insitu now is merged with 2.0.0

05bd067e · incardon · 8e5ec9fc · 23c94dfb · 05bd067e · 05bd067e
Commit 05bd067e authored Apr 17, 2019 by incardon
47 changed files
--- a/.gitlab-ci.yml_bck
+++ b/.gitlab-ci.yml_bck
+centos_build:
+  stage: build
+  tags:
+    - centos
+  artifacts:
+    paths:
+      - ./openfpm_vcluster/build/src/vcluster_test
+  script:
+    - ./build.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS $CI_COMMIT_REF_NAME
+
+centos_run:
+  stage: test
+  tags:
+    - centos
+  dependencies:
+    - centos_build
+  script:
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 3 $CI_COMMIT_REF_NAME
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 4 $CI_COMMIT_REF_NAME
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 5 $CI_COMMIT_REF_NAME
+
+
+mac_build:
+  stage: build
+  tags:
+    - mac
+  artifacts:
+    paths:
+      - ./openfpm_vcluster/build/src/vcluster_test
+  script:
+    - ./build.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS $CI_COMMIT_REF_NAME
+
+mac_run:
+  stage: test
+  tags:
+    - mac
+  dependencies:
+    - mac_build
+  script:
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 3 $CI_COMMIT_REF_NAME
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 4 $CI_COMMIT_REF_NAME
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 5 $CI_COMMIT_REF_NAME
+
+ubuntu_build:
+  stage: build
+  tags:
+    - ubuntu
+  artifacts:
+    paths:
+      - ./openfpm_vcluster/build/src/vcluster_test
+  script:
+    - ./build.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS $CI_COMMIT_REF_NAME
+
+ubuntu_run:
+  stage: test
+  tags:
+    - ubuntu
+  dependencies:
+    - ubuntu_build
+  script:
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 3 $CI_COMMIT_REF_NAME
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 4 $CI_COMMIT_REF_NAME
+    - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS 5 $CI_COMMIT_REF_NAME
+
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
+cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
+project(openfpm_pdata LANGUAGES C CXX)
+
+list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake_modules/)
+
+set(BOOST_INCLUDE ${Boost_INCLUDE_DIR} CACHE PATH "Include directory for BOOST")
+set(SE_CLASS1 CACHE BOOL "Activate compilation with SE_CLASS1")
+set(SE_CLASS2 CACHE BOOL "Activate compilation with SE_CLASS2")
+set(SE_CLASS3 CACHE BOOL "Activate compilation with SE_CLASS3")
+set(PETSC_ROOT CACHE PATH "If compiling with linear algebra indicate the PETSC root directory")
+
+set(ENV{PETSC_DIR} ${PETSC_ROOT})
+
+set (CMAKE_CXX_STANDARD 11)
+set (CMAKE_CUDA_STANDARD 11)
+
+if (ENABLE_GPU)
+	enable_language(CUDA)
+	find_package(CUDA)
+
+        if (CUDA_VERSION_MAJOR EQUAL 9 AND CUDA_VERSION_MINOR EQUAL 2)
+                message("CUDA is compatible")
+                set(WARNING_SUPPRESSION_AND_OPTION_NVCC  -Xcudafe "--display_error_number --diag_suppress=611 --diag_suppress=2885 --diag_suppress=2886  --diag_suppress=2887  --diag_suppress=2888 --diag_suppress=186 --diag_suppress=111" --expt-extended-lambda)
+        elseif ( CUDA_VERSION_MAJOR EQUAL 10 AND CUDA_VERSION_MINOR EQUAL 1 )
+                message("CUDA is compatible")
+                set(WARNING_SUPPRESSION_AND_OPTION_NVCC  -Xcudafe "--display_error_number --diag_suppress=2915 --diag_suppress=2912 --diag_suppress=2913 --diag_suppress=111 --diag_suppress=186 --diag_suppress=611 " --expt-extended-lambda)
+
+        else()
+                message(FATAL_ERROR "CUDA is incompatible, version 9.2 is only supported")
+        endif()
+
+endif()
+
+find_package(Boost 1.66.0 REQUIRED COMPONENTS unit_test_framework iostreams program_options)
+find_package(MPI REQUIRED)
+find_package(PETSc)
+
+if(CUDA_FOUND)
+	set(OPENFPM_INIT_FILE "initialize/initialize_wrapper_cuda.cu")
+else()
+	set(OPENFPM_INIT_FILE "initialize/initialize_wrapper_cuda.cpp")
+endif()
+
+###### CONFIG.h FILE ######
+
+if(SE_CLASS1)
+	set(DEFINE_SE_CLASS1 "#define SE_CLASS1")
+endif()
+
+if(SE_CLASS2)
+	set(DEFINE_SE_CLASS2 "#define SE_CLASS2")
+endif()
+
+if(SE_CLASS3)
+	set(DEFINE_SE_CLASS3 "#define SE_CLASS3")
+endif()
+
+if(PETSC_FOUND)
+	set(DEFINE_HAVE_PETSC "#define HAVE_PETSC")
+endif()
+
+if(CUDA_FOUND)
+	set(DEFINE_CUDA_GPU "#define CUDA_GPU")
+endif()
+
+if(MPI_FOUND)
+	set(DEFINE_HAVE_MPI "#define HAVE_MPI")
+else()
+	message( FATAL_ERROR "MPI is required in order to install OpenFPM" )
+endif()
+
+if (Boost_FOUND)
+	set(DEFINE_HAVE_BOOST "#define HAVE_BOOST")
+	set(DEFINE_HAVE_BOOST_IOSTREAMS "#define HAVE_BOOST_IOSTREAMS")
+	set(DEFINE_HAVE_BOOST_PROGRAM_OPTIONS "#define HAVE_BOOST_PROGRAM_OPTIONS")
+	set(DEFINE_HAVE_BOOST_UNIT_TEST_FRAMEWORK "#define HAVE_BOOST_UNIT_TEST_FRAMEWORK")
+else()
+	message( FATAL_ERROR "BOOST is required in order to install OpenFPM" )
+endif()
+
+
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/src/config/config_cmake.h.in ${CMAKE_CURRENT_SOURCE_DIR}/src/config/config.h)
+
+include_directories(SYSTEM ${MPI_INCLUDE_PATH})
+
+add_subdirectory (src)
+
--- a/Jenkinsfile_mpi
+++ b/Jenkinsfile_mpi
+#!groovy
+
+parallel (
+
+
+"cifarm-centos-node" : {node ('cifarm-centos-node')
+                  {
+                    deleteDir()
+                    checkout scm
+                    stage ('build centos')
+                    {
+                      sh "./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+                    }
+
+                    stage ('run centos')
+                    {
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 2 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 3 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 4 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 5 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./success.sh 2 centos openfpm_vcluster"
+                    }
+                  }
+                 },
+
+
+
+
+"cifarm-mac-node" : {node ('cifarm-mac-node')
+                  {
+                    deleteDir()
+                    checkout scm
+                    stage ('build mac')
+                    {
+                      sh "./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+                    }
+
+                    stage ('run mac')
+                    {
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 2 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 3 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 4 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 5 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 6 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 7 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./success.sh 2 mac openfpm_vcluster"
+                    }
+                  }
+                 },
+
+"cifarm-ubuntu-node" : {node ('cifarm-ubuntu-node')
+                  {
+                    deleteDir()
+                    checkout scm
+                    stage ('build ubuntu')
+                    {
+                      sh "./build.sh $WORKSPACE $NODE_NAME $BRANCH_NAME"
+                    }
+
+                    stage ('run ubuntu')
+                    {
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 2 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 3 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 4 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 5 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 6 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./run.sh $WORKSPACE $NODE_NAME 7 $BRANCH_NAME"
+                      sh "cd openfpm_vcluster && ./success.sh 2 ubuntu openfpm_vcluster"
+                    }
+                  }
+                 }
+
+)
+
--- a/Makefile.am
+++ b/Makefile.am
-SUBDIRS = src
-
-bin_PROGRAMS = 
\ No newline at end of file
--- a/autogen.sh
+++ b/autogen.sh
--- a/build.sh
+++ b/build.sh
 #! /bin/bash

 # Make a directory in /tmp/openfpm_data
+#
+
+workspace=$1
+hostname=$(hostname)
+branch=$3
+
+
+echo "Directory: $workspace"
+echo "Machine: $hostname"
+echo "Branch: $branch"

-echo "$PATH"
-echo "Directory: $1"
-echo "Machine: $2"
-echo "Branch: $3"

 mkdir /tmp/openfpm_vcluster
 mv * .[^.]* /tmp/openfpm_vcluster
@@ -13,25 +19,49 @@ mv /tmp/openfpm_vcluster openfpm_vcluster

 mkdir openfpm_vcluster/src/config

+## It is equivalent to the git modules
+
 git clone git@git.mpi-cbg.de:/openfpm/openfpm_devices.git openfpm_devices
 git clone git@git.mpi-cbg.de:/openfpm/openfpm_data.git openfpm_data
 cd openfpm_data
-git checkout 6c2a5911ac16f93ab0ae1e7ac14723c952aa5c16
+git checkout master
 cd ..
 cd openfpm_devices
-git checkout 46e4994c5dff879a71e6ae090c50b2f23235d435
+git checkout master
 cd ..

-cd "$1/openfpm_vcluster"
+cd "$workspace/openfpm_vcluster"

-source $HOME/openfpm_vars_$3
+# install MPI and BOOST  LIBHILBERT if needed

-if [ "$2" == "gin" ]; then
+if [ ! -d $HOME/openfpm_dependencies/openfpm_vcluster/LIBHILBERT ]; then
+        ./install_LIBHILBERT.sh $HOME/openfpm_dependencies/openfpm_vcluster/ 4
+fi
+
+
+if [ ! -d $HOME/openfpm_dependencies/openfpm_vcluster/BOOST ]; then
+        if [ x"$hostname" == x"cifarm-mac-node" ]; then
+                echo "Compiling for OSX"
+                ./install_BOOST.sh $HOME/openfpm_dependencies/openfpm_vcluster/ 4 darwin
+        else
+                echo "Compiling for Linux"
+                ./install_BOOST.sh $HOME/openfpm_dependencies/openfpm_vcluster/ 4 gcc
+        fi
+fi
+
+
+if [ ! -d $HOME/openfpm_dependencies/openfpm_vcluster/MPI ]; then
+	./install_MPI.sh $HOME/openfpm_dependencies/openfpm_vcluster/ 4
+fi
+
+export PATH="$PATH:$HOME/openfpm_dependencies/openfpm_vcluster/MPI/bin"
+
+if [ "$hostname" == "gin" ]; then
 echo "Compiling on gin\n"
 module load gcc/4.9.2
 module load openmpi/1.8.1

-elif [ "$2" == "wetcluster" ]; then
+elif [ "$hostname" == "wetcluster" ]; then
 echo "Compiling on wetcluster"

 ## produce the module path
@@ -53,7 +83,7 @@ exit(0)\n"

 bsub -o output_compile.%J -K -n 1 -J compile sh ./compile_script

-elif [ "$2" == "taurus" ]; then
+elif [ "$hostname" == "taurus" ]; then
 echo "Compiling on taurus"

 echo "$PATH"
@@ -75,8 +105,8 @@ else
 echo "$PATH"
 echo "Compiling general"
 sh ./autogen.sh
- sh ./configure  CXX=mpic++
- make
+ sh ./configure  CXX=mpic++ --with-boost=$HOME/openfpm_dependencies/openfpm_vcluster/BOOST
+ make VERBOSE=1 -j 4
 if [ $? -ne 0 ]; then exit 1 ; fi

 fi

--- a/cmake_modules/CorrectWindowsPaths.cmake
+++ b/cmake_modules/CorrectWindowsPaths.cmake
+# CorrectWindowsPaths - this module defines one macro
+#
+# CONVERT_CYGWIN_PATH( PATH )
+#  This uses the command cygpath (provided by cygwin) to convert
+#  unix-style paths into paths useable by cmake on windows
+
+macro (CONVERT_CYGWIN_PATH _path)
+  if (WIN32)
+    EXECUTE_PROCESS(COMMAND cygpath.exe -m ${${_path}}
+      OUTPUT_VARIABLE ${_path})
+    string (STRIP ${${_path}} ${_path})
+  endif (WIN32)
+endmacro (CONVERT_CYGWIN_PATH)
+
--- a/cmake_modules/FindPETSc.cmake
+++ b/cmake_modules/FindPETSc.cmake
--- a/cmake_modules/FindPackageMultipass.cmake
+++ b/cmake_modules/FindPackageMultipass.cmake
+# PackageMultipass - this module defines two macros
+#
+# FIND_PACKAGE_MULTIPASS (Name CURRENT
+#  STATES VAR0 VAR1 ...
+#  DEPENDENTS DEP0 DEP1 ...)
+#
+#  This function creates a cache entry <UPPERCASED-Name>_CURRENT which
+#  the user can set to "NO" to trigger a reconfiguration of the package.
+#  The first time this function is called, the values of
+#  <UPPERCASED-Name>_VAR0, ... are saved.  If <UPPERCASED-Name>_CURRENT
+#  is false or if any STATE has changed since the last time
+#  FIND_PACKAGE_MULTIPASS() was called, then CURRENT will be set to "NO",
+#  otherwise CURRENT will be "YES".  IF not CURRENT, then
+#  <UPPERCASED-Name>_DEP0, ... will be FORCED to NOTFOUND.
+#  Example:
+#    find_path (FOO_DIR include/foo.h)
+#    FIND_PACKAGE_MULTIPASS (Foo foo_current
+#      STATES DIR
+#      DEPENDENTS INCLUDES LIBRARIES)
+#    if (NOT foo_current)
+#      # Make temporary files, run programs, etc, to determine FOO_INCLUDES and FOO_LIBRARIES
+#    endif (NOT foo_current)
+#
+# MULTIPASS_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS LANGUAGE)
+#  Always runs the given test, use this when you need to re-run tests
+#  because parent variables have made old cache entries stale. The LANGUAGE
+#  variable is either C or CXX indicating which compiler the test should
+#  use.
+# MULTIPASS_C_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS)
+#  DEPRECATED! This is only included for backwards compatability. Use
+#  the more general MULTIPASS_SOURCE_RUNS instead.
+#  Always runs the given test, use this when you need to re-run tests
+#  because parent variables have made old cache entries stale.
+
+macro (FIND_PACKAGE_MULTIPASS _name _current)
+  string (TOUPPER ${_name} _NAME)
+  set (_args ${ARGV})
+  list (REMOVE_AT _args 0 1)
+
+  set (_states_current "YES")
+  list (GET _args 0 _cmd)
+  if (_cmd STREQUAL "STATES")
+    list (REMOVE_AT _args 0)
+    list (GET _args 0 _state)
+    while (_state AND NOT _state STREQUAL "DEPENDENTS")
+      # The name of the stored value for the given state
+      set (_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
+      if (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+        set (_states_current "NO")
+      endif (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+      set (${_stored_var} "${${_NAME}_${_state}}" CACHE INTERNAL "Stored state for ${_name}." FORCE)
+      list (REMOVE_AT _args 0)
+      list (GET _args 0 _state)
+    endwhile (_state AND NOT _state STREQUAL "DEPENDENTS")
+  endif (_cmd STREQUAL "STATES")
+
+  set (_stored ${_NAME}_CURRENT)
+  if (NOT ${_stored})
+    set (${_stored} "YES" CACHE BOOL "Is the configuration for ${_name} current?  Set to \"NO\" to reconfigure." FORCE)
+    set (_states_current "NO")
+  endif (NOT ${_stored})
+
+  set (${_current} ${_states_current})
+  if (NOT ${_current} AND PACKAGE_MULTIPASS_${_name}_CALLED)
+    message (STATUS "Clearing ${_name} dependent variables")
+    # Clear all the dependent variables so that the module can reset them
+    list (GET _args 0 _cmd)
+    if (_cmd STREQUAL "DEPENDENTS")
+      list (REMOVE_AT _args 0)
+      foreach (dep ${_args})
+        set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+      endforeach (dep)
+    endif (_cmd STREQUAL "DEPENDENTS")
+    set (${_NAME}_FOUND "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+  endif ()
+  set (PACKAGE_MULTIPASS_${name}_CALLED YES CACHE INTERNAL "Private" FORCE)
+endmacro (FIND_PACKAGE_MULTIPASS)
+
+
+macro (MULTIPASS_SOURCE_RUNS includes libraries source runs language)
+  include (Check${language}SourceRuns)
+  # This is a ridiculous hack.  CHECK_${language}_SOURCE_* thinks that if the
+  # *name* of the return variable doesn't change, then the test does
+  # not need to be re-run.  We keep an internal count which we
+  # increment to guarantee that every test name is unique.  If we've
+  # gotten here, then the configuration has changed enough that the
+  # test *needs* to be rerun.
+  if (NOT MULTIPASS_TEST_COUNT)
+    set (MULTIPASS_TEST_COUNT 00)
+  endif (NOT MULTIPASS_TEST_COUNT)
+  math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
+  set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
+  set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+  set (CMAKE_REQUIRED_INCLUDES ${includes})
+  set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+  if(${language} STREQUAL "C")
+    check_c_source_runs ("${source}" ${testname})
+  elseif(${language} STREQUAL "CXX")
+    check_cxx_source_runs ("${source}" ${testname})
+  endif()
+  set (${runs} "${${testname}}")
+endmacro (MULTIPASS_SOURCE_RUNS)
+
+macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
+  multipass_source_runs("${includes}" "${libraries}" "${source}" ${runs} "C")
+endmacro (MULTIPASS_C_SOURCE_RUNS)
--- a/cmake_modules/ResolveCompilerPaths.cmake
+++ b/cmake_modules/ResolveCompilerPaths.cmake
+# ResolveCompilerPaths - this module defines two macros
+#
+# RESOLVE_LIBRARIES (XXX_LIBRARIES LINK_LINE)
+#  This macro is intended to be used by FindXXX.cmake modules.
+#  It parses a compiler link line and resolves all libraries
+#  (-lfoo) using the library path contexts (-L/path) in scope.
+#  The result in XXX_LIBRARIES is the list of fully resolved libs.
+#  Example:
+#
+#    RESOLVE_LIBRARIES (FOO_LIBRARIES "-L/A -la -L/B -lb -lc -ld")
+#
+#  will be resolved to
+#
+#    FOO_LIBRARIES:STRING="/A/liba.so;/B/libb.so;/A/libc.so;/usr/lib/libd.so"
+#
+#  if the filesystem looks like
+#
+#    /A:       liba.so         libc.so
+#    /B:       liba.so libb.so
+#    /usr/lib: liba.so libb.so libc.so libd.so
+#
+#  and /usr/lib is a system directory.
+#
+#  Note: If RESOLVE_LIBRARIES() resolves a link line differently from
+#  the native linker, there is a bug in this macro (please report it).
+#
+# RESOLVE_INCLUDES (XXX_INCLUDES INCLUDE_LINE)
+#  This macro is intended to be used by FindXXX.cmake modules.
+#  It parses a compile line and resolves all includes
+#  (-I/path/to/include) to a list of directories.  Other flags are ignored.
+#  Example:
+#
+#    RESOLVE_INCLUDES (FOO_INCLUDES "-I/A -DBAR='\"irrelevant -I/string here\"' -I/B")
+#
+#  will be resolved to
+#
+#    FOO_INCLUDES:STRING="/A;/B"
+#
+#  assuming both directories exist.
+#  Note: as currently implemented, the -I/string will be picked up mistakenly (cry, cry)
+include (CorrectWindowsPaths)
+
+macro (RESOLVE_LIBRARIES LIBS LINK_LINE)
+  string (REGEX MATCHALL "((-L|-l|-Wl)([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))" _all_tokens "${LINK_LINE}")
+  set (_libs_found "")
+  set (_directory_list "")
+  foreach (token ${_all_tokens})
+    if (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+      # If it's a library path, add it to the list
+      string (REGEX REPLACE "^-L" "" token ${token})
+      string (REGEX REPLACE "//" "/" token ${token})
+      convert_cygwin_path(token)
+      list (APPEND _directory_list ${token})
+    elseif (token MATCHES "^(-l([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))")
+      # It's a library, resolve the path by looking in the list and then (by default) in system directories
+      if (WIN32) #windows expects "libfoo", linux expects "foo"
+        string (REGEX REPLACE "^-l" "lib" token ${token})
+      else (WIN32)
+        string (REGEX REPLACE "^-l" "" token ${token})
+      endif (WIN32)
+      set (_root "")
+      if (token MATCHES "^/")	# We have an absolute path
+        #separate into a path and a library name:
+        string (REGEX MATCH "[^/]*\\.(a|so|dll|lib)$" libname ${token})
+        string (REGEX MATCH ".*[^${libname}$]" libpath ${token})
+        convert_cygwin_path(libpath)
+        set (_directory_list ${_directory_list} ${libpath})
+        set (token ${libname})
+      endif (token MATCHES "^/")
+      set (_lib "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+      find_library (_lib ${token} HINTS ${_directory_list} ${_root})
+      if (_lib)
+	string (REPLACE "//" "/" _lib ${_lib})
+        list (APPEND _libs_found ${_lib})
+      else (_lib)
+        message (STATUS "Unable to find library ${token}")
+      endif (_lib)
+    endif (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+  endforeach (token)
+  set (_lib "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+  # only the LAST occurence of each library is required since there should be no circular dependencies
+  if (_libs_found)
+    list (REVERSE _libs_found)
+    list (REMOVE_DUPLICATES _libs_found)
+    list (REVERSE _libs_found)
+  endif (_libs_found)
+  set (${LIBS} "${_libs_found}")
+endmacro (RESOLVE_LIBRARIES)
+
+macro (RESOLVE_INCLUDES INCS COMPILE_LINE)
+  string (REGEX MATCHALL "-I([^\" ]+|\"[^\"]+\")" _all_tokens "${COMPILE_LINE}")
+  set (_incs_found "")
+  foreach (token ${_all_tokens})
+    string (REGEX REPLACE "^-I" "" token ${token})
+    string (REGEX REPLACE "//" "/" token ${token})
+    convert_cygwin_path(token)
+    if (EXISTS ${token})
+      list (APPEND _incs_found ${token})
+    else (EXISTS ${token})
+      message (STATUS "Include directory ${token} does not exist")
+    endif (EXISTS ${token})
+  endforeach (token)
+  list (REMOVE_DUPLICATES _incs_found)
+  set (${INCS} "${_incs_found}")
+endmacro (RESOLVE_INCLUDES)
--- a/configure
+++ b/configure
--- a/configure.ac
+++ b/configure.ac
-#                                               -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-
-AC_PREREQ(2.59)
-AC_INIT(OpenFPM_vcluster, 1.0.0, BUG-REPORT-ADDRESS)
-AC_CANONICAL_SYSTEM
-AC_CONFIG_SRCDIR([src/main.cpp])
-
-
-AM_INIT_AUTOMAKE([subdir-objects])
-AC_CONFIG_HEADER([src/config/config.h])
-m4_ifdef([ACX_PTHREAD],,[m4_include([m4/acx_pthread.m4])])
-m4_ifdef([ACX_MPI],,[m4_include([m4/acx_mpi.m4])])
-m4_ifdef([AX_OPENMP],,[m4_include([m4/ax_openmp.m4])])
-m4_ifdef([AX_CUDA],,[m4_include([m4/ax_cuda.m4])])
-m4_ifdef([AX_BOOST_BASE],,[m4_include([m4/ax_boost_base.m4])])
-m4_ifdef([AX_BOOST_IOSTREAMS],,[m4_include([m4/ax_boost_iostreams.m4])])
-m4_ifdef([AX_BOOST_PROGRAM_OPTIONS],,[m4_include([m4/ax_boost_program_options.m4])])
-m4_ifdef([AX_BOOST_UNIT_TEST_FRAMEWORK],,[m4_include([m4/ax_boost_unit_test_framework.m4])])
-
-
-case $host_os in
-   *cygwin*)
-        # Do something specific for cygwin
-        CXXFLAGS+=" --std=gnu++11 "
-        ;;
-    *)
-        #Default Case
-        CXXFLAGS+=" --std=c++11 "
-        ;;
-esac
-
-CXXFLAGS+=" -march=native -mtune=native -Wno-unused-local-typedefs -Wextra -Wno-unused-parameter "
-NVCCFLAGS=" "
-INCLUDES_PATH=" "
-
-# set default prefix
-if test "$prefix" = "NONE"; then
-   prefix="/usr/local"
-fi
-
-# Add openfpm_vcluster to prefix forlder (if prefix end if openfpm_pdata remove that path)
-if [ echo "$prefix" | grep -qE "/openfpm_pdata$" ]; then
-  prefix=$(echo "$prefix" | sed 's/\(.*\)\/openfpm_pdata$/\1/g')
-fi
-
-prefix="$prefix/openfpm_vcluster"
-echo "Installation dir is: $prefix"
-
-LT_INIT
-
-# Checks for programs.
-AC_PROG_CXX
-
-# Checks g++ flags
-
-AC_CANONICAL_HOST
-
-###### Check for verbose
-
-AC_MSG_CHECKING(whether to build with verbose print)
-verbose=no
-AC_ARG_ENABLE(verbose,
-	AC_HELP_STRING(
-	    [--enable-verbose],
-	    [enable verbose print (def=no)]
-	),
-  	verbose="$enableval"
-)
-
-
-
-AC_MSG_RESULT($verbose)
-if test x"$verbose" = x"yes"; then
-	AC_DEFINE([VERBOSE_TEST],[],[Verbose test])
-fi
-
-###### Check for debug compilation
-
-AC_MSG_CHECKING(whether to build with debug information)
-debuger=no
-AC_ARG_ENABLE(debug,
-	AC_HELP_STRING(
-	    [--enable-debug],
-	    [enable debug data generation (def=no)]
-	),
-  	debuger="$enableval"
-)
-
-
-
-AC_MSG_RESULT($debuger)
-if test x"$debuger" = x"yes"; then
-	AC_DEFINE([DEBUG_MODE],[],[Debug])
-	AC_DEFINE([DEBUG],[],[Debug])
-	CXXFLAGS="$CXXFLAGS -g3  -Wall -O0 "
-	NVCCFLAGS+="$NVCCFLAGS -g -O0 "
-else
-	CXXFLAGS="$CXXFLAGS -Wall -O3 -g3 -funroll-loops "
-	NVCCFLAGS+="$NVCCFLAGS -O3 "
-fi
-
-###### Check for se-class1
-
-AC_MSG_CHECKING(whether to build with security enhancement class1)
-se_class1=no
-AC_ARG_ENABLE(se-class1,
-        AC_HELP_STRING(
-            [--enable-se-class1],
-            [enable security enhancement class1]
-        ),
-        se_class1="$enableval"
-)
-
-
-
-AC_MSG_RESULT($se_class1)
-if test x"$se_class1" = x"yes"; then
-        AC_DEFINE([SE_CLASS1],[],[Security enhancement class 1])
-fi
-
-
-###### Check for se-class 2
-
-AC_MSG_CHECKING(whether to build with security enhancement class 2)
-se_class2=no
-AC_ARG_ENABLE(se-class2,
-        AC_HELP_STRING(
-            [--enable-se-class2],
-            [enable security enhancement class 2]
-        ),
-        se_class2="$enableval"
-)
-
-
-AC_MSG_RESULT($se_class2)
-if test x"$se_class2" = x"yes"; then
-        AC_DEFINE([SE_CLASS2],[],[Security enhancement class 2])
-fi
-
-###### Check for se-class 3
-
-AC_MSG_CHECKING(whether to build with security enhancement class 3)
-se_class3=no
-AC_ARG_ENABLE(se-class3,
-        AC_HELP_STRING(
-            [--enable-se-class3],
-            [enable security enhancement class 3]
-        ),
-        se_class3="$enableval"
-)
-
-
-
-AC_MSG_RESULT($se_class3)
-if test x"$se_class3" = x"yes"; then
-        AC_DEFINE([SE_CLASS3],[],[Security enhancement class 3])
-fi
-
-###### Check for test coverage
-
-AC_MSG_CHECKING(whether to build with test coverage)
-test_cov=no
-AC_ARG_ENABLE(test-coverage,
-        AC_HELP_STRING(
-            [--enable-test-coverage],
-            [enable test coverage]
-        ),
-        test_cov="$enableval"
-)
-
-
-
-AC_MSG_RESULT($test_cov)
-if test x"$test_cov" = x"yes"; then
-        AC_DEFINE([TEST_COVERAGE_MODE],[],[Test coverage mode])
-        CXXFLAGS="$CXXFLAGS  -fprofile-arcs -ftest-coverage "
-fi
-
-