.gitignore

@@ -25,6 +25,7 @@
 *.log
 *.sql
 *.sqlite
+*.xml
 
 # OS generated files #
 ######################
@@ -36,41 +37,42 @@
 ehthumbs.db
 Thumbs.db
 
+# CLion IDE-related
+.idea/
+cmake-build-debug/
+cmake-build-release/
+
+# Script-generated build folder
+build/
+
 ###### Other
 
-AUTHORS
-COPYING
-INSTALL
-NEWS
-README
 **/vtk/Makefile
 **/src/Makefile
 ./Makefile
 Makefile.in
-config.status
-configure
-numerics
+Makefile
 **/.deps
 **/src/config
-aclocal.m4
-**/autom4te.cache
 example.mk
 src/pdata
-vtk/cart_dec
-vtk/dom_box
-vtk/metis_dec
-.autotools
 .cproject
 .project
 .settings
-ar-lib
-compile
-config.guess
-config.sub
-depcomp
-install-sh
-missing
-install_dir
 **/*.vtk
 !**/test_data/*.vtk
 *.csv
+*.h5
+*.json
+*.html
+Makefile
+/build
+
+*CMake*
+*cmake*
+**/*cmake*
+**/*CMake*
+
+**/.gitignore
+.gitignore
+/doxygen/

.gitmodules

-[submodule "openfpm_vcluster"]
-	path = openfpm_vcluster
-	url = ssh://git@git.mpi-cbg.de/openfpm/openfpm_vcluster.git
-[submodule "openfpm_devices"]
-	path = openfpm_devices
-	url = ssh://git@git.mpi-cbg.de/openfpm/openfpm_devices.git
-[submodule "openfpm_io"]
-	path = openfpm_io
-	url = ssh://git@git.mpi-cbg.de/openfpm/openfpm_io.git
-[submodule "openfpm_data"]
-	path = openfpm_data
-	url = ssh://git@git.mpi-cbg.de/openfpm/openfpm_data.git
-[submodule "openfpm_numerics"]
-	path = openfpm_numerics
-	url = ssh://git@git.mpi-cbg.de/openfpm/openfpm_numerics.git

CHANGELOG.md

-# Change Log
-All notable changes to this project will be documented in this file.
-
-## [0.7.0] 15 December 2016
-
-### Added
-- Symmetric cell-list/verlet list Crossing scheme
-- VCluster examples
-- cell-list crossing scheme
-
-### Fixed
-- CRITICAL BUG: OpenFPM has a bug handling decomposition when a processor has a disconnected domains
-                (By experience this case has been seen on big number of processors). Please update to
-                0.7.0 or apply the patch to upgrade to 0.6.1
-- Found and fixed a memory leak when using complex properties
-
-### Changed
-- The file VCluster has been mooved #include "VCluster.hpp" must be changed to #include "VCluster/VCluster.hpp"
-  BECAUSE OF THIS, PLEASE CLEAN THE OPENFPM FOLDER OTHERWISE YOU WILL END TO HAVE 2 VCLUSTER.HPP
-
-## [0.6.0] - 5 November 2016
-
-### Added
-- Symmetric cell-list/verlet list
-- Multi-phase cell-list and Multi-phase cell-list
-- Added ghost_get that keep properties
-- Examples: 1_ghost_get_put it show how to use ghost_get and put with the new options
-            4_multiphase_celllist_verlet completely rewritten for new Cell-list and multiphase verlet
-	    5_molecular_dynamic use case of symmetric cell-list and verlet list with ghost put
-	    6_complex_usage It show how the flexibility of openfpm can be used to debug your program
-- Plotting system can export graph in svg (to be included in the paper)
-
- 
-### Fixed
-- Option NO_POSITION was untested
-- Regression: Examples code compilation was broken on OSX (Affect only 0.5.1)
-              (Internal: Added OSX examples compilarion/running test in the release pipeline)
-- gray_scott example code (variable not initialized)
-
-
-### Changes
-
-
-## [0.5.1] - 27 September 2016
-
-### Added
-- ghost_put support for particles
-- Full-Support for complex property on vector_dist (Serialization)
-- Added examples for serialization of complex properties 4_Vector
-- improved speed of the iterators
-
-### Fixed
-- Installation PETSC installation fail in case of preinstalled MPI
-- Miss-compilation of SUITESPARSE on gcc-6.2
-- vector_dist with negative domain (Now supported)
-- Grid 1D has been fixed
-- One constructor of Box had arguments inverted.
-  PLEASE CAREFULL ON THIS BUG
-     float xmin[] = {0.0,0.0};
-     float xmax[] = {1.0,1.0};
-     // Box<2,float> box(xmax,xmin)    BUG IT WAS xmax,xmin
-	 Box<2,float> box(xmin,xmax)  <--- NOW IT IS xmin,xmax
-	 Box<2,float> box({0.0,0.0},{1.0,1.0}) <---- This constructor is not affected by the BUG
-
-### Changed
-- On gcc the -fext-numeric-literals compilation flag is now mandatory
-
-## [0.5.0] - 15 August 2016
-
-### Added
-- map communicate particles across processors mooving the information of all the particle map_list give the possibility to give a list of property to move from one to another processor
-- Numeric: Finite Differences discretization with matrix contruction and parallel solvers (See example ... )
-- vector_dist now support complex object like Point VectorS Box ... , with no limitation
-   and more generic object like std::vector ... (WARNING TEMPORARY LIMITATION: Communication is not supported property must be excluded from communication using map_list and ghost_get)
-- vector_dist support expressions (See example ...)
-- No limit to ghost extension (they can be arbitrary extended)
-- Multi-phase CellList
-- Hilber curve data and computation reordering for cache firndliness
-
-### Fixed
-- Removed small crash for small grid and big number of processors
-
-### Changed
-
-### Known Bugs
-
-- On gcc 6.1 the project does not compile
-- Distributed grids on 1D do not work
-
-
-## [0.4.0] - 26-05-2016
-
-### Added
-- Grid with periodic boundary conditions
-- VTK Writer for distributed vector, now is the default writer
-- Installation of linear algebra packages
-- More user friendly installation (No environment variables to add in your bashrc, installation report less verbose)
-
-### Fixed
-- GPU compilation
-- PARMetis automated installation
-- Critical Bug in getCellList, it was producing Celllist with smaller spacing
-
-### Changed
-
-
-## [0.3.0] - 16-04-2016
-
-### Added
-- Molacular Dynamic example
-- addUpdateCell list for more optimal update of the cell list instead of recreate the CellList
-
-### Fixed
-- Nothing to report
-
-### Changed
-- Eliminated global_v_cluster, init_global_v_cluster, delete_global_v_cluster, 
-  substituted by 
-  create_vcluster, openfpm_init, openfpm_finalize
-- CartDecomposition parameter for the distributed structures is now optional
-- template getPos<0>(), substituted by getPos()
-
-## [0.2.1] - 01-04-2016
-
-### Changed
-- GoogleChart name function changed: AddPointGraph to AddLinesGraph and AddColumsGraph to AddHistGraph
-
-## [0.2.0] - 2016-03-25
-### Added
-- Added Load Balancing and Dynamic Load Balancing on Beta
-- PSE 1D example with multiple precision
-- Plot example for GoogleChart plotting
-- Distributed data structure now support 128bit floating point precision (on Beta)
-
-### Fixed
-- Detection 32 bit system and report as an error
-- Bug in rounding off for periodic boundary condition
-
-### Changed
-- Nothing to report
-
-## [0.1.0] - 2016-02-05
-### Added
-- PSE 1D example
-- Cell list example
-- Verlet list example
-- Kickstart for OpenFPM_numeric
-- Automated dependency installation for SUITESPRASE EIGEN OPENBLAS(LAPACK)
-
-
-### Fixed
-- CRITICAL BUG in periodic bondary condition
-- BOOST auto updated to 1.60
-- Compilation with multiple .cpp files
-
-### Changed
-- Nothing to report
-
-
-
-# Planned in the next Releases
-
-## [0.9.0] - Mid March
-
-- Algebraic Multigrid solver
-- Parallel VTK, improved visualization
-
-## [0.8.0] - Mid January 2017
-
-### Added
-- Dynamic Load Balancies examples and interface fixation
-- Check Point restart
-- More example and documentations
-
-## [0.7.0] - December of October
-
-### Added
-- Asynchronous communication
-- Support for Microsoft Windows with Cygwin
-- Support for Docker/codenvy
-- Defining a domain an invalid domain like Box<2,float> box({0.0,1.0},{0.0,1.0}) (the correct is {0.0,0.0},{1.0,1.0}  )
-           produce dead-lock or unclear error message in SE_CLASS1, not hint is given, added usefull error message
-
-
-

CMakeLists.txt

+cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
+project(openfpm_pdata LANGUAGES C CXX)
+
+if (POLICY CMP0074)
+	cmake_policy(SET CMP0074 NEW)
+endif()
+
+set(openfpm_VERSION 5.0.0)
+
+if (METIS_FOUND)
+	set(DEFINE_HAVE_METIS "#define HAVE_METIS 1")
+else()
+	message( FATAL_ERROR "Metis is required in order to install OpenFPM" )
+endif()
+
+if (PARMETIS_FOUND)
+	set(DEFINE_HAVE_PARMETIS "#define HAVE_PARMETIS 1")
+else()
+	message( FATAL_ERROR "ParMetis is required in order to install OpenFPM")
+endif()
+
+add_subdirectory (src)
+
+file(READ ${CMAKE_CURRENT_SOURCE_DIR}/src/cmake/openfpmConfig-configure.cmake CMAKE_OPENFPM_CONFIG_VARS)
+set(CMAKE_OPENFPM_CONFIG_VARS "${CMAKE_OPENFPM_CONFIG_VARS}\nmessage(STATUS \"Found OpenFPM version ${openfpm_VERSION} (\$\{CMAKE_CURRENT_LIST_FILE\})\")")
+set(CMAKE_OPENFPM_CONFIG_VARS "${CMAKE_OPENFPM_CONFIG_VARS}\nset(OPENFPM_CUDA_ON_BACKEND \"${CUDA_ON_BACKEND}\")")
+file(WRITE ${CMAKE_CURRENT_SOURCE_DIR}/src/cmake/openfpmConfig-Vars.cmake "${CMAKE_OPENFPM_CONFIG_VARS}")
+
+get_directory_property(hasParent PARENT_DIRECTORY)
+if(hasParent)
+	set(DEFINE_HAVE_METIS ${DEFINE_HAVE_METIS} CACHE INTERNAL "")
+	set(DEFINE_HAVE_PARMETIS ${DEFINE_HAVE_PARMETIS} CACHE INTERNAL "")
+endif()
+

Common Mistake

-Common Mistake
-1) Overshoot aggregate
-2) Forget .template
-3) Missing const

FAQ

-* Try to install OpenFPM I get "cannot recover from this error"
-It mean that the configuration phase has failed. Something has failed, what has failed should be reported some line before. We are trying to track the causes to understand if it is possible to produce a better error message but it seem that most of the time this error has been seen on OSX having a very old X-Code.
-
-* I get a huge number of error
-It can happen in compilation phase. The installation system in general should detect potential known incompatibility and try in the best case to silently workaround the problem, in the middle case provide an automatic solution and ask to the user the permission to perform it, in the worst case report to the user for manual fixation. Unfortunately the number of systems and possible configuration/missconfiguration make this task impossible to control.
-
-* The program generate the file openfpm_vars in my "holy" home folder. why ?
-If you show the hidden folder in your "holy" home, you will see how many program actually "violate" your home folder. They do costantly Creating/Reading/Writing such folder every time you open them, they are just hiding. OpenFPM create such text file only one time in installation and report it, mooving such file somewhere else after installation will bring the home folder to be "virgin" from OpenFPM forever.
-
-* The examples does not scale on my 4 - x core PC.
-Not all example are made for scalability. In particular example that do not have computation inside like the 0_simple_ ... . If instead is an example that has computation inside, when you are benchmarking in particular using all the cores of your PC, close all applications, like Browser, IDE, pdf reader, ..., unusefull shell running command (anything that could consume resources, consider that the Desktop environment consume resources, in particular if you have OpenGL/3D effects, disable them. The best would be close the X-server/Desktop environment). Check also that no program are running in background using resources, use top/Task manager to check this. Consider also that 99.9% of Laptop/Desktop today can adjust their frequency dynamically. In particular it is common that the system increase the CPU frequency at higher level when only one-core is used compared to N-core, and this can significantly affect scalability.
- 

Jenkins_high_scal_test

-#!groovy
-
-node ('taurus')
-{
-  deleteDir()
-  checkout scm
-  stage ('build_taurus')
-  {
-    sh "./build.sh $WORKSPACE $NODE_NAME pdata"
-  }
-
-  stage ('run_taurus')
-  {
-    parallel (
-      "24" : {sh "./run.sh $WORKSPACE $NODE_NAME 24 1 24"},
-      "48" : {sh "./run.sh $WORKSPACE $NODE_NAME 48 2 24"},
-      "96" : {sh "./run.sh $WORKSPACE $NODE_NAME 96 4 24"},
-      "192" : {sh "./run.sh $WORKSPACE $NODE_NAME 192 8 24"},
-      "240" : {sh "./run.sh $WORKSPACE $NODE_NAME 240 10 24"}
-    )
-  }
-}
-                 
-
-

Jenkins_med_scal_test

-#!groovy
-
-node ('gin')
-{
-  deleteDir()
-  checkout scm
-  stage ('build_gin')
-  {
-    sh "./build.sh $WORKSPACE $NODE_NAME pdata"
-  }
-
-  stage ('run_gin')
-  {
-    sh "./run.sh $WORKSPACE $NODE_NAME 5"
-    sh "./run.sh $WORKSPACE $NODE_NAME 6"
-    sh "./run.sh $WORKSPACE $NODE_NAME 7"
-    sh "./run.sh $WORKSPACE $NODE_NAME 8"
-    sh "./run.sh $WORKSPACE $NODE_NAME 9"
-    sh "./run.sh $WORKSPACE $NODE_NAME 10"
-    sh "./run.sh $WORKSPACE $NODE_NAME 11"
-  }
-}
-

Jenkins_sec_compilers

-#!groovy
-
-node ('taurus')
-{
-  deleteDir()
-  checkout scm
-  stage ('build_taurus')
-  {
-    sh "./build_sec_compilers.sh $WORKSPACE $NODE_NAME pdata"
-  }
-
-//  stage ('run_taurus')
-//  {
-//      ./run.sh $WORKSPACE $NODE_NAME 24 1 24"
-//  }
-}
-                 
-
-