Squash merge hacc/integrate-subfind.

A detailed commit history of the branch follows:

commit bad906d93f9e76d22599f8c80b09e8a1ff58d0ce
Merge: f107b94 fcbd530
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu Jun 5 19:39:15 2014 +0000

    Merge branch 'master' into integrate-subfind

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2111 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit f107b940e9bc6ad03a207c16921e96d500cbae28
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 30 21:53:12 2014 +0000

    STYLE: Guard printouts within an ifdef DEBUG

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2094 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 6b6507cb608e5b9516d9386f5b6534feb69431b6
Merge: 7b3900d 783e039
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 30 21:30:17 2014 +0000

    Merge branch 'master' into integrate-subfind

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2093 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 7b3900d91798c651f7448ff15bd623ba73bac7ea
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 17:39:12 2014 +0000

    ENH: Add SUBFIND to HaloTestP.

    This commit adds the ability to call the SUBFIND algorithm for
    sub-halo finding from HaloTestP. This is triggered by a
    new parameter in the HaloTestP input, USE_SUBFIND, which can be
    set to "1" to control which sub-halo finder to use.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2058 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 4d62a8186bd365bf6978faeba1f477fc50e68b92
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 17:39:09 2014 +0000

    ENH: Integrate SUBFIND in to in situ wrapper.

    This commit adds an additional option, USE_SUBFIND,
    for sub-halo finding. This allows the user to switch
    between the particular algorithm to use for sub-halo
    finding. Further, changes to the in situ halofinder
    wrapper class are added to call the appropriate algorithm
    for sub-halo finding based on the user-supplied parameter
    from the configuration file.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2057 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a0397cbb8eb58717b3325394a8177d0479672e9a
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 17:39:07 2014 +0000

    ENH: Additional SetParticles method for SUBFIND.

    Added method to the SUBFIND class that passes the
    particles as raw pointers instead of pointers to
    vectors, which is how normally the particle information
    for each process is propagated when running in situ.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2056 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 32fdcfcf5fa3636603dcb59f665bc4914189551b
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 17:39:05 2014 +0000

    COMP: Add SUBFIND into the make and cmake build

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2055 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit f9ace5440eb5820041c38ce0ff231dbaa66c311d
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 14:05:43 2014 +0000

    ENH: Importing Pat Fasel's SUBFIND implementation

    From: Patricia K. Fasel <pkf@lanl.gov>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2054 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit e6b94de9f6bf8e0bd82c99b57a19a58598933885
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 16 13:57:56 2014 +0000

    Creating branch:integrate-subfind

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/integrate-subfind@2053 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@2112 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf
Squash merge hacc/gpu-halofinder.

A detailed commit history of the branch follows:

commit 4bd9b0f1682cc0478e698b085c3e517e19a97410
Merge: fc183de f534f52
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu Jun 5 19:54:08 2014 +0000

    Merge branch 'master' into gpu-halofinder

    Conflicts:
    	cosmotools/framework/LANLHaloFinderInSituAlgorithm.cxx

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2114 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit fc183de51d7ca43b87829848763083ba1a6ae9f0
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Jun 2 18:52:47 2014 +0000

    COMP: Fix environment for titan

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2098 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a7a240985e5a828226ba742bc7919df15e97e8d0
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Jun 2 17:51:50 2014 +0000

    COMP: Update CUDA target to reflect build changes

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2096 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit f52e9f612cc8f4c59db7c31f3dcbb64ee187e15d
Merge: 1e303a1 783e039
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Jun 2 17:51:42 2014 +0000

    Merge branch 'master' into gpu-halofinder

    Conflicts:
    	cosmotools/Makefile
    	nbody/common/Makefile
    	nbody/halo_finder/Makefile
    	nbody/opencl/Makefile
    	nbody/simulation/Makefile

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2095 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 1e303a163aa8859ccd0a680e44e00a57756dff01
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon May 12 15:32:34 2014 +0000

    ENH: Use thrust-based MBP center-finder in situ

    This commit modifies the halo-finder in situ wrapper class,
    such that, when the code is compiled with trust, the code
    will use the thrust based MBP center finder. Further, modified
    the Makefiles of the hacc n-body module, such that, when the
    CUDA thrust backend is used, the code would link in
    cosmotools_nvcc.a, as well as, the necessary cuda library dependencies.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2051 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 9e9f3215f1b571ad7206d335d9d1f641e0b3f45e
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sat May 10 20:05:46 2014 +0000

    COMP: Fix error due to redefinition of centerIndex

    Fixed issue when compiling without CUDA or THRUST-OMP due to
    redefinition of the centerIndex variable.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2050 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 4bb12893a45cae81e79432401acf889e103a2c09
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Sat May 10 20:05:44 2014 +0000

    COMP: Use different HACC_PLATFORM

    This commit changes the hacc platform for each environment on
    agora, such that, binaries from different builds can co-exist
    and to better indicate the type of build.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2049 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 97748f8660c17e1cf6539f65d84a67c0144ef287
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 9 21:10:33 2014 +0000

    COMP: Updated build to handle CUDA sources

    This commit adds support for compiling cuda sources in CosmoTools.
    All CUDA sources in CosmoTools are compiled in a single static library
    `libcosmotools_nvcc.a`. Then, executables can be linked against this
    library.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2048 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit bc76ef1ff0127bbca6c66e329aba41a02c69e0d7
Merge: ea7fe3f db4763f
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 9 14:54:10 2014 +0000

    Merge branch 'master' into gpu-halofinder

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2047 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit ea7fe3f8ef89f955b606f4ef7ca6ad2d1224f703
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Fri May 9 14:54:06 2014 +0000

    WIP: Compiling with cuda

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2046 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit dfde0f6a597ce9d0e0a86fda465d5e4183fddfa0
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Apr 29 17:55:57 2014 +0000

    ENH: local environment with CUDA

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2029 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 16a5e999378ea5a8154c5097da80ea7505576d05
Merge: 6104a45 a6a0200
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Tue Apr 29 14:52:14 2014 +0000

    Merge branch 'master' into gpu-halofinder

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2028 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 6104a45522d7468fd5e9a6f51892b0d2a3e221e7
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 19:10:01 2014 +0000

    COMP: Initial env file for titan w/opencl+thrust

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2025 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 6bcf14c3e100cdc0ed6491f6f247a9e909ac057e
Merge: a66d1a1 818fb4c
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 18:14:29 2014 +0000

    Merge branch 'master' into gpu-halofinder

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2024 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit a66d1a1199ed11c1204cdd2039e8718b23a6e13d
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 16:59:10 2014 +0000

    ENH: Restructure code to always time MBP

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2021 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 8012566cf8af5d2c5b9b95cfe44f515a9fc64ae4
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 16:50:27 2014 +0000

    ENH: Use thrust-based center-finder in HaloTestP

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2020 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 205556c7a28e137fe9f40023ad349ef80613399b
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 16:50:25 2014 +0000

    COMP: Add old center-finder method enum definition.

    Add older center-finder method enum b/c it is still being used
    by this code. This should be updated later.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2019 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 963f67df89d0ff7cb009f44c7af439ff1592e52f
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 16:50:23 2014 +0000

    COMP: Build thrust-based piston halo/center finder

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2018 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 5f519014a8c5698690051da7a9d5ec45d7c1870e
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 16:50:20 2014 +0000

    COMP: Add local environment with thrust

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2017 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit de413419261fe44b37280c150c19ba72051674b8
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 16:50:18 2014 +0000

    COMP: Put thrust halo-finder in a cxx file

    This commit moves the thrust-based halo/center finder to a CXX file. Then,
    a corresponding *.cu file is added that includes the *.cxx file. That way,
    we can transparently compile to different device backends, i.e., CPU or
    GPU.

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2016 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 7e8216e92bd044bde23436a91483cd75f359b2ad
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 16:50:16 2014 +0000

    ENH: Add thrust-based halo/center finder

    From: Chris Sewell <csewell@lanl.gov>

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2015 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 1d895646ea1fa3ed17ec3d6d561191f2df761f93
Merge: 154afde 95d9d95
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Mon Apr 28 13:49:45 2014 +0000

    Merge branch 'master' into gpu-halofinder

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

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2014 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf

commit 154afde4b8e27cadc19ff7be1042dce39a945a76
Author: gzagaris <gzagaris@952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf>
Date:   Thu Apr 24 20:05:21 2014 +0000

    Creating branch:gpu-halofinder

    git-svn-id: https://svn.alcf.anl.gov/repos/DarkUniverse/hacc/branches/gpu-halofinder@2008 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@2115 952bdfbe-fa2e-45c0-a9ae-ac90d4a62daf
Merge branch 'svn/trunk'