Squash merge hacc/tess-updates

A detailed commit history of the branch follows:

commit b57ec90c6236a1cd07df66b0c69ad257fa97564e
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu May 29 14:16:52 2014 +0000

    COMP: Use ifdef __xlC__ instead of __bgq__

    Mapping of the GCC builtins to the corresponding IBM builtins
    is specific to the xlc compiler and not to the BG/Q platform
    (for which there are other compilers). This commit changes the
    "ifdef" statement to check for the compiler that is being used
    instead of the underlying platform.

    From: Hal Finkel <hfinkel@anl.gov>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2089 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 8398e7bc3fad34d2fa847b106a85fec1be8bef67
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Wed May 28 18:25:54 2014 +0000

    COMP: Minor env fixes to port on the BG/Q

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2088 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 1b7d2bbd602e985126b93d8bd04305c0127a5821
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Wed May 28 18:00:13 2014 +0000

    COMP: Use IBM built-ins on the BQ/Q instead of GCC

    Fixed issue wherein CGAL was using GCC built-in functions that
    the IBM compiler could not resolve. Now, if we are compiling
    on the BG/Q, the GCC built-in functions are mapped to the
    corresponding IBM built-in functions.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2087 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit be365aed0cdc97d998a3c9998a6ca9f3972e443f
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu May 22 17:56:42 2014 +0000

    COMP: Allow BOOST_LDFLAGS to be user-supplied

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2085 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 3cab388cce3de555dce2cada53c4021bef877d91
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu May 22 17:56:41 2014 +0000

    COMP: Update stack tracer for BG/Q

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2084 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit b04b76ed994b5a1aa22580e217fde06bdcdc5af0
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu May 22 17:56:40 2014 +0000

    ENH: Script building all dependencies on mira.

    A script to build all dependencies on mira, e.g., CGAL,
    DIY, Qhull, etc. with an XL C/C++ toolchain.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2083 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 6d8a5c51241f641faf486600d246452ecd6115c9
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu May 22 17:56:38 2014 +0000

    ENH: mira env scripts for tess using cgal or qhull

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2082 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 0e8bd0be5e84afb647f142b799cc3da128ebcd1b
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue May 20 20:09:54 2014 +0000

    Make bold echo portable to different terminals.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2080 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a4a1e8dba2a968480b239dfb24ef80bf9f2560a4
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue May 20 20:09:53 2014 +0000

    ENH: mira env script to build with tess and qhull

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2079 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit bff16b01ef65923576a70b2e4e82fdd71da63436
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 20:35:37 2014 +0000

    ENH: Update tess-cgal & add tess-qhull env script

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2078 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 36b9575abb8468368049b7cc2ee97be07b6039e0
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 20:35:35 2014 +0000

    COMP: Include boost in HACC_COSMOTOOLS_LDFLAGS

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2077 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 9134fd238dedb83dc6e786fd523e3982366fe099
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 20:13:32 2014 +0000

    ENH: Distinguish between CGAL and Qhull versions

    Fixed build such that it will build either tess-qhull or
    tess-cgal depending on which flavor of tess is being build.
    This is controlled via the environment, the user can set
    for example TESS_USE_QHULL or TESS_USE_CGAL to indicate
    which one to use. Further, also included boost in the build,
    since CGAL needs to link to boost_system and boost_thread.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2076 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit d6d689b2d2ada77602cc58a6acde7296a411ed27
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 20:13:30 2014 +0000

    ENH: Remove old tess.cxx

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2075 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit c43c7bffaa2b0a9541efa53aae7d6186ffc406da
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 20:13:28 2014 +0000

    ENH: More updates to tess in situ wrapper

    Updated code that initializes tess and removed old
    cell size and ghost zone size parameters.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2074 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit ffe954493a5f4dcf99cfd92372dcdb51659a208e
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 17:55:32 2014 +0000

    COMP: More plumbing to get things compiling

    Added HACC_COSMOTOOLS_LDFLAGS in the environment to propagate
    CosmoTools third-party dependencies, e.g., CGAL,PnetCDF, DIY, etc.,
    when building the nbody module.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2073 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 43dc19a30cadda28904dc41e9b0dcc7fb2aaba90
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 17:55:28 2014 +0000

    COMP: Enclose C libraries within an extern "C"

    When including pnetcdf and qhull, enclose the include directive
    within an "extern "C"" if we are compiling with a C++ compiler.
    Also, removed older version of io.cxx, which is no longer used.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2072 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit da319d4c21d4e7e96f81f77adae975094cafe95f
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 17:55:26 2014 +0000

    ENH: Update tess in situ wrapper

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2071 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 458ad8e6a9e4b32835e0fad90ce4a25814ac030e
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 17:55:24 2014 +0000

    COMP: Update to conform to latest DIY_Init API

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2070 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 497d54f2fb26e990708b661214f505499dbeb5f2
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 19 17:55:22 2014 +0000

    COMP: Fix rules and dependencies for tess

    Updated the way the list of objects and programs to be compiled
    is constructed. Now, files with *.cpp *.c and *.cxx extensions
    are includes to the object list and programs list transparently.
    Further, added the use_mpfr.mk, which is needed by the CGAL version
    of tess.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2069 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit db773628560a8a4c103c80b95d8abf159516a83b
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun May 18 20:18:02 2014 +0000

    COMP: Propagate tess deps from the environment

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2068 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit e176afec58c7ae91ab7d2a5598eec5d5e860b5dd
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun May 18 20:18:00 2014 +0000

    COMP: Add use_*.mk files for tess dependencies

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2067 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 0dc63fe4aaddc3e3e7756163701c321c169819f4
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun May 18 20:17:58 2014 +0000

    ENH: Modularize raw makefile build.

    Put sections of the Makefile in different *.mk files to
    avoid spaghettifing the master Makefile. There are two
    types of *.mk files: (a) setup_*.mk files, which control
    the global build environment and settings, and (b) the
    use_*.mk files which detect dependecies from the user's
    environment and update the COSMOTOOLS_INCLUDE and
    COSMOTOOLS_LDFLAGS accordingly.

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2066 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 6e077a978f0d2605bae840895a1d11439232f3c7
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun May 18 20:17:55 2014 +0000

    ENH: Put cmake cross-compile in resources/cmake

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2065 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 5bc1a9c7ac8fda2a3d33a53360332fb64e083f9e
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun May 18 20:17:53 2014 +0000

    ENH: Put cmake/make stuff in a "resources" folder

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2064 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a32eff97cd3504596e72bba49cd708986a804343
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sun May 18 20:17:47 2014 +0000

    COMP: Temporarilly disable tess from CMake build

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2063 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 9371f128d02f0633cbfd62ac29f9a79c068e501f
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 20:23:18 2014 +0000

    COMP: Update makefile build for latest tess

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2061 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 67efe79cd4ab5edafae5bae7094fe0ed9c16263b
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 20:23:16 2014 +0000

    ENH: Move drivers into a programs dir within tess

    From: George Zagaris <george.zagaris@kitware.com>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2060 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 3e5ff68f9281125eeac613059e5b868bf729e766
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 18:57:41 2014 +0000

    ENH: Update to latest tess code

    From: Tom Peterka <tpeterka@mcs.anl.gov>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2059 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit b7d19956671d6febe606c2af98f6003d963cb4d2
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 13:57:19 2014 +0000

    Creating branch:tess-updates

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/tess-updates@2052 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

From: George Zagaris <george.zagaris@kitware.com>

git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/trunk/cosmotools@2091 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf
Merge branch 'svn/trunk'