Initial commit.

##---------------------------------------------------------------------------##

## Profugus/CMakeLists.txt

##---------------------------------------------------------------------------##

## Copyright (C) 2011 Oak Ridge National Laboratory, UT-Battelle, LLC.

##---------------------------------------------------------------------------##

##---------------------------------------------------------------------------##

# A) Define your project name and set up major project options

##---------------------------------------------------------------------------##

INCLUDE(${CMAKE_SOURCE_DIR}/ProjectName.cmake)

# CMake requires that you declare the CMake project in the top-level file and

# not in an include file :-(

PROJECT(${PROJECT_NAME} NONE)

# Add support for extra repositories; everything handled by native above

SET(${PROJECT_NAME}_SUPPORT_EXTRA_REPOS FALSE)

# Disable Tribits generating HTML dependencies webpage and xml files

SET(${PROJECT_NAME}_DEPS_XML_OUTPUT_FILE OFF CACHE BOOL "" )

# Disable Tribits export system to save time configuring

SET(${PROJECT_NAME}_ENABLE_INSTALL_CMAKE_CONFIG_FILES OFF CACHE BOOL "")

# Disable Tribits export makefiles system to save time configuring

SET(${PROJECT_NAME}_ENABLE_EXPORT_MAKEFILES OFF CACHE BOOL "")

##---------------------------------------------------------------------------##

# B) Pull in the TriBITS system and execute

##---------------------------------------------------------------------------##

# Just use the TriBITS system in Trilinos

SET(${PROJECT_NAME}_TRIBITS_DIR

  "${CMAKE_CURRENT_SOURCE_DIR}/TriBITS/tribits" CACHE PATH "" )

MESSAGE("${PROJECT_NAME}_TRIBITS_DIR = '${${PROJECT_NAME}_TRIBITS_DIR}'")

INCLUDE(${${PROJECT_NAME}_TRIBITS_DIR}/TriBITS.cmake)

# CMake requires this be in the top file and not in an include file :-(

CMAKE_MINIMUM_REQUIRED(VERSION ${TRIBITS_CMAKE_MINIMUM_REQUIRED})

# Default to building shared libraries if user hasn't specified.

#

# Note that if you define BUILD_SHARED_LIBS using a configure option file

# with -D PROFUGUS_PROJECT_CONFIGURE_FILE:PATH=config.cmake,

# then you'll have to use the FORCE keyword in that file because it gets read

# during TRIBITS_PROJECT().

#

#   SET(BUILD_SHARED_LIBS OFF CACHE BOOL "" FORCE)

#

# (Alternatively, use 'cmake -C config.cmake' to read in BUILD_SHARED_LIBS

# *before* this point.)

IF(NOT DEFINED BUILD_SHARED_LIBS)

  SET(BUILD_SHARED_LIBS_DEFAULT ON)

  IF(DEFINED BUILD_SHARED)

    SET(BUILD_SHARED_LIBS_DEFAULT ${BUILD_SHARED})

  ENDIF()

  SET(BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS_DEFAULT}

    CACHE BOOL

    "Build shared libraries.")

  UNSET(BUILD_SHARED_LIBS_DEFAULT)

ENDIF()

# Do all of the processing for this Tribits project

TRIBITS_PROJECT()

# Add the final documentation

#add_subdirectory(doc)

##---------------------------------------------------------------------------##

## end of CMakeLists.txt

##---------------------------------------------------------------------------##

Copyright (c) 2014, Computational Engineering & Energy Sciences Group

All rights reserved.

Redistribution and use in source and binary forms, with or without

modification, are permitted provided that the following conditions are met:

* Redistributions of source code must retain the above copyright notice, this

  list of conditions and the following disclaimer.

* Redistributions in binary form must reproduce the above copyright notice,

  this list of conditions and the following disclaimer in the documentation

  and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE

IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE

FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL

DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR

SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER

CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,

OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE

OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

##---------------------------------------------------------------------------##

## Profugus/PackagesList.cmake

## Thomas M. Evans

## Monday December 2 21:24:6 2013

##---------------------------------------------------------------------------##

##---------------------------------------------------------------------------##

## PACKAGES PROVIDED

##---------------------------------------------------------------------------##

TRIBITS_REPOSITORY_DEFINE_PACKAGES(

  Utils     packages/Utils     SS

  CudaUtils packages/CudaUtils SS

  Matprop   packages/Matprop   SS

  SPn       packages/SPn       SS

  MC        packages/MC        SS

  Alea      packages/Alea      SS

  )

##---------------------------------------------------------------------------##

## PLATFORM SUPPORT

##---------------------------------------------------------------------------##

TRIBITS_DISABLE_PACKAGE_ON_PLATFORMS(Profugus Windows)

##---------------------------------------------------------------------------##

## end of PackagesList.cmake

##---------------------------------------------------------------------------##

##---------------------------------------------------------------------------##

## Profugus/ProjectName.cmake

## Thomas M. Evans

## Tuesday August 7 16:1:14 2012

##---------------------------------------------------------------------------##

# Must set the project name as a varaible at very beginning before including

# anything else

SET(PROJECT_NAME Profugus)

##---------------------------------------------------------------------------##

## end of Profugus/ProjectName.cmake

##---------------------------------------------------------------------------##

Description

***********

Profugus is an open-source mini-application (mini-app) for radiation

transport and reactor applications.  It contains the fundamental

computational kernels used in the Exnihilo code suite from Oak Ridge

National Laboratory. However, Exnihilo is production code with a

substantial user base. Furthermore, Exnihilo is export controlled.

This makes collaboration with computer scientists and computer

engineers difficult.  Profugus is designed to bridge that gap.  By

encapsulating the core numerical algorithms in an abbreviated code

base that is open-source, computer scientists can analyze the

algorithms and easily make code-architectural changes to test

performance without compromising the production code values of

Exnihilo.

Profugus is **not** meant to be production software with respect to

problem analysis.  The computational kernels in Profugus are designed

to analyze *performance*, not *correctness*.  Nonetheless, users of

Profugus can setup and run problems with enough *real-world* features

to be useful as proof-of-concept for actual production work.

Profugus is also used as a test-bed mini-app for the ASCR projects

XPRESS and MCREX.

Profugus Development Team

=========================

Profugus contains the computational kernels from the Exnihilo code

base. The core Exnihilo development team consists of the following

scientists (listed alphabetically)

* Kevin Clarno <clarnokt@ornl.gov>

* Greg Davidson <davidsongg@ornl.gov>

* Tom Evans <evanstm@ornl.gov>

* Steven Hamilton <hamiltonsr@ornl.gov>

* Seth Johnson <johnsonsr@ornl.gov>

* Tara Pandya <pandyatm@ornl.gov>

* Stuart Slattery <slatterysr@ornl.gov>

* Rachel Slaybaugh <slaybaugh@berkeley.edu>

Profugus is developed and maintained by the following team:

* Tom Evans <evanstm@ornl.gov>

* Steven Hamilton <hamiltonsr@ornl.gov>

* Stuart Slattery <slatterysr@ornl.gov>

Profugus Packages

=================

Profugus constains the following code mini-apps:

**SPn**

   Mini-app of Simplified Spherical Harmonics ("SPn") computational

   kernel.

**MC**

   Mini-app of Monte Carlo computational kernel.

Documentation on the mini-apps (methods and execution) are given in

*Running The Mini-Applications*. There are several support packages

that are used by the mini-apps.  These are:

**Utils**

   Utilities and testing framework used by other packages.

**Matprop**

   Data structures for storing material properties (cross-sections).

Profugus is designed to build and run with a minimum of dependencies.

However, there are some requirements.  The third-party software (TPLs)

necessary to build Profugus is all open-source and freely available.

The TPLs for Profugus are listed in the following table:

+-----------------------+---------------+---------------------------------------+

| TPL                   | Required      | Comments                              |

+=======================+===============+=======================================+

| TriBITS               | Yes           | TriBITS is the Trilinos build system  |

+-----------------------+---------------+---------------------------------------+

| Trilinos              | Yes           | Trilinos is an open-source solvers    |

+-----------------------+---------------+---------------------------------------+

| BLAS/LAPACK           | Yes           | Use vendor-specific implementation    |

+-----------------------+---------------+---------------------------------------+

| MPI                   | No            | OpenMPI and MPICH are suggested       |

+-----------------------+---------------+---------------------------------------+

| HDF5                  | No            | Parallel HDF5 will allow output of    |

+-----------------------+---------------+---------------------------------------+

Building The Code

*****************

The most straightforward method for building Profugus is to use the

scripts in `Profugus/install`.  Profugus uses the `TriBITS` build

system.  This system is a set of package-based extensions to standard

cmake.  So, first you need to obtain *Trilinos* and *TriBITS* and put

them in your top-level Profugus directory::

   > cd Profugus

   > git clone https://github.com/TriBITSPub/TriBITS.git

   > ln -s $PATH_TO_TRILINOS .

The preferred mechanism for using the build scripts is to make a

*target* directory where the build is to be performed::

   > pwd

     /home/me

   > mkdir debug

   > cd debug

   > mkdir target

   > cd target

   > pwd

     /home/me/debug/target

The `install` directory contains several example build scripts.

General options for all platforms (which can be overridden at

configure time) are specified in the `install/base.cmake`::

   ##---------------------------------------------------------------------------##

   ## CMAKE BASE FILE

   ##---------------------------------------------------------------------------##

   # Default build all packages

   SET(Profugus_ENABLE_Utils   ON CACHE BOOL "")

   SET(Profugus_ENABLE_Matprop ON CACHE BOOL "")

   SET(Profugus_ENABLE_SPn     ON CACHE BOOL "")

   SET(Profugus_ENABLE_MC      ON CACHE BOOL "")

   # Turn on tests

   SET(Profugus_ENABLE_TESTS ON CACHE BOOL "")

   SET(Profugus_TEST_CATEGORIES "BASIC" CACHE STRING "")

   # Turn on SS code and optional packages by default

   SET(Profugus_ENABLE_ALL_FORWARD_DEP_PACKAGES OFF CACHE BOOL "")

   SET(Profugus_ENABLE_ALL_OPTIONAL_PACKAGES    ON  CACHE BOOL "")

   SET(Profugus_ENABLE_SECONDARY_STABLE_CODE    ON  CACHE BOOL "")

   # Up the max num procs

   SET(MPI_EXEC_MAX_NUMPROCS 8 CACHE STRING "")

   # Turn off binutils

   SET(Teuchos_ENABLE_BinUtils OFF CACHE BOOL "")

   # Turn off Zoltan2

   SET(Profugus_ENABLE_Zoltan2 OFF CACHE BOOL "")

   # Compiler options

   SET(BUILD_SHARED_LIBS ON CACHE BOOL "")

   SET(CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated-declarations" CACHE STRING "")

   SET(Profugus_ENABLE_CXX11:BOOL=ON)

   # TriBITS stuff

   SET(Profugus_ENABLE_INSTALL_CMAKE_CONFIG_FILES OFF CACHE BOOL "")

   SET(Profugus_DEPS_XML_OUTPUT_FILE "" CACHE FILEPATH "")

By default, all of the packages inside of Profugus are turned on.

Furthermore, *C++-11* is **required**.  The default options specify

the appropriate compiler flags for gcc.  The tests are also turned on

by default; to disable tests in any upstream package simply do not

explicitly *ENABLE* that package.  For example, to build the *SPn*

package and all of its tests but only include required *source* from

upstream packages, the user would specify::

   SET(Profugus_ENABLE_SPn ON CACHE BOOL "")

In this case, only the pieces of *Utils* needed to build *SPn* are

compiled. All tests can be turned off by setting

**Profugus_ENABLE_TESTS** to **OFF**.

The `install` directory contains several build scripts that are all

suffixed by the platform name.  For example, to build on a Linux

*x86_64* system the "install/cmake_x86_64.sh" script can be used::

   #!/bin/sh

   ##---------------------------------------------------------------------------##

   ## CMAKE FOR X86_64

   ##---------------------------------------------------------------------------##

   # CLEANUP

   rm -rf CMakeCache.txt

   rm -rf CMakeFiles

   # SOURCE AND INSTALL

   SOURCE=<SET_SOURCE_DIR>

   INSTALL=<SET_INSTALL_DIR>

   # BUILD OPTIONS

   BUILD="DEBUG"

   MPI="ON"

   # TPL PATHS

   HDF5_PATH="/vendors/hdf5_parallel"

   MPI_PATH="/opt/openmpi/gcc/current"

   ##---------------------------------------------------------------------------##

   cmake \

   -DCMAKE_BUILD_TYPE:STRING="$BUILD" \

   -DTPL_ENABLE_MPI:BOOL=$MPI \

   -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL \

   \

   -DMPI_BASE_DIR:PATH=$MPI_PATH \

   \

   -DTPL_ENABLE_HDF5:BOOL=ON \

   -DHDF5_INCLUDE_DIRS:PATH=$HDF5_PATH/include \

   -DHDF5_LIBRARY_DIRS:PATH=$HDF5_PATH/lib \

   \

   -DBLAS_LIBRARY_DIRS:PATH=/vendors/gcc/atlas/lib \

   -DLAPACK_LIBRARY_DIRS:PATH=/vendors/gcc/atlas/lib \

   -DBLAS_LIBRARY_NAMES:STRING="f77blas;cblas;atlas" \

   -DLAPACK_LIBRARY_NAMES:STRING="lapack" \

   \

   -DProfugus_CONFIGURE_OPTIONS_FILE:FILEPATH="${SOURCE}/install/base.cmake" \

   -DProfugus_ASSERT_MISSING_PACKAGES:BOOL=OFF \

   \

   ${SOURCE}

   ##---------------------------------------------------------------------------##

   ## end of cmake_x86_64.sh

   ##---------------------------------------------------------------------------##

The source and install locations must be set. Also, to enable a

optimized build set **BUILD** to **RELEASE**.  Adjust the paths and

libraries for LAPACK to fit your platform.  The example assumes that

the ATLAS LAPACK is available.  Any standard LAPACK distribution will

work. HDF5 is **not** required, to build/run/test the applications;

however, problem output will be severely curtailed if a parallel HDF5

option is not provided.  If HDF5 is not available, setting::

   -DTPL_ENABLE_HDF5:BOOL=OFF \

will disable HDF5.

To complete the configuration, execute this script inside the *target*

directory and then make/test/install::

   > pwd

     /home/me/debug/target

   > sh /home/me/Profugus/install/cmake_x86_64.sh

   > make -j 8

   > ctest -j 8

   > make -j 8 install