public

CMakeLists.txt

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+# CMake makefile.
+# To build the program, do
+# mkdir -p build/
+# cd build/
+# cmake ..
+# make
+
+cmake_minimum_required (VERSION 2.6)
+project (MDengine)
+
+#set(Boost_DEBUG 1)
+#find_package(Boost
+#	REQUIRED
+#    1.62.0
+#	COMPONENTS python 
+#	)
+# Set the version number
+set (VERSION_MAJOR 0)
+set (VERSION_MINOR 4)
+
+# Activate debug output of called with -DDEBUG=1
+if (DEBUG)
+    set (CMAKE_BUILD_TYPE "DEBUG")
+    set (CUDA_VERBOSE_BUILD ON)
+    set (CMAKE_VERBOSE_MAKEFILE ON)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -pedantic")
+    set (CUDA_NVCC_DEBUG_FLAGS -Xcompiler -Wall;)
+endif (DEBUG)
+
+
+if (CMAKE_BUILD_TYPE MATCHES "RELEASE")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
+endif ()
+
+set (CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules")
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -fpic")
+
+# Find CUDA
+find_package(CUDA REQUIRED)
+set (CUDA_PROPAGATE_HOST_FLAGS OFF)
+set (custom_cuda_flags -std=c++11; -Xcompiler -fpic; --use_fast_math; --prec-div=true; --prec-sqrt=true;)
+#set (custom_cuda_flags -std=c++11; -Xcompiler -fpic; )
+list (APPEND CUDA_NVCC_FLAGS ${custom_cuda_flags})
+list (APPEND CUDA_NVCC_FLAGS ${CUDA_NVCC_DEBUG_FLAGS})
+get_filename_component (CUDA_CUFFT_LIBRARY_PATH ${CUDA_CUFFT_LIBRARIES} DIRECTORY)
+
+# Find Python libraries
+
+#set (PYTHON_LIBRARY "/software/python-2.7-2014q1-el6-x86_64/lib")
+#set (PYTHON_INCLUDE_DIR "/software/python-2.7-2014q1-el6-x86_64/include/python2.7")
+#set (PYTHON_LIBRARIES
+    #    "/software/python-2.7-2014q1-el6-x86_64/lib/libpython2.7.so")
+find_package (PythonLibs 2.7 REQUIRED)
+include_directories (${PYTHON_INCLUDE_DIR}) #removed an S here
+#get_filename_component (PYTHON_LIBRARY_PATH ${PYTHON_LIBRARIES} DIRECTORY)
+
+# Find boost
+find_package (Boost 
+    #1.62 
+    REQUIRED COMPONENTS python)
+
+# Require Boost MPI.
+
+
+message (STATUS "Building MD_engine Version ${VERSION_MAJOR}.${VERSION_MINOR}")
+
+
+# Create configuration file
+configure_file (
+    "${PROJECT_SOURCE_DIR}/Config.h.in"
+    "${PROJECT_BINARY_DIR}/Config.h"
+)
+include_directories ("${PROJECT_BINARY_DIR}")
+
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}")
+set (MD_ENGINE_LIB_NAME DASH)
+
+add_subdirectory (src)
+#add src directory
+
+# Install Python library
+add_subdirectory (python)

CMakeLists_midway.txt

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+# CMake makefile.
+# To build the program, do
+# mkdir -p build/
+# cd build/
+# cmake ..
+# make
+
+cmake_minimum_required (VERSION 2.6)
+project (MDengine)
+
+# Set the version number
+set (VERSION_MAJOR 0)
+set (VERSION_MINOR 4)
+
+# Activate debug output of called with -DDEBUG=1
+if (DEBUG)
+    set (CMAKE_BUILD_TYPE "DEBUG")
+    set (CUDA_VERBOSE_BUILD ON)
+    set (CMAKE_VERBOSE_MAKEFILE ON)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -pedantic")
+    set (CUDA_NVCC_DEBUG_FLAGS -Xcompiler -Wall;)
+endif (DEBUG)
+
+
+if (CMAKE_BUILD_TYPE MATCHES "RELEASE")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
+endif ()
+
+set (CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules")
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -fpic")
+
+# Find CUDA
+find_package(CUDA REQUIRED)
+set (CUDA_PROPAGATE_HOST_FLAGS OFF)
+set (custom_cuda_flags -std=c++11; -Xcompiler -fpic; --use_fast_math; --prec-div=true; --prec-sqrt=true;)
+#set (custom_cuda_flags -std=c++11; -Xcompiler -fpic; )
+list (APPEND CUDA_NVCC_FLAGS ${custom_cuda_flags})
+list (APPEND CUDA_NVCC_FLAGS ${CUDA_NVCC_DEBUG_FLAGS})
+get_filename_component (CUDA_CUFFT_LIBRARY_PATH ${CUDA_CUFFT_LIBRARIES} DIRECTORY)
+
+# Find Python libraries
+
+#set (PYTHON_LIBRARY "/software/python-2.7-2014q1-el6-x86_64/lib")
+set (PYTHON_INCLUDE_DIR "/software/python-2.7-2014q1-el6-x86_64/include/python2.7")
+set (PYTHON_LIBRARIES
+    "/software/python-2.7-2014q1-el6-x86_64/lib/libpython2.7.so")
+#find_package (PythonLibs 2.7 REQUIRED)
+include_directories (${PYTHON_INCLUDE_DIR}) #removed an S here
+#get_filename_component (PYTHON_LIBRARY_PATH ${PYTHON_LIBRARIES} DIRECTORY)
+
+# Find boost
+find_package (Boost 1.62.0 COMPONENTS python REQUIRED)
+
+
+message (STATUS "Building MD_engine Version ${VERSION_MAJOR}.${VERSION_MINOR}")
+
+
+# Create configuration file
+configure_file (
+    "${PROJECT_SOURCE_DIR}/Config.h.in"
+    "${PROJECT_BINARY_DIR}/Config.h"
+)
+include_directories ("${PROJECT_BINARY_DIR}")
+
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}")
+set (MD_ENGINE_LIB_NAME DASH)
+
+add_subdirectory (src)
+#add src directory
+
+# Install Python library
+add_subdirectory (python)
+# Add tests

CMakeLists_midway2.txt

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+# CMake makefile.
+# To build the program, do
+# mkdir -p build/
+# cd build/
+# cmake ..
+# make
+
+cmake_minimum_required (VERSION 2.6)
+project (MDengine)
+
+# Set the version number
+set (VERSION_MAJOR 0)
+set (VERSION_MINOR 4)
+
+# Activate debug output of called with -DDEBUG=1
+if (DEBUG)
+    set (CMAKE_BUILD_TYPE "DEBUG")
+    set (CUDA_VERBOSE_BUILD ON)
+    set (CMAKE_VERBOSE_MAKEFILE ON)
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -pedantic")
+    set (CUDA_NVCC_DEBUG_FLAGS -Xcompiler -Wall;)
+endif (DEBUG)
+
+
+if (CMAKE_BUILD_TYPE MATCHES "RELEASE")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3")
+endif ()
+
+set (CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules")
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -fpic")
+
+# Find CUDA
+find_package(CUDA REQUIRED)
+set (CUDA_PROPAGATE_HOST_FLAGS OFF)
+set (custom_cuda_flags -std=c++11; -Xcompiler -fpic; --use_fast_math; --prec-div=true; --prec-sqrt=true;)
+#set (custom_cuda_flags -std=c++11; -Xcompiler -fpic; )
+list (APPEND CUDA_NVCC_FLAGS ${custom_cuda_flags})
+list (APPEND CUDA_NVCC_FLAGS ${CUDA_NVCC_DEBUG_FLAGS})
+get_filename_component (CUDA_CUFFT_LIBRARY_PATH ${CUDA_CUFFT_LIBRARIES} DIRECTORY)
+
+# Find Python libraries
+
+#set (PYTHON_LIBRARY "/software/python-2.7-2014q1-el6-x86_64/lib")
+set (PYTHON_INCLUDE_DIR "/software/python-2.7.12-el7-x86_64/include/python2.7")
+set (PYTHON_LIBRARIES
+    "/software/python-2.7.12-el7-x86_64/lib/libpython2.7.so")
+include_directories (${PYTHON_INCLUDE_DIR}) #removed an S here
+#get_filename_component (PYTHON_LIBRARY_PATH ${PYTHON_LIBRARIES} DIRECTORY)
+
+# Find boost
+find_package (Boost 1.62.0 COMPONENTS python REQUIRED)
+
+
+message (STATUS "Building MD_engine Version ${VERSION_MAJOR}.${VERSION_MINOR}")
+
+
+# Create configuration file
+configure_file (
+    "${PROJECT_SOURCE_DIR}/Config.h.in"
+    "${PROJECT_BINARY_DIR}/Config.h"
+)
+include_directories ("${PROJECT_BINARY_DIR}")
+
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}")
+set (MD_ENGINE_LIB_NAME DASH)
+
+add_subdirectory (src)
+#add src directory
+
+# Install Python library
+add_subdirectory (python)

Config.h.in

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+// Read Version number from CMakeLists.txt
+#define VERSION_MAJOR @VERSION_MAJOR@
+#define VERSION_MINOR @VERSION_MINOR@

Eigen/Array

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+#ifndef EIGEN_ARRAY_MODULE_H
+#define EIGEN_ARRAY_MODULE_H
+
+// include Core first to handle Eigen2 support macros
+#include "Core"
+
+#ifndef EIGEN2_SUPPORT
+  #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.
+#endif
+
+#endif // EIGEN_ARRAY_MODULE_H

Eigen/Cholesky

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+#ifndef EIGEN_CHOLESKY_MODULE_H
+#define EIGEN_CHOLESKY_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \defgroup Cholesky_Module Cholesky module
+  *
+  *
+  *
+  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+  * Those decompositions are accessible via the following MatrixBase methods:
+  *  - MatrixBase::llt(),
+  *  - MatrixBase::ldlt()
+  *
+  * \code
+  * #include <Eigen/Cholesky>
+  * \endcode
+  */
+
+#include "src/misc/Solve.h"
+#include "src/Cholesky/LLT.h"
+#include "src/Cholesky/LDLT.h"
+#ifdef EIGEN_USE_LAPACKE
+#include "src/Cholesky/LLT_MKL.h"
+#endif
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLESKY_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */

Eigen/CholmodSupport

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+#ifndef EIGEN_CHOLMODSUPPORT_MODULE_H
+#define EIGEN_CHOLMODSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+extern "C" {
+  #include <cholmod.h>
+}
+
+/** \ingroup Support_modules
+  * \defgroup CholmodSupport_Module CholmodSupport module
+  *
+  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * It provides the two following main factorization classes:
+  * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
+  * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
+  *
+  * For the sake of completeness, this module also propose the two following classes:
+  * - class CholmodSimplicialLLT
+  * - class CholmodSimplicialLDLT
+  * Note that these classes does not bring any particular advantage compared to the built-in
+  * SimplicialLLT and SimplicialLDLT factorization classes.
+  *
+  * \code
+  * #include <Eigen/CholmodSupport>
+  * \endcode
+  *
+  * In order to use this module, the cholmod headers must be accessible from the include paths, and your binary must be linked to the cholmod library and its dependencies.
+  * The dependencies depend on how cholmod has been compiled.
+  * For a cmake based project, you can use our FindCholmod.cmake module to help you in this task.
+  *
+  */
+
+#include "src/misc/Solve.h"
+#include "src/misc/SparseSolve.h"
+
+#include "src/CholmodSupport/CholmodSupport.h"
+
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLMODSUPPORT_MODULE_H
+