184,9 +204,9 @@ class Ascent(Package):
                 raise RuntimeError(msg)
             cmake_exe = cmake_exe.path
 
-        host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
-                                             sys_type,
-                                             spec.compiler)
+        host_cfg_fname = "%s-%s-%s-ascent.cmake" % (socket.gethostname(),
+                                                    sys_type,
+                                                    spec.compiler)
 
         cfg = open(host_cfg_fname, "w")
         cfg.write("##################################\n")
@@ -246,10 +266,10 @@ class Ascent(Package):
             cfg.write("# python from spack \n")
             cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE",
                       spec['python'].command.path))
-            # install module to standard style site packages dir
-            # so we can support spack activate
-            cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
-                                        site_packages_dir))
+            # only set dest python site packages dir if passed
+            if py_site_pkgs_dir:
+                cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
+                                            py_site_pkgs_dir))
         else:
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
 
@@ -260,10 +280,6 @@ class Ascent(Package):
             sphinx_build_exe = join_path(spec['py-sphinx'].prefix.bin,
                                          "sphinx-build")
             cfg.write(cmake_cache_entry("SPHINX_EXECUTABLE", sphinx_build_exe))
-
-            cfg.write("# doxygen from uberenv\n")
-            doxygen_exe = spec['doxygen'].command.path
-            cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
         else:
             cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
 
@@ -280,6 +296,10 @@ class Ascent(Package):
                                         spec['mpi'].mpicxx))
             cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
                                         spec['mpi'].mpifc))
+            mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+            if os.path.isfile(mpiexe_bin):
+                cfg.write(cmake_cache_entry("MPIEXEC",
+                                            mpiexe_bin))
         else:
             cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
 
diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
index 6793a391c3..2ce7edc8cd 100644
--- a/var/spack/repos/builtin/packages/conduit/package.py
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -108,9 +108,10 @@ class Conduit(Package):
     # experienced on BGQ. When on, the static build tries
     # to link against shared libs.
     #
-    # we are not using hdf5's mpi or fortran features.
-    depends_on("hdf5~cxx~mpi~fortran", when="+hdf5+shared")
-    depends_on("hdf5~shared~cxx~mpi~fortran", when="+hdf5~shared")
+    # Use HDF5 1.8, for wider output compatibly
+    # variants reflect we are not using hdf5's mpi or fortran features.
+    depends_on("hdf5@1.8.19:1.8.999~cxx~mpi~fortran", when="+hdf5+shared")
+    depends_on("hdf5@1.8.19:1.8.999~shared~cxx~mpi~fortran", when="+hdf5~shared")
 
     # we are not using silo's fortran features
     depends_on("silo~fortran", when="+silo+shared")
@@ -148,7 +149,13 @@ class Conduit(Package):
         Build and install Conduit.
         """
         with working_dir('spack-build', create=True):
-            host_cfg_fname = self.create_host_config(spec, prefix)
+            py_site_pkgs_dir = None
+            if "+python" in spec:
+                py_site_pkgs_dir = site_packages_dir
+
+            host_cfg_fname = self.create_host_config(spec,
+                                                     prefix,
+                                                     py_site_pkgs_dir)
             cmake_args = []
             # if we have a static build, we need to avoid any of
             # spack's default cmake settings related to rpaths
@@ -163,14 +170,26 @@ class Conduit(Package):
             cmake(*cmake_args)
             make()
             make("install")
+            # install copy of host config for provenance
+            install(host_cfg_fname, prefix)
 
-    def create_host_config(self, spec, prefix):
+    def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
         """
         This method creates a 'host-config' file that specifies
         all of the options used to configure and build conduit.
 
-        For more details see about 'host-config' files see:
+        For more details about 'host-config' files see:
             http://software.llnl.gov/conduit/building.html
+
+        Note:
+          The `py_site_pkgs_dir` arg exists to allow a package that
+          subclasses this package provide a specific site packages
+          dir when calling this function. `py_site_pkgs_dir` should
+          be an absolute path or `None`.
+
+          This is necessary because the spack `site_packages_dir`
+          var will not exist in the base class. For more details
+          on this issue see: https://github.com/spack/spack/issues/6261
         """
 
         #######################
@@ -209,9 +228,9 @@ class Conduit(Package):
                 raise RuntimeError(msg)
             cmake_exe = cmake_exe.path
 
-        host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
-                                             sys_type,
-                                             spec.compiler)
+        host_cfg_fname = "%s-%s-%s-conduit.cmake" % (socket.gethostname(),
+                                                     sys_type,
+                                                     spec.compiler)
 
         cfg = open(host_cfg_fname, "w")
         cfg.write("##################################\n")
@@ -256,10 +275,10 @@ class Conduit(Package):
             cfg.write("# python from spack \n")
             cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE",
                       spec['python'].command.path))
-            # install module to standard style site packages dir
-            # so we can support spack activate
-            cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
-                                        site_packages_dir))
+            # only set dest python site packages dir if passed
+            if py_site_pkgs_dir:
+                cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
+                                            py_site_pkgs_dir))
         else:
             cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
 
@@ -290,6 +309,10 @@ class Conduit(Package):
                                         spec['mpi'].mpicxx))
             cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
                                         spec['mpi'].mpifc))
+            mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+            if os.path.isfile(mpiexe_bin):
+                cfg.write(cmake_cache_entry("MPIEXEC",
+                                            mpiexe_bin))
         else:
             cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
 
diff --git a/var/spack/repos/builtin/packages/vtkh/package.py b/var/spack/repos/builtin/packages/vtkh/package.py
index 9073c1f6f3..35883547b1 100644
--- a/var/spack/repos/builtin/packages/vtkh/package.py
+++ b/var/spack/repos/builtin/packages/vtkh/package.py
@@ -24,6 +24,7 @@
 ##############################################################################
 
 from spack import *
+import os
 
 
 class Vtkh(Package):
@@ -67,7 +68,9 @@ class Vtkh(Package):
                 mpicxx = spec['mpi'].mpicxx
                 cmake_args.extend(["-DMPI_C_COMPILER={0}".format(mpicc),
                                    "-DMPI_CXX_COMPILER={0}".format(mpicxx)])
-
+                mpiexe_bin = join_path(spec['mpi'].prefix.bin, 'mpiexec')
+                if os.path.isfile(mpiexe_bin):
+                    cmake_args.append("-DMPIEXEC={0}".format(mpiexe_bin))
             # tbb support
             if "+tbb" in spec:
                 cmake_args.append("-DTBB_DIR={0}".format(spec["tbb"].prefix))