Merge pull request #2533 from ComputationalRadiationPhysics/release-0.3.2

psychocoderHPC · web-flow · commit d8afdf347fea · 2018-02-16T22:08:59.000+01:00
Release 0.3.2: Phase Space Momentum, ADIOS One-Particle Dumps &amp; Field Names
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,47 @@
 Change Log / Release Log for PIConGPU
 ================================================================
 
+0.3.2
+-----
+**Date:** 2018-02-16
+
+Phase Space Momentum, ADIOS One-Particle Dumps & Field Names
+
+This release fixes a bug in the phase space plugin which derived a too-low
+momentum bin for particles below the typical weighting (and too-high for above
+it). ADIOS dumps crashed on one-particle dumps and in the name of on-the-fly
+particle-derived fields species name and field name were in the wrong order.
+The plugins libSplash (1.6.0) and PNGwriter (0.6.0) need exact versions,
+later releases will require a newer version of PIConGPU.
+
+### Changes to "0.3.1"
+
+**Bug Fixes:**
+ - PIConGPU:
+   - wrong border with current background field #2326
+ - libPMacc:
+   - cuSTL: missing include in `ForEach` #2406
+   - warning concerning forward declarations of `pmacc::detail::Environment` #2489
+   - `pmacc::math::Size_t<0>::create()` in Visual Studio #2513
+ - plugins:
+   - phase space plugin: weighted particles' momentum #2428
+   - calorimeter: validate `minEnergy` #2512
+   - ADIOS:
+     - one-particle dumps #2437
+     - `FieldTmp`: derived field name #2461
+   - exact versions of libSplash 1.6.0 & PNGwriter 0.6.0
+ - tools:
+   - tbg: wrong quoting of `'` #2419
+   - CMake: false-positive on in-source build check #2407
+   - pic-configure: cmakeFlags return code #2323
+
+**Misc:**
+ - Hypnos (HZDR): new modules #2521 #2524
+
+Thanks to Axel Huebl, René Widera, Sergei Bastrakov and Sebastian Hahn
+for contributing to this release!
+
+
 0.3.1
 -----
 **Date:** 2017-10-20
diff --git a/INSTALL.rst b/INSTALL.rst
@@ -133,7 +133,7 @@ We recommend to install at least **pngwriter** and either **libSplash** (HDF5) o
 
 pngwriter
 """""""""
-- 0.5.6+
+- 0.6.0 (exact!)
 - *Spack:* ``spack install pngwriter``
 - *from source:*
 
@@ -145,7 +145,7 @@ pngwriter
   - example:
 
     - ``mkdir -p ~/src ~/build ~/lib``
-    - ``git clone https://github.com/pngwriter/pngwriter.git ~/src/pngwriter/``
+    - ``git clone https://github.com/pngwriter/pngwriter.git --branch 0.6.0 ~/src/pngwriter/``
     - ``cd ~/build``
     - ``cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/pngwriter ~/src/pngwriter``
     - ``make install``
@@ -157,14 +157,14 @@ pngwriter
 
 libSplash
 """""""""
-- 1.6.0+ (requires *HDF5*, *boost program-options*)
+- 1.6.0 (exact! requires *HDF5*, *boost program-options*)
 - *Debian/Ubuntu dependencies:* ``sudo apt-get install libhdf5-openmpi-dev libboost-program-options-dev``
 - *Arch Linux dependencies:* ``sudo pacman --sync hdf5-openmpi boost``
 - *Spack:* ``spack install libsplash ^hdf5~fortran``
 - *from source:*
 
   - ``mkdir -p ~/src ~/build ~/lib``
-  - ``git clone https://github.com/ComputationalRadiationPhysics/libSplash.git ~/src/splash/``
+  - ``git clone https://github.com/ComputationalRadiationPhysics/libSplash.git --branch v1.6.0 ~/src/splash/``
   - ``cd ~/build``
   - ``cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/splash ~/src/splash``
   - ``make install``
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -89,9 +89,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = u'0.3.1'
+version = u'0.3.2'
 # The full version, including alpha/beta/rc tags.
-release = u'0.3.1'
+release = u'0.3.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
diff --git a/pic-configure b/pic-configure
@@ -83,7 +83,12 @@ if [ ! -d "$extension_param" ] ; then
 fi
 #check for cmakeFlags file (interprete with sh)
 if [ -f "$extension_param/cmakeFlags" ] ; then
-    cmake_flags=`$extension_param/cmakeFlags $cmakeFlagsNr`
+    cmake_flags=$($extension_param/cmakeFlags $cmakeFlagsNr)
+    if [ $? -ne 0 ] ; then
+        echo "ERROR: Executing '$extension_param/cmakeFlags' failed!" >&2
+        echo "       Is the file executable? (chmod u+x cmakeFlags)" >&2
+        exit 2
+    fi
 fi
 
 #set default install path if no path is set by paramater
diff --git a/src/libPMacc/PMaccConfig.cmake b/src/libPMacc/PMaccConfig.cmake
@@ -277,6 +277,7 @@ endif()
 # Boost 1.55 added support for a define that makes result_of look for
 # the result<> template and falls back to decltype if none is found. This is
 # great for the transition from the "wrong" usage to the "correct" one as
+message(STATUS "Boost: result_of with TR1 style and decltype fallback")
 set(PMacc_DEFINITIONS ${PMacc_DEFINITIONS} -DBOOST_RESULT_OF_USE_TR1_WITH_DECLTYPE_FALLBACK)
 
 # Boost >= 1.60.0 and CUDA != 7.5 failed when used with C++11
@@ -290,13 +291,16 @@ if( (Boost_VERSION GREATER 105999) AND
 endif()
 
 if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+    message(STATUS "Boost: Disable variadic templates")
+    message(STATUS "Boost: Do not use fenv.h from standard library")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_VARIADIC_TEMPLATES")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_CXX11_VARIADIC_TEMPLATES")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_FENV_H")
 elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
     # suppress boost error
     # 'no member named "impl" in "boost::detail::thread_move_t<boost::detail::nullary_function<void ()> >"'
     # in 'boost/thread/detail/nullary_function.hpp'
+    message(STATUS "Boost: Do not use C++11 smart pointers from standard library")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_CXX11_SMART_PTR")
 endif()
 
@@ -306,6 +310,7 @@ endif()
 if( ("${PMACC_CUDA_COMPILER}" STREQUAL "nvcc") AND
     (Boost_VERSION EQUAL 106400) AND
     (CUDA_VERSION VERSION_EQUAL 8.0) )
+    message(STATUS "Boost: Disable C++11 noexcept")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DBOOST_NO_CXX11_NOEXCEPT")
 endif()
 
diff --git a/src/libPMacc/examples/gameOfLife2D/CMakeLists.txt b/src/libPMacc/examples/gameOfLife2D/CMakeLists.txt
@@ -108,7 +108,7 @@ set(LIBS ${LIBS} ${Boost_LIBRARIES})
 ################################################################################
 
 # find PNGwriter installation
-find_package(PNGwriter 0.5.6 REQUIRED)
+find_package(PNGwriter 0.6.0 EXACT REQUIRED)
 
 if(PNGwriter_FOUND)
     include_directories(SYSTEM ${PNGwriter_INCLUDE_DIRS})
diff --git a/src/libPMacc/include/cuSTL/algorithm/kernel/detail/ForeachKernel.hpp b/src/libPMacc/include/cuSTL/algorithm/kernel/detail/ForeachKernel.hpp
@@ -21,6 +21,9 @@
 
 #pragma once
 
+#include <boost/preprocessor.hpp>
+
+
 namespace PMacc
 {
 namespace algorithm
diff --git a/src/libPMacc/include/dataManagement/DataConnector.hpp b/src/libPMacc/include/dataManagement/DataConnector.hpp
@@ -216,7 +216,7 @@ namespace PMacc
 
     private:
 
-        friend class detail::Environment;
+        friend struct detail::Environment;
 
         static DataConnector&
         getInstance()
diff --git a/src/libPMacc/include/eventSystem/Manager.hpp b/src/libPMacc/include/eventSystem/Manager.hpp
@@ -76,7 +76,7 @@ namespace PMacc
 
     private:
 
-        friend class detail::Environment;
+        friend struct detail::Environment;
 
         inline ITask* getPassiveITaskIfNotFinished(id_t taskId) const;
 
diff --git a/src/libPMacc/include/eventSystem/events/EventPool.hpp b/src/libPMacc/include/eventSystem/events/EventPool.hpp
@@ -96,7 +96,7 @@ namespace PMacc
 
     private:
 
-        friend class detail::Environment;
+        friend struct detail::Environment;
 
         static EventPool& getInstance( )
         {
diff --git a/src/libPMacc/include/eventSystem/streams/StreamController.hpp b/src/libPMacc/include/eventSystem/streams/StreamController.hpp
@@ -111,7 +111,7 @@ namespace PMacc
 
     private:
 
-        friend class detail::Environment;
+        friend struct detail::Environment;
 
         /**
          * Constructor.
diff --git a/src/libPMacc/include/eventSystem/tasks/Factory.hpp b/src/libPMacc/include/eventSystem/tasks/Factory.hpp
@@ -164,7 +164,7 @@ namespace PMacc
 
     private:
 
-        friend class detail::Environment;
+        friend struct detail::Environment;
 
         Factory() {};
 
diff --git a/src/libPMacc/include/eventSystem/transactions/TransactionManager.hpp b/src/libPMacc/include/eventSystem/transactions/TransactionManager.hpp
@@ -87,7 +87,7 @@ class TransactionManager
 
 private:
 
-    friend class detail::Environment;
+    friend struct detail::Environment;
 
     TransactionManager();
 
diff --git a/src/libPMacc/include/mappings/simulation/EnvironmentController.hpp b/src/libPMacc/include/mappings/simulation/EnvironmentController.hpp
@@ -64,7 +64,7 @@ class EnvironmentController
 
 private:
 
-    friend class detail::Environment;
+    friend struct detail::Environment;
 
     /*! Default constructor.
      */
diff --git a/src/libPMacc/include/math/vector/Vector.hpp b/src/libPMacc/include/math/vector/Vector.hpp
@@ -521,6 +521,15 @@ struct Vector<Type, 0 >
     {
         return false;
     }
+
+    HDINLINE
+    static Vector create(Type)
+    {
+        /* this method should never be actually called,
+         * it exists only for Visual Studio to handle pmacc::math::Size_t< 0 >
+         */
+        PMACC_CASSERT_MSG(Vector_dim_0_create_cannot_be_called, false);
+    }
 };
 
 template<typename Type, int dim, typename Accessor, typename Navigator>
diff --git a/src/libPMacc/include/nvidia/memory/MemoryInfo.hpp b/src/libPMacc/include/nvidia/memory/MemoryInfo.hpp
@@ -108,7 +108,7 @@ class MemoryInfo
 
 private:
 
-    friend class detail::Environment;
+    friend struct detail::Environment;
 
     static MemoryInfo& getInstance()
     {
diff --git a/src/libPMacc/include/particles/tasks/ParticleFactory.hpp b/src/libPMacc/include/particles/tasks/ParticleFactory.hpp
@@ -68,7 +68,7 @@ namespace PMacc
 
     private:
 
-        friend class detail::Environment;
+        friend struct detail::Environment;
 
         /**
          * returns the instance of this factory
diff --git a/src/libPMacc/include/pluginSystem/PluginConnector.hpp b/src/libPMacc/include/pluginSystem/PluginConnector.hpp
@@ -213,7 +213,7 @@ namespace PMacc
 
     private:
 
-        friend class detail::Environment;
+        friend struct detail::Environment;
 
         static PluginConnector& getInstance()
         {
diff --git a/src/libPMacc/include/simulationControl/SimulationDescription.hpp b/src/libPMacc/include/simulationControl/SimulationDescription.hpp
@@ -112,7 +112,7 @@ class SimulationDescription
 
 private:
 
-    friend class detail::Environment;
+    friend struct detail::Environment;
 
     static SimulationDescription& getInstance()
     {
diff --git a/src/picongpu/CMakeLists.txt b/src/picongpu/CMakeLists.txt
@@ -62,7 +62,7 @@ set(CMAKE_CXX_STANDARD 11)
 
 get_filename_component(SOURCE_DIR_ROOT ${PIConGPU_SOURCE_DIR}/../.. ABSOLUTE)
 string(FIND "${PIConGPU_BINARY_DIR}"
-            "${SOURCE_DIR_ROOT}" IN_SRC_POS)
+            "${SOURCE_DIR_ROOT}/" IN_SRC_POS)
 if(IN_SRC_POS GREATER -1)
   message(FATAL_ERROR
     "PICoNGPU requires an out of source build. "
@@ -272,7 +272,7 @@ endif()
 # find libSplash installation
 # prefer static libraries over shared ones (but do not force them)
 set(Splash_USE_STATIC_LIBS ON)
-find_package(Splash 1.6.0 COMPONENTS PARALLEL)
+find_package(Splash 1.6.0 EXACT COMPONENTS PARALLEL)
 
 if(Splash_FOUND)
     include_directories(SYSTEM ${Splash_INCLUDE_DIRS})
@@ -287,7 +287,7 @@ endif(Splash_FOUND)
 ################################################################################
 
 # find PNGwriter installation
-find_package(PNGwriter 0.5.6)
+find_package(PNGwriter 0.6.0 EXACT)
 
 if(PNGwriter_FOUND)
     include_directories(SYSTEM ${PNGwriter_INCLUDE_DIRS})
diff --git a/src/picongpu/include/fields/background/cellwiseOperation.hpp b/src/picongpu/include/fields/background/cellwiseOperation.hpp
@@ -52,16 +52,17 @@ namespace cellwiseOperation
             class FieldBox,
             class Mapping>
         DINLINE void
-        operator()( FieldBox field, T_OpFunctor opFunctor, T_ValFunctor valFunctor, const DataSpace<simDim> totalCellOffset,
+        operator()( FieldBox field, T_OpFunctor opFunctor, T_ValFunctor valFunctor, const DataSpace<simDim> totalDomainOffset,
             const uint32_t currentStep, Mapping mapper ) const
         {
             const DataSpace<simDim> block( mapper.getSuperCellIndex( DataSpace<simDim>( blockIdx ) ) );
             const DataSpace<simDim> blockCell = block * MappingDesc::SuperCellSize::toRT();
+            const DataSpace<simDim> guardCells = mapper.getGuardingSuperCells( ) * SuperCellSize::toRT( );
 
             const DataSpace<simDim> threadIndex( threadIdx );
 
             opFunctor( field( blockCell + threadIndex ),
-                       valFunctor( blockCell + threadIndex + totalCellOffset,
+                       valFunctor( blockCell + threadIndex + totalDomainOffset - guardCells,
                                    currentStep )
                      );
         }
@@ -98,25 +99,19 @@ namespace cellwiseOperation
                 return;
 
             const SubGrid<simDim>& subGrid = Environment<simDim>::get().SubGrid();
-            /** offset due to being the n-th GPU */
-            DataSpace<simDim> totalCellOffset(subGrid.getLocalDomain().offset);
+            // offset to the local domain relative to the origin of the global domain
+            DataSpace<simDim> totalDomainOffset(subGrid.getLocalDomain().offset);
             const uint32_t numSlides = MovingWindow::getInstance().getSlideCounter( currentStep );
 
             /** Assumption: all GPUs have the same number of cells in
              *              y direction for sliding window */
-            totalCellOffset.y() += numSlides * subGrid.getLocalDomain().size.y();
-            /* the first block will start with less offset if started in the GUARD */
-            if( T_Area & GUARD)
-                totalCellOffset -= m_cellDescription.getSuperCellSize() * m_cellDescription.getGuardingSuperCells();
-            /* if we run _only_ in the CORE we have to add the BORDER's offset */
-            else if( T_Area == CORE )
-                totalCellOffset += m_cellDescription.getSuperCellSize() * m_cellDescription.getBorderSuperCells();
+            totalDomainOffset.y( ) += numSlides * subGrid.getLocalDomain().size.y( );
 
             /* start kernel */
             AreaMapping<T_Area, MappingDesc> mapper(m_cellDescription);
             PMACC_KERNEL(KernelCellwiseOperation{})
                     (mapper.getGridDim(), SuperCellSize::toRT())
-                    (field->getDeviceDataBox(), opFunctor, valFunctor, totalCellOffset, currentStep, mapper);
+                    (field->getDeviceDataBox(), opFunctor, valFunctor, totalDomainOffset, currentStep, mapper);
         }
     };
 
diff --git a/src/picongpu/include/plugins/PhaseSpace/PhaseSpace.tpp b/src/picongpu/include/plugins/PhaseSpace/PhaseSpace.tpp
@@ -239,13 +239,16 @@ namespace picongpu
         const float_64 unit = UNIT_CHARGE / UNIT_VOLUME;
 
         /* (momentum) p range: unit is m_species * c
-         *   During the kernels we calculate with a typical MAKRO momentum range
-         *   to avoid over- / underflows. Now for the dump the meta information
+         *   During the kernels we calculate with a typical single/real
+         *   momentum range. Now for the dump the meta information of units
          *   on the p-axis should be scaled to represent single/real particles.
-         *   \see PhaseSpaceMulti::pluginLoad( ) */
-        float_64 pRange_unit = float_64( frame::getMass<typename Species::FrameType>() ) *
-                               float_64( SPEED_OF_LIGHT ) *
-                               UNIT_MASS * UNIT_SPEED;
+         *   \see PhaseSpaceMulti::pluginLoad( )
+         */
+        float_64 const pRange_unit =
+            float_64( frame::getMass<typename Species::FrameType>() ) *
+            float_64( SPEED_OF_LIGHT ) *
+            ( UNIT_MASS * float_64( particles::TYPICAL_NUM_PARTICLES_PER_MACROPARTICLE ) ) *
+            UNIT_SPEED;
 
         DumpHBuffer dumpHBuffer;
 
diff --git a/src/picongpu/include/plugins/PhaseSpace/PhaseSpaceFunctors.hpp b/src/picongpu/include/plugins/PhaseSpace/PhaseSpaceFunctors.hpp
@@ -98,7 +98,7 @@ namespace picongpu
             const float_PS particleChargeDensity =
               precisionCast<float_PS>( charge / CELL_VOLUME );
 
-            const float_X rel_bin = (mom_i - axis_p_range.first)
+            const float_X rel_bin = (mom_i / weighting - axis_p_range.first)
                                   / (axis_p_range.second - axis_p_range.first);
             int p_bin = int( rel_bin * float_X(num_pbins) );
 
diff --git a/src/picongpu/include/plugins/PhaseSpace/PhaseSpaceMulti.tpp b/src/picongpu/include/plugins/PhaseSpace/PhaseSpaceMulti.tpp
diff --git a/src/picongpu/include/plugins/adios/ADIOSWriter.hpp b/src/picongpu/include/plugins/adios/ADIOSWriter.hpp
diff --git a/src/picongpu/include/plugins/particleCalorimeter/ParticleCalorimeter.hpp b/src/picongpu/include/plugins/particleCalorimeter/ParticleCalorimeter.hpp
diff --git a/src/picongpu/include/simulationControl/MySimulation.hpp b/src/picongpu/include/simulationControl/MySimulation.hpp
diff --git a/src/picongpu/include/version.hpp b/src/picongpu/include/version.hpp
diff --git a/src/picongpu/submit/hypnos-hzdr/picongpu.profile.example b/src/picongpu/submit/hypnos-hzdr/picongpu.profile.example
diff --git a/src/tools/bin/tbg b/src/tools/bin/tbg
diff --git a/src/tools/png2gas/CMakeLists.txt b/src/tools/png2gas/CMakeLists.txt
diff --git a/src/tools/splash2txt/CMakeLists.txt b/src/tools/splash2txt/CMakeLists.txt

Original file line number	Diff line number	Diff line change
`@@ -21,6 +21,9 @@`
`21`	`21`
`22`	`22`	`#pragma once`
`23`	`23`
	`24`	`+#include <boost/preprocessor.hpp>`
	`25`	`+`
	`26`	`+`
`24`	`27`	`namespace PMacc`
`25`	`28`	`{`
`26`	`29`	`namespace algorithm`
Original file line number	Diff line number	Diff line change
`@@ -96,7 +96,7 @@ namespace PMacc`
`96`	`96`
`97`	`97`	`private:`
`98`	`98`
`99`		`- friend class detail::Environment;`
	`99`	`+ friend struct detail::Environment;`
`100`	`100`
`101`	`101`	`static EventPool& getInstance( )`
`102`	`102`	`{`