Merge pull request #206 from ComputationalRadiationPhysics/dev

Release 1.3.0: openPMD Types and h5py

Author: f-schmitt-zih

.travis.yml

@@ -32,8 +32,7 @@ script:
 # compile and run tests/
   - cmake -DWITH_MPI=$SPLASHMPI $SRC/tests
   - make
-
-after_script:
+# run tests
   - $SRC/tests/run_tests $BUILD
   - $SRC/tests/run_parallel_tests $BUILD
 
@@ -42,6 +41,7 @@ before_script:
   - lsb_release -a
   - echo "$SRC"
   - ls -hal $SRC
+  - ls -hal /usr/include
 # PPA providing hdf5 >= 1.8.6 and OpenMPI >= 1.5.1
 # -> remove legacy hdf5 and mpi packages/deps from travis
   - sudo apt-get remove -qq libhdf5* libopenmpi* openmpi-bin
@@ -58,4 +58,12 @@ before_script:
   - sudo apt-get install -qq -f libboost-program-options-dev
   - sudo apt-get -t o=LP-PPA-james-page-openmpi install -q -f $APTMPI
   - sudo apt-get -t o=LP-PPA-axel-huebl-libsplash install -q -f $APTHDF5
+  - sudo apt-get install python-numpy cython
+  - sudo -H pip install --upgrade pip
+#   numpy and cython should be already satisfied
+  - export HDF5_DIR=/usr
+  - export C_INCLUDE_PATH=/usr/lib/openmpi/include
+  - pip install --user h5py
+  - python -c "import numpy; print(numpy.version.version)"
+  - python -c "import h5py; print(h5py.version.version)"
   - mkdir -p $BUILD ~/lib

CHANGELOG.md

@@ -1,6 +1,53 @@
 Change Log for libSplash
 ================================================================
 
+Release 1.3.0
+-------------
+**Date:** 2015-11-12
+
+This release adds functionality for users to fulfill formatting for
+`openPMD`. Support for array attributes, strings/chars, bools and
+further `h5py` compatibility have been added. Additionally, read
+functionality has improved by new meta calls to determine type
+and size of a data set before reading.
+The internal format was increased to version 3.3
+
+**New Features**
+
+ - bool types are now h5py compatible #153 #198
+ - new interface `readMeta` in `DataCollector`s to determine type 
+   and size before reading #203
+ - new interfaces for `DataCollector`s `writeGlobalAttribute` to support
+   arrays via HDF5 simple data spaces (h5py compatible) #170 #171
+ - `splashVersion` and `splashFormat` are now written to `/header` #183
+ - header define `SPLASH_HDF5_VERSION` remembers HDF5 version of build #177
+ - `char`s, fixed and variable length `string` support added #167
+
+
+**Interface Changes**
+
+ - `ParallelDataCollector::writeGlobalAttribute` now writes to `/` instead of
+   `/custom` (`SerialDataCollector` unchanged) #182
+
+
+**Misc**
+
+ - term "iteration" is now consequently preferred over
+   "time step" #157 #187 #188 #204
+ - public includes do not throw on `-Wshadow` any more #201
+ - `/header/compression` attribute in new bool representation #199
+ - CMake:
+   - shared library detection refactored #192
+   - FindHDF5 shipped with version support (pre CMake 3.3.0) #176 #169
+ - doxygen project name updated #178
+ - `DataSpace` refactored: prefer `DSP_DIM_MAX` over magic numbers #175
+ - test scripts
+   - CI (travis) false-positive fixed #172
+   - output improved #166
+   - warn on missing dir argument #185
+ - `INSTALL.md` now in project's root directory #158
+
+
 Release 1.2.4
 -------------
 **Date:** 2015-01-25

CMakeLists.txt

@@ -1,5 +1,5 @@
  #
- # Copyright 2013-2014 Felix Schmitt, Axel Huebl
+ # Copyright 2013-2015 Felix Schmitt, Axel Huebl
  #
  # This file is part of libSplash. 
  # 
@@ -39,6 +39,9 @@ PROJECT(libSplash)
 SET(CMAKE_PREFIX_PATH "/usr/lib/x86_64-linux-gnu/" "$ENV{MPI_ROOT}"
                       "$ENV{HDF5_ROOT}")
 
+# own modules for find_packages
+set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/ ${CMAKE_MODULE_PATH})
+
 #-------------------------------------------------------------------------------
 
 # install prefix
@@ -70,18 +73,17 @@ MESSAGE(STATUS "Building libSplash version ${SPLASH_VERSION}")
 #-------------------------------------------------------------------------------
 
 # HDF5 is required package
-FIND_PACKAGE(HDF5 REQUIRED)
+FIND_PACKAGE(HDF5 1.8.6 REQUIRED)
 INCLUDE_DIRECTORIES(SYSTEM ${HDF5_INCLUDE_DIR})
 
-# check if static version of HDF5 is used
-#   CMake prefers .so/shared libraries                 
-#   if we find a static HDF5 lib in the ${HDF5_LIBRARIES}
-#   it means there is only a static version installed
-SET(HDF5_IS_STATIC ON)
-STRING(FIND "${HDF5_LIBRARIES}" "hdf5.a" HDF5_IS_STATIC_POS)
-IF(${HDF5_IS_STATIC_POS} EQUAL -1)
-    SET(HDF5_IS_STATIC OFF)
-ENDIF(${HDF5_IS_STATIC_POS} EQUAL -1)
+# check if shared version of HDF5 can be used
+#   CMake prefers .so/shared libraries over static ones
+SET(HDF5_HAS_SHARED ON)
+STRING(FIND "${HDF5_LIBRARIES}" "hdf5.so" HDF5_HAS_SHARED_POS)
+IF(${HDF5_HAS_SHARED_POS} EQUAL -1)
+    SET(HDF5_HAS_SHARED OFF)
+ENDIF()
+UNSET(HDF5_HAS_SHARED_POS)
 
 #-------------------------------------------------------------------------------
 
@@ -109,7 +111,7 @@ ENDIF(NOT SPLASH_RELEASE)
 SET(SPLASH_LIBS z ${HDF5_LIBRARIES})
 
 # serial or parallel version of libSplash
-SET(SPLASH_CLASSES logging DCAttribute DCDataSet DCGroup HandleMgr SerialDataCollector DomainCollector)
+SET(SPLASH_CLASSES logging DCAttribute DCDataSet DCGroup HandleMgr SerialDataCollector DomainCollector SDCHelper)
 IF(HDF5_IS_PARALLEL)
     #parallel version 
     MESSAGE(STATUS "Parallel HDF5 found. Building parallel version")
@@ -144,22 +146,22 @@ AUX_SOURCE_DIRECTORY("${CMAKE_CURRENT_SOURCE_DIR}/tools" TOOLS_SOURCES)
 #-------------------------------------------------------------------------------
 
 # build libsplash shared (if shared HDF5 is used)
-IF(HDF5_IS_STATIC)
+IF(NOT HDF5_HAS_SHARED)
     MESSAGE(WARNING "Skipping dynamic libSplash because HDF5 library is static")
-ELSE(HDF5_IS_STATIC)
+ELSE()
     ADD_LIBRARY(splash SHARED ${LIBRARY_SOURCES})
     TARGET_LINK_LIBRARIES(splash ${SPLASH_LIBS})
-ENDIF(HDF5_IS_STATIC)
+ENDIF()
 
 # build libsplash static
 ADD_LIBRARY(splash_static STATIC ${LIBRARY_SOURCES})
 SET_TARGET_PROPERTIES(splash_static PROPERTIES OUTPUT_NAME splash)
 TARGET_LINK_LIBRARIES (splash_static ${SPLASH_LIBS})
 
 # install libs
-IF(NOT HDF5_IS_STATIC)
+IF(HDF5_HAS_SHARED)
     INSTALL(TARGETS splash LIBRARY DESTINATION lib)
-ENDIF(NOT HDF5_IS_STATIC)
+ENDIF()
 
 INSTALL(TARGETS splash_static ARCHIVE DESTINATION lib)
 
@@ -169,8 +171,15 @@ INSTALL(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/src/include/."
   PATTERN ".svn" EXCLUDE
   PATTERN ".git" EXCLUDE
   PATTERN "splash_*.h" EXCLUDE
+  PATTERN "version.hpp" EXCLUDE
 )
 
+# version.hpp file with SPLASH_HDF5_VERSION set accordingly
+configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/src/include/splash/version.hpp
+                ${CMAKE_CURRENT_BINARY_DIR}/splash/version.hpp )
+INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/splash/version.hpp
+        DESTINATION include/splash)
+
 # install correct splash header file
 # (will be executed after the POST_BUILD copies of splash.h)
 INSTALL(FILES ${CMAKE_CURRENT_BINARY_DIR}/splash/splash.h
@@ -210,7 +219,11 @@ OPTION(WITH_TOOLS "enable splashtools" ON)
 IF(WITH_TOOLS)
     MESSAGE(STATUS "Building splashtools")
 
-    SET(TOOLS_LIBS ${TOOLS_LIBS} splash_static)
+    IF(HDF5_HAS_SHARED)
+        SET(TOOLS_LIBS ${TOOLS_LIBS} splash)
+    ELSE()
+        SET(TOOLS_LIBS ${TOOLS_LIBS} splash_static)
+    ENDIF()
     INCLUDE_DIRECTORIES(${CMAKE_CURRENT_BINARY_DIR})
 
     # MPI for tools

doc/INSTALL.md INSTALL.mddoc/INSTALL.md renamed to INSTALL.md

@@ -17,7 +17,8 @@ To use the CMakeLists.txt file which comes with the source code, you must have
 The splashtools and some tests also require an **MPI 2.2** compatible MPI library,
 e.g. **OpenMPI 1.5.1** or higher.
 
-Tests require the development version of the **CppUnit** library.
+Our *tests* require the development version of the **CppUnit** library and
+python support for `h5py` & `numpy`.
 
 
 Compiling

README.md

@@ -46,7 +46,7 @@ Licences can be found in [GPL](COPYING) or [LGPL](COPYING.LESSER), respectively.
 Install
 -------
 
-See our notes in [INSTALL.md](doc/INSTALL.md).
+See our notes in [INSTALL.md](INSTALL.md).
 
 
 Usage