ComputationalRadiationPhysics · psychocoderHPC · Feb 20, 2015 · Feb 17, 2015 · Feb 17, 2015 · Feb 17, 2015
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -302,6 +302,11 @@ Please **add the according license header** snippet to your *new files*:
 - the default project name ist `PIConGPU` (case sensitive!) and adds the GPLv3+
   only.
 
+Files in the directory `thirdParty/` are only imported from remote repositories
+as written in our [LICENSE](LICENSE.md). If you want to improve them, submit
+your pull requests there and open an issue for our **maintainers** to update
+to a new version of the according software.
+
 *******************************************************************************
 
 Commit Rules

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,17 +1,23 @@
  PIConGPU - Licenses
 ================================================================================
 
-**Copyright 2009-2014** Florian Berninger, Heiko Burau, Robert Dietrich, Wen Fu,
-                        Anton Helm, Wolfgang Hoehnig, Axel Huebl, Remi Lehe,
-                        Richard Pausch, Felix Schmitt, Benjamin Schneider,
-                        Joseph Schuchart, Klaus Steiniger, Rene Widera
+**Copyright 2009-2015** Florian Berninger, Heiko Burau, Michael Bussmann,
+                        Alexander Debus, Robert Dietrich, Carlchristian Eckert,
+                        Wen Fu, Marco Garten, Anton Helm, Wolfgang Hoehnig,
+                        Axel Huebl, Maximilian Knespel, Remi Lehe,
+                        Richard Pausch, Felix Schmitt, Conrad Schumann,
+                        Benjamin Schneider, Joseph Schuchart, Klaus Steiniger,
+                        Rene Widera, Benjamin Worpitz
 
 See [active team](README.md#active-team).
 
 PIConGPU is a program collection containing the main simulation, independent
 scripts and auxiliary libraries. If not stated otherwise explicitly, the
 following licenses apply:
 
+
+### PIConGPU
+
 The **main simulation** is licensed under the **GPLv3+**. See
 [COPYING](COPYING). If not stated otherwise explicitly, that affects:
  - `buildsystem`
@@ -20,17 +26,46 @@ The **main simulation** is licensed under the **GPLv3+**. See
  - `src/picongpu`
  - `src/tools` (without `splash2txt`)
  - `src/mpiInfo`
+
+
+### PMacc & splash2txt
 
 All **libraries** are *dual licensed* under the **GLPv3+ and LGPLv3+**. See
 [COPYING](COPYING) and [COPYING.LESSER](COPYING.LESSER).
 If not stated otherwise explicitly, that affects:
  - `src/libPMacc`
  - `src/tools/splash2txt`
 
-**other licenses**:
- - `src/cuda_memtest`:
+
+### Third party software and other licenses
+
+We include a list of (GPL-) compatible third party software for the sake
+of an easier install of `PIConGPU`. Contributions to these parts of the
+repository should *not* be made in the `thirdParty/` directory but in
+*their according repositories* (that we import).
+
+ - `thirdParty/mallocMC`:
+   mallocMC is a fast memory allocator for many core accelerators and was
+   originally forked from the `ScatterAlloc` project.
+   It is licensed under the *MIT License*.
+   Please visit
+     https://github.com/ComputationalRadiationPhysics/mallocMC
+   for further details and contributions.
+
+ - `thirdParty/cmake-modules`:
+   we published a set of useful CMake modules that are not in the
+   CMake mainline under the *ISC license* at
+     https://github.com/ComputationalRadiationPhysics/cmake-modules
+   for contributions or inclusion in PIConGPU and other projects.
+
+ - `thirdParty/cuda_memtest`:
    CUDA MemTest is an *independent program* developed by the University
    Illinois, published under the *Illinois Open Source License*.
-   Please refer to the file `src/cuda_memtest/README` for license information.
+   Please refer to the file `thirdParty/cuda_memtest/README` for license information.
    We redistribute this modified version of CUDA MemTest under the same license
-   [src/cuda_memtest/README](src/cuda_memtest/README).
+   [thirdParty/cuda_memtest/README](thirdParty/cuda_memtest/README).
+   The original release was published at
+     http://sourceforge.net/projects/cudagpumemtest
+   and our modified version is hosted at
+     https://github.com/ComputationalRadiationPhysics/cuda_memtest
+   for further reference.
diff --git a/src/libPMacc/examples/gameOfLife2D/CMakeLists.txt b/src/libPMacc/examples/gameOfLife2D/CMakeLists.txt
@@ -39,7 +39,8 @@ project (GameOfLife)
 set(CMAKE_PREFIX_PATH "/usr/lib/x86_64-linux-gnu/" "$ENV{MPI_ROOT}" "$ENV{CUDA_ROOT}" "$ENV{BOOST_ROOT}")
 
 # own modules for find_packages
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/../../../cmake/)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
+    ${CMAKE_CURRENT_SOURCE_DIR}/../../../../thirdParty/cmake-modules/)
 
 IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
     SET(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}" CACHE PATH "install prefix" FORCE)

diff --git a/src/picongpu/CMakeLists.txt b/src/picongpu/CMakeLists.txt
@@ -36,7 +36,8 @@ set(CMAKE_PREFIX_PATH "/usr/lib/x86_64-linux-gnu/" "$ENV{MPI_ROOT}"
     "$ENV{CUDA_ROOT}" "$ENV{BOOST_ROOT}" "$ENV{HDF5_ROOT}" "$ENV{VT_ROOT}")
 
 # own modules for find_packages
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${CMAKE_CURRENT_SOURCE_DIR}/../cmake/)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
+    ${CMAKE_CURRENT_SOURCE_DIR}/../../thirdParty/cmake-modules/)
 
 
 ################################################################################
@@ -84,6 +85,20 @@ if(CUDA_KEEP_FILES)
 endif(CUDA_KEEP_FILES)
 
 
+################################################################################
+# Find mallocMC
+################################################################################
+
+find_package(mallocMC 2.1.0)
+
+if(mallocMC_FOUND)
+  include_directories(SYSTEM ${mallocMC_INCLUDE_DIRS})
+else(mallocMC_FOUND)
+  message(STATUS "Using mallocMC from thirdParty/ directory")
+  include_directories(SYSTEM ${CMAKE_CURRENT_SOURCE_DIR}/../../thirdParty/mallocMC/src/include)
+endif(mallocMC_FOUND)
+
+
 ################################################################################
 # VampirTrace
 ################################################################################
@@ -286,7 +301,7 @@ endif(PARAM_OVERWRITES)
 set(SAME_NVCC_FLAGS_IN_SUBPROJECTS OFF)
 find_path(CUDA_MEMTEST_DIR
         NAMES CMakeLists.txt
-        PATHS "${CMAKE_CURRENT_SOURCE_DIR}/../cuda_memtest"
+        PATHS "${CMAKE_CURRENT_SOURCE_DIR}/../../thirdParty/cuda_memtest"
         DOC "path to cuda_memtest"
         )
 

diff --git a/src/tools/png2gas/CMakeLists.txt b/src/tools/png2gas/CMakeLists.txt
@@ -43,7 +43,7 @@ set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g -Wall -Wno-pmf-conversions -Wno-depre
 
 # own modules for find_packages
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
-    ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake/)
+    ${CMAKE_CURRENT_SOURCE_DIR}/../../../thirdParty/cmake-modules/)
 
 
 ################################################################################

diff --git a/src/tools/splash2txt/CMakeLists.txt b/src/tools/splash2txt/CMakeLists.txt
@@ -37,7 +37,7 @@ set(CMAKE_PREFIX_PATH "/usr/lib/x86_64-linux-gnu/" "$ENV{BOOST_ROOT}" "$ENV{HDF5
 
 # own modules for find_packages
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}
-    ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake/)
+    ${CMAKE_CURRENT_SOURCE_DIR}/../../../thirdParty/cmake-modules/)
 
 include_directories(include)
 

diff --git a/src/cmake/FindADIOS.cmake → thirdParty/cmake-modules/FindADIOS.cmake b/src/cmake/FindADIOS.cmake → thirdParty/cmake-modules/FindADIOS.cmake
diff --git a/src/cmake/FindPNGwriter.cmake → thirdParty/cmake-modules/FindPNGwriter.cmake b/src/cmake/FindPNGwriter.cmake → thirdParty/cmake-modules/FindPNGwriter.cmake
diff --git a/src/cmake/FindSplash.cmake → thirdParty/cmake-modules/FindSplash.cmake b/src/cmake/FindSplash.cmake → thirdParty/cmake-modules/FindSplash.cmake
diff --git a/src/cmake/FindmallocMC.cmake → thirdParty/cmake-modules/FindmallocMC.cmake b/src/cmake/FindmallocMC.cmake → thirdParty/cmake-modules/FindmallocMC.cmake
diff --git a/src/cuda_memtest/CMakeLists.txt → thirdParty/cuda_memtest/CMakeLists.txt b/src/cuda_memtest/CMakeLists.txt → thirdParty/cuda_memtest/CMakeLists.txt
diff --git a/src/cuda_memtest/Makefile → thirdParty/cuda_memtest/Makefile b/src/cuda_memtest/Makefile → thirdParty/cuda_memtest/Makefile
diff --git a/src/cuda_memtest/README → thirdParty/cuda_memtest/README b/src/cuda_memtest/README → thirdParty/cuda_memtest/README
diff --git a/src/cuda_memtest/RELEASE → thirdParty/cuda_memtest/RELEASE b/src/cuda_memtest/RELEASE → thirdParty/cuda_memtest/RELEASE
diff --git a/src/cuda_memtest/cmake/FindNVML.cmake → thirdParty/cuda_memtest/cmake/FindNVML.cmake b/src/cuda_memtest/cmake/FindNVML.cmake → thirdParty/cuda_memtest/cmake/FindNVML.cmake
diff --git a/src/cuda_memtest/cuda_memtest.cu → thirdParty/cuda_memtest/cuda_memtest.cu b/src/cuda_memtest/cuda_memtest.cu → thirdParty/cuda_memtest/cuda_memtest.cu
diff --git a/src/cuda_memtest/cuda_memtest.h → thirdParty/cuda_memtest/cuda_memtest.h b/src/cuda_memtest/cuda_memtest.h → thirdParty/cuda_memtest/cuda_memtest.h
diff --git a/src/cuda_memtest/doc/saahpc_09.pdf → thirdParty/cuda_memtest/doc/saahpc_09.pdf b/src/cuda_memtest/doc/saahpc_09.pdf → thirdParty/cuda_memtest/doc/saahpc_09.pdf
diff --git a/src/cuda_memtest/misc.cpp → thirdParty/cuda_memtest/misc.cpp b/src/cuda_memtest/misc.cpp → thirdParty/cuda_memtest/misc.cpp
diff --git a/src/cuda_memtest/misc.h → thirdParty/cuda_memtest/misc.h b/src/cuda_memtest/misc.h → thirdParty/cuda_memtest/misc.h
diff --git a/src/cuda_memtest/ocl_memtest.cpp → thirdParty/cuda_memtest/ocl_memtest.cpp b/src/cuda_memtest/ocl_memtest.cpp → thirdParty/cuda_memtest/ocl_memtest.cpp
diff --git a/src/cuda_memtest/ocl_memtest_kernels.cpp → ...arty/cuda_memtest/ocl_memtest_kernels.cpp b/src/cuda_memtest/ocl_memtest_kernels.cpp → ...arty/cuda_memtest/ocl_memtest_kernels.cpp
diff --git a/src/cuda_memtest/ocl_tests.cpp → thirdParty/cuda_memtest/ocl_tests.cpp b/src/cuda_memtest/ocl_tests.cpp → thirdParty/cuda_memtest/ocl_tests.cpp
diff --git a/src/cuda_memtest/ocl_tests.h → thirdParty/cuda_memtest/ocl_tests.h b/src/cuda_memtest/ocl_tests.h → thirdParty/cuda_memtest/ocl_tests.h
diff --git a/src/cuda_memtest/sanity_check.sh → thirdParty/cuda_memtest/sanity_check.sh b/src/cuda_memtest/sanity_check.sh → thirdParty/cuda_memtest/sanity_check.sh
diff --git a/src/cuda_memtest/tests.cu → thirdParty/cuda_memtest/tests.cu b/src/cuda_memtest/tests.cu → thirdParty/cuda_memtest/tests.cu
diff --git a/thirdParty/mallocMC/.gitignore b/thirdParty/mallocMC/.gitignore
@@ -0,0 +1,16 @@
+# Compiled Object files
+*.slo
+*.lo
+*.o
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+
+*~
+/nbproject
diff --git a/thirdParty/mallocMC/.travis.yml b/thirdParty/mallocMC/.travis.yml
@@ -0,0 +1,31 @@
+language: cpp
+
+compiler:
+  - gcc
+
+env:
+  global:
+    - INSTALL_DIR=~/mylibs
+
+script:
+  - mkdir build_tmp && cd build_tmp
+  - cmake -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR $TRAVIS_BUILD_DIR
+  - make
+  - make install
+  - make examples
+
+before_script:
+  - sudo apt-get update -qq
+  - sudo apt-get install -qq build-essential
+  - sudo apt-get install -qq gcc-4.4 g++-4.4
+  - sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.4 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.4
+  - gcc --version && g++ --version
+  - sudo apt-get install -qq nvidia-common
+  - sudo apt-get install -qq nvidia-current
+  - sudo apt-get install -qq nvidia-cuda-toolkit nvidia-cuda-dev
+  - sudo apt-get install -qq libboost1.48-dev
+  - sudo find /usr/ -name libcuda*.so
+
+after_script:
+  - ls -halR $INSTALL_DIR
+
diff --git a/thirdParty/mallocMC/CHANGELOG.md b/thirdParty/mallocMC/CHANGELOG.md
@@ -0,0 +1,98 @@
+Change Log / Release Log for mallocMC
+================================================================
+
+2.1.0crp
+-------------
+**Date:** 2015-02-11
+
+This release fixes some bugs that occured after the release of 2.0.1crp and reduces the interface to improve interoperability with the default CUDA allocator.
+We closed all issues documented in
+[Milestone *New Features*](https://github.com/ComputationalRadiationPhysics/mallocMC/issues?milestone=3&state=closed)
+
+### Changes to mallocMC 2.0.1crp
+
+**Features**
+ - the possibility to overwrite the default implementation of new/delete and malloc/free was removed #72. **This changes the interface**, since users are now always forced to call `mallocMC::malloc()` and `mallocMC::free()`. This is intended to improve readability and allows to use the CUDA allocator inside mallocMC.
+ - the policy *Scatter* now places the onpagetables data structure at the end of a page. This can greatly improve performance when using large pages and `resetfreedpages=true` #80
+
+**Bug fixes**
+ - in the policy *Scatter*, `fullsegments` and `additional_chunks` could grow too large in certain configurations #79
+
+**Misc:**
+ - See the full changes at https://github.com/ComputationalRadiationPhysics/mallocMC/compare/2.0.1crp...2.1.0crp
+
+
+2.0.1crp
+-------------
+**Date:** 2015-01-13
+
+This release fixes several bugs that occured after the release of 2.0.0crp.
+We closed all issues documented in
+[Milestone *Bugfixes*](https://github.com/ComputationalRadiationPhysics/mallocMC/issues?milestone=4&state=closed)
+
+### Changes to mallocMC 2.0.0crp
+
+**Bug fixes**
+ - page table metadata was not correctly initialized with 0 #70
+ - freeing pages would not work under certain circumstances #66
+ - the bitmask in a page table entry could be wrong due to a racecondition #62
+ - not all regions were initialized correctly #60
+ - getAvailableSlots could sometimes miss blocks #59
+ - the counter for elements in a page could get too high due to a racecondition #61
+ - Out of Memory (OOM) Policy sometimes did not recognize allocation failures correctly #67
+
+**Misc:**
+ - See the full changes at https://github.com/ComputationalRadiationPhysics/mallocMC/compare/2.0.0crp...2.0.1crp
+
+
+2.0.0crp
+-------------
+**Date:** 2014-06-02
+
+This release introduces mallocMC, which contains the previous algorithm and
+much code from ScatterAlloc 1.0.2crp. The project was renamed due to massive
+restructurization and because the code uses ScatterAlloc as a reference
+algorithm, but can be extended to include other allocators in the future.
+We closed all issues documented in
+[Milestone *Get Lib ready for PIConGPU*](https://github.com/ComputationalRadiationPhysics/mallocMC/issues?milestone=2&state=closed)
+
+### Changes to ScatterAlloc 1.0.2crp
+
+**Features**
+ - completely split into policies #17
+ - configuration through structs instead of macro #17
+ - function `getAvailableSlots()` #5
+ - selectable data alignment #14
+ - function `finalizeHeap()` #11
+
+**Bug fixes:**
+ - build warning for cmake #33
+
+**Misc:**
+ - verification code and examples #35
+ - install routines #4
+ - See the full changes at https://github.com/ComputationalRadiationPhysics/mallocMC/compare/1.0.2crp...2.0.0crp
+
+
+1.0.2crp
+-------------
+**Date:** 2014-01-07
+
+This is our first bug fix release.
+We closed all issues documented in
+[Milestone *Bug fixes*](https://github.com/ComputationalRadiationPhysics/mallocMC/issues?milestone=1&state=closed)
+
+### Changes to 1.0.1
+
+**Features:**
+  - added travis-ci.org support for compile tests #7
+
+**Bug fixes:**
+  - broken cmake/compile #1
+  - g++ warnings #10
+  - only N-1 access blocks used instead of N #2
+  - 32bit bug: allocate more than 4GB #12
+
+**Misc:**
+  See the full changes at
+  https://github.com/ComputationalRadiationPhysics/scatteralloc/compare/1.0.1...1.0.2crp