add package for conduit (#2670)

* add package for conduit

* try to fix main conduit docstring

* use join_path instead of pjoin

* address a few requests in pr #2670

change name of 'github-master' to 'master'

change 'docs' variant to 'doc', set default to False

remove explicit +shared variant spec for silo and hdf5 deps
(in the conduit +shared case) cases since they default to True

add reference to static rpath issue
(https://github.com/LLNL/spack/issues/2658)

* address pr #2670 requests

add todos and more info on why variants for deps where selected
use python module install python to enable spack activate
use .format instead of %s

1 files changed, 312 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/conduit/package.py b/var/spack/repos/builtin/packages/conduit/package.py
new file mode 100644
index 0000000000..ce1affc0cd
--- /dev/null
+++ b/var/spack/repos/builtin/packages/conduit/package.py
@@ -0,0 +1,312 @@
+##############################################################################
+# 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 socket
+import os
+
+import llnl.util.tty as tty
+
+
+def cmake_cache_entry(name, value):
+    """
+    Helper that creates CMake cache entry strings used in
+    'host-config' files.
+    """
+    return 'set("{0}" "{1}" CACHE PATH "")\n\n'.format(name, value)
+
+
+class Conduit(Package):
+    """Conduit is an open source project from Lawrence Livermore National
+    Laboratory that provides an intuitive model for describing hierarchical
+    scientific data in C++, C, Fortran, and Python. It is used for data
+    coupling between packages in-core, serialization, and I/O tasks."""
+
+    homepage = "http://software.llnl.gov/conduit"
+    url = "https://github.com/LLNL/conduit/archive/v0.2.0.tar.gz"
+
+    version('0.2.0', 'd595573dedf55514c11d7391092fd760')
+
+    version('master', git='https://github.com/LLNL/conduit.git')
+
+    ###########################################################################
+    # package variants
+    ###########################################################################
+
+    variant("shared", default=True, description="Build Conduit as shared libs")
+
+    variant("cmake", default=True,
+            description="Build CMake (if off, attempt to use cmake from PATH)")
+
+    # variants for python support
+    variant("python", default=True, description="Build Conduit Python support")
+
+    # variants for comm and i/o
+    variant("mpi", default=True, description="Build Conduit MPI Support")
+    variant("hdf5", default=True, description="Build Conduit HDF5 support")
+    variant("silo", default=True, description="Build Conduit Silo support")
+
+    # variants for dev-tools (docs, etc)
+    variant("doc", default=False, description="Build Conduit's documentation")
+
+    ###########################################################################
+    # package dependencies
+    ###########################################################################
+
+    #######################
+    # CMake
+    #######################
+    # cmake 3.3.1 is the version we tested
+    depends_on("cmake@3.3.1", when="+cmake")
+
+    #######################
+    # Python
+    #######################
+    extends("python", when="+python")
+    # TODO: blas and lapack are disabled due to build
+    # issues Cyrus experienced on OSX 10.11.6
+    depends_on("py-numpy~blas~lapack", when="+python")
+
+    #######################
+    # I/O Packages
+    #######################
+    # TODO: cxx variant is disabled due to build issue Cyrus
+    # experienced on BGQ. When on, the static build tries
+    # to link agains shared libs.
+    #
+    # we are not using hdf5's mpi or fortran features.
+    depends_on("hdf5~cxx~mpi~fortran", when="+shared")
+    depends_on("hdf5~shared~cxx~mpi~fortran", when="~shared")
+
+    # we are not using silo's fortran features
+    depends_on("silo~fortran", when="+shared")
+    depends_on("silo~shared~fortran", when="~shared")
+
+    #######################
+    # MPI
+    #######################
+    depends_on("mpi", when="+mpi")
+
+    #######################
+    # Documentation related
+    #######################
+    depends_on("py-sphinx", when="+python+doc")
+    depends_on("doxygen", when="+doc")
+
+    def install(self, spec, prefix):
+        """
+        Build and install Conduit.
+        """
+        with working_dir('spack-build', create=True):
+            host_cfg_fname = self.create_host_config(spec, prefix)
+            cmake_args = []
+            # if we have a static build, we need to avoid any of
+            # spack's default cmake settings related to rpaths
+            # (see: https://github.com/LLNL/spack/issues/2658)
+            if "+shared" in spec:
+                cmake_args.extend(std_cmake_args)
+            else:
+                for arg in std_cmake_args:
+                    if arg.count("RPATH") == 0:
+                        cmake_args.append(arg)
+            cmake_args.extend(["-C", host_cfg_fname, "../src"])
+            cmake(*cmake_args)
+            make()
+            make("install")
+
+    def create_host_config(self, spec, prefix):
+        """
+        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:
+            http://software.llnl.gov/conduit/building.html
+        """
+
+        #######################
+        # Compiler Info
+        #######################
+        c_compiler = env["SPACK_CC"]
+        cpp_compiler = env["SPACK_CXX"]
+        f_compiler = None
+
+        if self.compiler.fc:
+            # even if this is set, it may not exist so do one more sanity check
+            if os.path.isfile(env["SPACK_FC"]):
+                f_compiler = env["SPACK_FC"]
+
+        #######################################################################
+        # By directly fetching the names of the actual compilers we appear
+        # to doing something evil here, but this is necessary to create a
+        # 'host config' file that works outside of the spack install env.
+        #######################################################################
+
+        sys_type = spec.architecture
+        # if on llnl systems, we can use the SYS_TYPE
+        if "SYS_TYPE" in env:
+            sys_type = env["SYS_TYPE"]
+
+        ##############################################
+        # Find and record what CMake is used
+        ##############################################
+
+        if "+cmake" in spec:
+            cmake_exe = join_path(spec['cmake'].prefix.bin, "cmake")
+        else:
+            cmake_exe = which("cmake")
+            if cmake_exe is None:
+                msg = 'failed to find CMake (and cmake variant is off)'
+                raise RuntimeError(msg)
+            cmake_exe = cmake_exe.command
+
+        host_cfg_fname = "%s-%s-%s.cmake" % (socket.gethostname(),
+                                             sys_type,
+                                             spec.compiler)
+
+        cfg = open(host_cfg_fname, "w")
+        cfg.write("##################################\n")
+        cfg.write("# spack generated host-config\n")
+        cfg.write("##################################\n")
+        cfg.write("# {0}-{1}\n".format(sys_type, spec.compiler))
+        cfg.write("##################################\n\n")
+
+        # Include path to cmake for reference
+        cfg.write("# cmake from spack \n")
+        cfg.write("# cmake executable path: %s\n\n" % cmake_exe)
+
+        #######################
+        # Compiler Settings
+        #######################
+
+        cfg.write("#######\n")
+        cfg.write("# using %s compiler spec\n" % spec.compiler)
+        cfg.write("#######\n\n")
+        cfg.write("# c compiler used by spack\n")
+        cfg.write(cmake_cache_entry("CMAKE_C_COMPILER", c_compiler))
+        cfg.write("# cpp compiler used by spack\n")
+        cfg.write(cmake_cache_entry("CMAKE_CXX_COMPILER", cpp_compiler))
+
+        cfg.write("# fortran compiler used by spack\n")
+        if f_compiler is not None:
+            cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "ON"))
+            cfg.write(cmake_cache_entry("CMAKE_Fortran_COMPILER", f_compiler))
+        else:
+            cfg.write("# no fortran compiler found\n\n")
+            cfg.write(cmake_cache_entry("ENABLE_FORTRAN", "OFF"))
+
+        #######################
+        # Python
+        #######################
+
+        cfg.write("# Python Support\n")
+
+        if "+python" in spec:
+            python_exe = join_path(spec['python'].prefix.bin, "python")
+            cfg.write("# Enable python module builds\n")
+            cfg.write(cmake_cache_entry("ENABLE_PYTHON", "ON"))
+            cfg.write("# python from spack \n")
+            cfg.write(cmake_cache_entry("PYTHON_EXECUTABLE", python_exe))
+            # install module to standard style site packages dir
+            # so we can support spack activate
+            py_ver_short = "python{0}".format(spec["python"].version.up_to(2))
+            pym_prefix = join_path("${CMAKE_INSTALL_PREFIX}",
+                                   "lib",
+                                   py_ver_short,
+                                   "site-packages")
+            # use pym_prefix as the install path
+            cfg.write(cmake_cache_entry("PYTHON_MODULE_INSTALL_PREFIX",
+                                        pym_prefix))
+        else:
+            cfg.write(cmake_cache_entry("ENABLE_PYTHON", "OFF"))
+
+        if "+doc" in spec:
+            cfg.write(cmake_cache_entry("ENABLE_DOCS", "ON"))
+
+            cfg.write("# sphinx from spack \n")
+            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 = join_path(spec['doxygen'].prefix.bin, "doxygen")
+            cfg.write(cmake_cache_entry("DOXYGEN_EXECUTABLE", doxygen_exe))
+        else:
+            cfg.write(cmake_cache_entry("ENABLE_DOCS", "OFF"))
+
+        #######################
+        # MPI
+        #######################
+
+        cfg.write("# MPI Support\n")
+
+        if "+mpi" in spec:
+            cfg.write(cmake_cache_entry("ENABLE_MPI", "ON"))
+            cfg.write(cmake_cache_entry("MPI_C_COMPILER", spec['mpi'].mpicc))
+            # we use `mpicc` as `MPI_CXX_COMPILER` b/c we don't want to
+            # introduce linking deps to the MPI C++ libs (we aren't using
+            # C++ features of MPI) -- this happens with some versions of
+            # OpenMPI
+            cfg.write(cmake_cache_entry("MPI_CXX_COMPILER", spec['mpi'].mpicc))
+            cfg.write(cmake_cache_entry("MPI_Fortran_COMPILER",
+                                        spec['mpi'].mpifc))
+        else:
+            cfg.write(cmake_cache_entry("ENABLE_MPI", "OFF"))
+
+        #######################################################################
+        # I/O Packages
+        #######################################################################
+
+        cfg.write("# I/O Packages\n\n")
+
+        #######################
+        # HDF5
+        #######################
+
+        cfg.write("# hdf5 from spack \n")
+
+        if "+hdf5" in spec:
+            cfg.write(cmake_cache_entry("HDF5_DIR", spec['hdf5'].prefix))
+        else:
+            cfg.write("# hdf5 not built by spack \n")
+
+        #######################
+        # Silo
+        #######################
+
+        cfg.write("# silo from spack \n")
+
+        if "+silo" in spec:
+            cfg.write(cmake_cache_entry("SILO_DIR", spec['silo'].prefix))
+        else:
+            cfg.write("# silo not built by spack \n")
+
+        cfg.write("##################################\n")
+        cfg.write("# end spack generated host-config\n")
+        cfg.write("##################################\n")
+        cfg.close()
+
+        host_cfg_fname = os.path.abspath(host_cfg_fname)
+        tty.info("spack generated conduit host-config file: " + host_cfg_fname)
+        return host_cfg_fname