Merge branch 'release/v0.4.0'

* release/v0.4.0:
  fix error messages
  examples: boris: refactor logging initialization
  prepare Changelog for v0.4.0
  add Selman to mailmap file
  logging: immediately print PFASST++ version number on start
  cmake: adding version number as const-string
  examples: boris: fix Boris-PFASST configuration
  Add Matt's key.
  docu: adjusting installation instructions
  fixing a couple of CppCheck warnings related to style and performance
  examples: boris: deactivate same levels by default
  examples: boris: Boris-PFASST, is that all?
  hashstack: Bump hashstack version to get latest CMake.
  implicit: Use LU decomposition in sweeps.
  implicit: Add lu_decomposition (LU without pivoting).
  implicit: Tighten up the implicit sweeper.
  tests: Update vdP tests.
  examples: Use implicit sweeper in vdP instead of IMEX seeper.
  implicit: Added `implicit_sweeper.hpp`.
  logging: add MPI rank to logging output (iff MPI enabled)
  mpi: stupid me ...
  cmake: fix handling of mpi
  examples: mpi: a few beautifications
  docu: add walk-through for JUQUEEN
  cmake: first draft for JUQUEEN toolchain file
  cmake: rework how MPI compiler wrappers are handled
  cmake: use Boost's static libs when all other are static
  cmake: fftw-detection module can handle dir hints
  examples: advec: make mpi example take cmd options
  cleanup includes
  pfasst: Use Controller logger.
  pfasst: Make sure num of procs and time steps are consistent.
  advec: Call `set_options`.
  mpi: re-require the user to call MPI_Init
  logging: add '--quiet/-q' flag to disable stdout
  config: mpi: let only rank 0 print help message
  examples: boris: enable residual control for MLSDC
  Tidy whitespace.
  Remove z1.
  examples: boris: fixing boris MLSDC for different levels
  examples: boris: some code cleanup
  config: fix a small issue with cmd args
  tests: mpi test didn't wrote XML output
  tools: fix coverage report script
  cmake: adjust make targets for MPI
  examples: adjust the MPI example to improved init-function
  logging: make logging on MPI runs only go to per-rank-files
  done bug fixes in interface_impl and sdc_impl
  docu: fix capitalization of brief docs
  docu: using Twitter Bootstrap for generated HTML pages
  doxygen: update Doxyfile to new version of Doxygen
  update PGP key ID and fingerprint
  docu: fix multiple subpaging of changelog
  docu: small remark on docu section in style guide
  docu: examples: improve examples
  docu: improve controller interfaces
  docu: improve Encapsulation and EncapSweeper
  docu: improve quadrature stuff
  docu: improve utilities and general stuff
  docu: adding docu modules
  logging: adjust easylogging API
  logging: update easyloggingpp from v9.75 to v9.80
  logging: fix custom logger timestamp precision
  poly: Use a fixed number of DKW iterations for roots.
  fix: iostream needed by config.hpp
  reorderung: moving implementation files into separate directory tree
  reordering: moving controllers into own subfolder
  internals: splitting up decls/defs for encapsulation related stuff
  internals: splitting up decls/defs for quadrature classes
  internals: splitting up decls/defs for mpi communicator
  internals: splitting up decls/defs for pfasst controller
  internals: splitting up decls/defs for sdc controller
  internals: splitting up decls/defs for mlsdc controller
  internals: splitting up decls/defs for config options
  internals: splitting up decls/defs for controller
  internals: a few docu fixes/additions
  internals: unbroadening base exception classes
  internals: splitting up decls/defs for interfaces
  a few updates to the gitignore file
  tools: a few additional usability tweaks
  tools: move generate_coverage script to tools
  fix failure with tests not producing tracing data
  rewritten coverage report generation script
  cmake: specify minimum patch version
  fix a cmakefile bug with cmake 3.1.x
  tests: examples: boris: fix sweeper test
  examples: boris: tests: fix particle utility tests and bug in operators
  examples: boris: linearized particle cloud components
  docs: Update install instructions.
  config: Add abs/rel residual tolerances.
  examples: Update option initialization.
  config: Tidy and set defaults.
  config: Get rid of redundant `add_option`.
  config: Add two stage config/log init to `pfasst::init`.
  examples: boris: use and override `void residual(dt, dst) const`
  config: Revamp adding options.
  examples: advec: enable cmd arg for residual tolerances
  config: enable cmd args for residual tolerances
  examples: boris: analysis: a little more intuitive
  examples: boris: make tau correction 0-to-node and don't reintegrate
  examples: boris: make different MLSDC levels for Boris optional
  examples: boris: steps towards working Boris-MLSDC
  examples: boris: introducing MLSDC for Boris
  tests: Add RelativeAdaptiveErrorTest to test_advection_diffusion.cpp.
  mpi: Minor tidying.
  tests: Re-organise the adaptive MLSDC tests a bit.
  tests: Add AdaptiveErrorTest for AD example to MPI PFASST.
  examples: enable logging for autobuild example
  log: better logging for MLSDC
  log: adding ability to add further named loggers
  tests: Relax some tolerances.
  FAS: Test residual+FAS for AD example.
  examples: boris: prepare separation of left/right-is-node handling
  examples: boris: some tweaks and additions to python analysis
  examples: boris: adding IPython notebook for analysing
  examples: boris: minor bugfixes and header/impl split for sweeper
  imex: Fix inclusion of FAS corrections in residuals.
  mlsdc, pfasst: Call `post_step` on all levels.
  examples: boris: calculating distances is hard ...
  examples: boris: improving logging and consistency
  logging: remove auto-spacing
  logging improvements
  cmake: fix random seed
  examples: boris: tweaking logging and data output
  examples: boris: multi particle works!!! *yeah*
  encap: Compute relative residuals as well.
  imex: Add FAS corrections to residual.
  status: Bug fix.
  status: Move to blocking send/recv.
  examples: boris: some logging tweaks
  examples: boris: single-particle system works again *yeah*
  examples: boris: a bunch of debugging and fixing
  examples: boris: fixing compiler warnings
  status: Break iterations in PFASST when converged.
  status: Begin adding converged status MPI communication.
  examples: boris: at least not segfaulting anymore ...
  examples: boris: a few bug fixes
  examples: boris: fixed examples namespace for Boris
  examples: boris: remove legacy code
  examples: boris: adjust boris main and tests to recent changes
  examples: boris: adjust sweeper to reworked framework
  cmake: examples: adjustments for recent boris changes
  examples: boris: solver wrapper interface + example impl for example solver
  examples: boris: some tweaks to example solver library
  examples: boris: some tweaks to particle data structures
  tests: examples: boris: test cases for particle utility functions
  examples: boris: rewritten particle data structure
  examples: boris: simple physics solver as separate library
  examples: boris: a few logging related tweaks
  examples: boris: a few logging-related improvements
  examples: boris: fix computation of exact solution (+caching)
  examles: boris: variable renaming
  tests: examples: adding sweeper convergence tests for Boris
  examples: boris: using logging

Signed-off-by: Torbjörn Klatt <[email protected]>

Author: torbjoernk

.gitignore

@@ -5,6 +5,11 @@
 *.info
 /include/pfasst/site_config.hpp
 
+.python-version
+__pycache__
+.ipynb_checkpoints
+/run
+
 # Created by http://www.gitignore.io
 
 ### C ###
@@ -37,24 +42,14 @@
 # Compiled Object files
 *.slo
 *.lo
-*.o
-*.obj
 
 # Compiled Dynamic libraries
-*.so
-*.dylib
-*.dll
 
 # Compiled Static libraries
 *.lai
 *.la
-*.a
-*.lib
 
 # Executables
-*.exe
-*.out
-*.app
 
 
 ### Eclipse ###
@@ -123,11 +118,14 @@ tramp
 
 
 ### Linux ###
-*~
 
 # KDE directory preferences
 .directory
 
+# KDevelop
+*.kdev4
+.kdev4/
+
 
 ### OSX ###
 .DS_Store
@@ -200,3 +198,66 @@ atlassian-ide-plugin.xml
 # Crashlytics plugin (for Android Studio and IntelliJ)
 com_crashlytics_export_strings.xml
 
+# Created by https://www.gitignore.io
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+cppcheck.xml
+/cppcheck
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# IPython
+*.ipynb_checkpoints/
+

.mailmap

@@ -4,3 +4,4 @@ Matthew Emmett <[email protected]> <[email protected]>
 Daniel Ruprecht <[email protected]> danielru <[email protected]>
 Daniel Ruprecht <[email protected]> Daniel <[email protected]>
 Daniel Ruprecht <[email protected]> Daniel <[email protected]>
+Selman Terzi <[email protected]>

3rdparty/CMakeLists.txt

@@ -10,6 +10,11 @@ message(STATUS "----------------------------------------------------------------
 message(STATUS "Boost")
 
 set(Boost_USE_MULTITHREADED ON)
+if(${pfasst_BUILD_SHARED_LIBS})
+    set(Boost_USE_STATIC_LIBS OFF)
+else()
+    set(Boost_USE_STATIC_LIBS ON)
+endif()
 set(Boost_ADDITIONAL_VERSIONS "1.57" "1.57.0" ${Boost_ADDITIONAL_VERSIONS})
 
 if(${compiler_version_available} AND ${CMAKE_CXX_COMPILER_ID} MATCHES Clang)

CHANGELOG.md

@@ -1,9 +1,107 @@
 # Changelog                                                                        {#page_changelog}
 
+## v0.4.0 -- The Big Improvement (2015/04/17)
+
+DOI: [10.6084/m9.figshare.1381721](http://dx.doi.org/10.6084/m9.figshare.1381721)
+
+    $ git diff --stat v0.3.0..v0.4.0
+    > 131 files changed, 15182 insertions(+), 6940 deletions(-)
+
+### Notable Features
+
+* Iteration controll for PFASST via relative and absolute residual tolerances.
+  ([#139][], [#141][], [#142][])
+
+* Adding an implicit sweeper with support for LU decomposition of quadrature matrix.
+  ([#150][])
+
+* General improvements to the logging and configuration functionality.
+  ([#144][], [#145][], [#146][], [#148][], [#163][], [#168][], [#169][], [#177][])
+
+* Successful tests on supercomputers (i.e., JUQUEEN)
+  ([#168][], [#176][])
+
+* Improved code organization.
+  ([#156][], [#157][], [#158][], [#170][], [#181][])
+
+* Rewamped documentation.
+  ([#149][], [#160][], [#179][], [#183][])
+
+* Examples: Boris supports multiple particles and multi-level coarsening
+  ([#152][], [#172][], [#180][])
+
+### Details
+
+* logging framework [Easylogging][] has been updated from v9.75 to v9.80.
+  ([#163][])
+
+* root finding algorithm for polynomials uses fixed number of iterations or residual tolerance.
+  ([#162][])
+
+* reworked how `pfasst::init(...)` is used.
+  ([#148][])
+
+* minimum _CMake_ version bumped to 2.8.*6*
+  ([#153][])
+
+* `git describe`-based version number as `pfasst::VERSION`
+  ([#185][])
+
+* script to generate and compile test coverage report was rewritten in Python 3.x
+  ([#154][])
+
+[#139]: https://github.com/Parallel-in-Time/PFASST/pull/139
+[#141]: https://github.com/Parallel-in-Time/PFASST/pull/141
+[#142]: https://github.com/Parallel-in-Time/PFASST/pull/142
+[#144]: https://github.com/Parallel-in-Time/PFASST/pull/144
+[#145]: https://github.com/Parallel-in-Time/PFASST/pull/145
+[#146]: https://github.com/Parallel-in-Time/PFASST/pull/146
+[#148]: https://github.com/Parallel-in-Time/PFASST/pull/148
+[#149]: https://github.com/Parallel-in-Time/PFASST/pull/149
+[#150]: https://github.com/Parallel-in-Time/PFASST/pull/150
+[#152]: https://github.com/Parallel-in-Time/PFASST/pull/152
+[#153]: https://github.com/Parallel-in-Time/PFASST/pull/153
+[#154]: https://github.com/Parallel-in-Time/PFASST/pull/154
+[#156]: https://github.com/Parallel-in-Time/PFASST/pull/156
+[#157]: https://github.com/Parallel-in-Time/PFASST/pull/157
+[#158]: https://github.com/Parallel-in-Time/PFASST/pull/158
+[#160]: https://github.com/Parallel-in-Time/PFASST/pull/160
+[#162]: https://github.com/Parallel-in-Time/PFASST/pull/162
+[#163]: https://github.com/Parallel-in-Time/PFASST/pull/163
+[#168]: https://github.com/Parallel-in-Time/PFASST/pull/168
+[#169]: https://github.com/Parallel-in-Time/PFASST/pull/169
+[#170]: https://github.com/Parallel-in-Time/PFASST/pull/170
+[#172]: https://github.com/Parallel-in-Time/PFASST/pull/172
+[#176]: https://github.com/Parallel-in-Time/PFASST/pull/176
+[#177]: https://github.com/Parallel-in-Time/PFASST/pull/177
+[#180]: https://github.com/Parallel-in-Time/PFASST/pull/180
+[#181]: https://github.com/Parallel-in-Time/PFASST/pull/181
+[#183]: https://github.com/Parallel-in-Time/PFASST/pull/183
+[#185]: https://github.com/Parallel-in-Time/PFASST/pull/185
+
+### Contributors
+
+* Matthew Emmett, Lawrence Berkeley National Laboratory ([memmett][])
+* Torbjörn Klatt, Jülich Supercomputing Centre ([torbjoernk][])
+* Daniel Ruprecht, Institute of Computational Science, University of Lugano ([danielru][])
+* Robert Speck, Jülich Supercomputing Centre ([pancetta][])
+* Selman Terzi, Jülich Supercomputing Centre ([selmanTerzi][])
+
+[memmett]: https://github.com/memmett
+[torbjoernk]: https://github.com/torbjoernk
+[danielru]: https://github.com/danielru
+[pancetta]: https://github.com/pancetta
+[selmanTerzi]: https://github.com/selmanTerzi
+
+---
+
 ## v0.3.0 -- The Big Cleanup (2014/12/12)
 
 DOI: [10.5281/zenodo.13221](http://dx.doi.org/10.5281/zenodo.13221)
 
+    $ git diff --stat v0.2.0..v0.3.0
+    > 84 files changed, 7687 insertions(+), 1968 deletions(-)
+
 ### Notable Features
 
 * Complete rewrite of quadrature functions.
@@ -15,7 +113,7 @@ DOI: [10.5281/zenodo.13221](http://dx.doi.org/10.5281/zenodo.13221)
 * Introduced framework for passing command line parameters to programs using PFASST++.
   ([#88][])
 
-* Versatile and colourful logging framework based on [Easylogging++](https://github.com/easylogging/easyloggingpp).
+* Versatile and colourful logging framework based on [Easylogging++][].
   ([#105][], [#123][])
 
 * New Example: Boris-SDC.
@@ -91,6 +189,9 @@ DOI: [10.5281/zenodo.13221](http://dx.doi.org/10.5281/zenodo.13221)
 
 DOI: [10.5281/zenodo.11517](http://dx.doi.org/10.5281/zenodo.11517)
 
+    $ git diff --stat v0.1.0..v0.2.0
+    > 52 files changed, 3306 insertions(+), 875 deletions(-)
+
 ### Notable Features
 
 * Addition of MPI based PFASST.
@@ -129,7 +230,7 @@ DOI: [10.5281/zenodo.11517](http://dx.doi.org/10.5281/zenodo.11517)
 [#76]: https://github.com/Parallel-in-Time/PFASST/pull/76
 [#77]: https://github.com/Parallel-in-Time/PFASST/pull/77
 [#78]: https://github.com/Parallel-in-Time/PFASST/pull/78
-[#78]: https://github.com/Parallel-in-Time/PFASST/pull/81
+[#81]: https://github.com/Parallel-in-Time/PFASST/pull/81
 
 ### Contributors
 
@@ -176,3 +277,6 @@ DOI: [10.5281/zenodo.11047](http://dx.doi.org/10.5281/zenodo.11047)
 
 [memmett]: https://github.com/memmett
 [torbjoernk]: https://github.com/torbjoernk
+
+
+[Easylogging++]: https://github.com/easylogging/easyloggingpp

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.8)
+cmake_minimum_required(VERSION 2.8.6)
 project(pfasst)
 
 list(APPEND CMAKE_MODULE_PATH ${pfasst_SOURCE_DIR}/cmake)
@@ -14,17 +14,33 @@ list(APPEND CMAKE_FIND_ROOT_PATH ${pfasst_SOURCE_DIR}/stack)
 set_directory_properties(PROPERTIES EP_PREFIX ${CMAKE_BINARY_DIR}/3rdparty)
 
 option(pfasst_DISABLE_LIBCXX    "Disable use of LLVM's libc++ when compiling with Clang." ON )
-option(pfasst_BUILD_SHARED_LIBS "Build shared libraries."                                 OFF)
+option(pfasst_BUILD_SHARED_LIBS "Build shared libraries."                                 ON )
 option(pfasst_BUILD_EXAMPLES    "Build example programs."                                 ON )
 CMAKE_DEPENDENT_OPTION(pfasst_INSTALL_EXAMPLES "Install example programs." ON
     "pfasst_BUILD_EXAMPLES" OFF)
 option(pfasst_BUILD_TESTS       "Build test suite for PFASST."                            ON )
 option(pfasst_WITH_MPI          "Build with MPI enabled."                                 OFF)
 option(pfasst_WITH_GCC_PROF     "Enable excessive debugging & profiling output with GCC." OFF)
+option(pfasst_DEFAULT_RAND_SEED "Using a hardcoded random seed"                           ON )
 
 if(${pfasst_WITH_MPI})
     find_package(MPI REQUIRED)
-    message(STATUS "Using MPI C++ Compiler: ${MPI_CXX_COMPILER}")
+    if(NOT "${CMAKE_CXX_COMPILER}" STREQUAL "${MPI_CXX_COMPILER}" OR 
+       NOT "${CMAKE_C_COMPILER}" STREQUAL "${MPI_C_COMPILER}")
+        message(STATUS "C++ Compiler: ${CMAKE_CXX_COMPILER}")
+        message(STATUS "MPI C++ Compiler Wrapper: ${MPI_CXX_COMPILER}")
+        message(WARNING "Please make sure to set CXX and CC to the MPI compiler wrappers!")
+        set(CMAKE_CXX_COMPILER "${MPI_CXX_COMPILER}")
+        set(CMAKE_C_COMPILER "${MPI_C_COMPILER}")
+        message(STATUS "Set default compilers to MPI compilers.")
+    endif()
+    message(STATUS "Using MPI C++ Compiler Wrapper: ${MPI_CXX_COMPILER}")
+    message(STATUS "USing MPI C Compiler Wrapper: ${MPI_C_COMPILER}")
+    add_definitions(-DWITH_MPI)
+endif()
+
+if(pfasst_DEFAULT_RAND_SEED)
+    set(pfasst_RANDOM_SEED "42")
 endif()
 
 # Check for C++11 support
@@ -103,6 +119,12 @@ if(${CMAKE_CXX_COMPILER_ID} MATCHES GNU)
         "build-in profiling support"
     )
 endif()
+if(pfasst_RANDOM_SEED)
+    add_feature_info(DefaultRandomSeed
+        pfasst_RANDOM_SEED
+        "using specific default random seed ${pfasst_RANDOM_SEED}"
+    )
+endif()
 
 set(3rdparty_INCLUDES)
 set(3rdparty_DEPENDEND_LIBS)
@@ -129,18 +151,24 @@ message(STATUS "Configuring 3rd party libraries")
 #  - FFTW_LIBRARIES (if pfasst_BUILD_EXAMPLES)
 add_subdirectory(3rdparty)
 
+message(STATUS "********************************************************************************")
+message(STATUS "Configuring sources")
+update_site_config()
+
+add_custom_target(set_version ALL
+    COMMAND ${pfasst_SOURCE_DIR}/tools/get_pfasst_version.sh
+    WORKING_DIRECTORY ${pfasst_SOURCE_DIR}
+    COMMENT "Updating PFASST++ version number"
+    USES_TERMINAL
+)
+set(pfasst_DEPENDEND_TARGETS set_version ${pfasst_DEPENDEND_TARGETS})
+
 list(LENGTH pfasst_DEPENDEND_LIBS pfasst_NUM_DEPENDEND_LIBS)
 list(LENGTH pfasst_DEPENDEND_TARGETS pfasst_NUM_DEPENDEND_TARGETS)
 list(LENGTH pfasst_TESTS_DEPENDEND_TARGETS pfasst_TESTS_NUM_DEPENDEND_TARGETS)
 
-message(STATUS "********************************************************************************")
-message(STATUS "Configuring sources")
-set(WARNING_COMMENT "/*\n * DO NOT ALTER THIS FILE\n *\n * It will get rewritten on CMake's next run\n *\n */")
-configure_file(
-    "${pfasst_SOURCE_DIR}/cmake/site_config.hpp.in"
-    "${CMAKE_CURRENT_SOURCE_DIR}/include/pfasst/site_config.hpp"
-)
 add_subdirectory(include)
+add_subdirectory(src)
 
 if(pfasst_BUILD_EXAMPLES)
     message(STATUS "********************************************************************************")
@@ -163,6 +191,10 @@ install(DIRECTORY include/
     DESTINATION include
     FILES_MATCHING PATTERN "*.hpp"
 )
+install(DIRECTORY src/
+    DESTINATION include
+    FILES_MATCHING PATTERN "*.hpp"
+)
 
 if(pfasst_BUILD_EXAMPLES AND pfasst_INSTALL_EXAMPLES)
     message(STATUS "  example programs:    <PREFIX>/bin")