Merge pull request ComputationalRadiationPhysics#2520 from ax3l/topic-libSplash170

psychocoderHPC · web-flow · commit 65457a88cdae · 2018-02-09T10:54:02.000+01:00
Splash: 1.7.0
diff --git a/.travis.yml b/.travis.yml
@@ -36,17 +36,11 @@ install:
       mkdir -p $SPACK_ROOT &&
       git clone --depth 50 https://github.com/spack/spack.git $SPACK_ROOT &&
       echo -e "config:""\n  build_jobs:"" 2" > $SPACK_ROOT/etc/spack/config.yaml;
-      echo -e "packages:""\n  cmake:"
-              "\n    paths:"
-              "\n      cmake@3.9.2$COMPILERSPEC arch=linux-ubuntu14.04-x86_64:"
-              " $(dirname $(which cmake))"
-              "\n    buildable:"" False" > $SPACK_ROOT/etc/spack/packages.yaml;
     fi
   - spack compiler add
   - travis_wait spack install
-      cmake@3.9.2
+      cmake@3.10.0~openssl~ncurses
       $COMPILERSPEC
-      # ~openssl~ncurses
   - travis_wait spack install
       boost@1.62.0~date_time~graph~iostreams~locale~log~random~thread~timer~wave
       $COMPILERSPEC
diff --git a/INSTALL.rst b/INSTALL.rst
@@ -48,7 +48,7 @@ gcc
 
 CMake
 """""
-- 3.7.0 or higher
+- 3.10.0 or higher
 - *Debian/Ubuntu:* ``sudo apt-get install cmake file cmake-curses-gui``
 - *Arch Linux:* ``sudo pacman --sync cmake``
 - *Spack:* ``spack install cmake``
@@ -171,12 +171,12 @@ pngwriter
 
   - *environment:* (assumes install from source in ``$HOME/lib/pngwriter``)
 
-    - ``export PNGWRITER_ROOT=$HOME/lib/pngwriter``
-    - ``export LD_LIBRARY_PATH=$PNGWRITER_ROOT/lib:$LD_LIBRARY_PATH``
+    - ``export CMAKE_PREFIX_PATH=$HOME/lib/pngwriter:$CMAKE_PREFIX_PATH``
+    - ``export LD_LIBRARY_PATH=$HOME/lib/pngwriter/lib:$LD_LIBRARY_PATH``
 
 libSplash
 """""""""
-- 1.6.0+ (requires *HDF5*, *boost program-options*)
+- 1.7.0+ (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``
@@ -185,13 +185,13 @@ libSplash
   - ``mkdir -p ~/src ~/build ~/lib``
   - ``git clone https://github.com/ComputationalRadiationPhysics/libSplash.git ~/src/splash/``
   - ``cd ~/build``
-  - ``cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/splash ~/src/splash``
+  - ``cmake -DCMAKE_INSTALL_PREFIX=$HOME/lib/splash -DSplash_USE_MPI=ON -DSplash_USE_PARALLE=ON ~/src/splash``
   - ``make install``
 
 - *environment:* (assumes install from source in ``$HOME/lib/splash``)
 
-  - ``export SPLASH_ROOT=$HOME/lib/splash``
-  - ``export LD_LIBRARY_PATH=$SPLASH_ROOT/lib:$LD_LIBRARY_PATH``
+  - ``export CMAKE_PREFIX_PATH=$HOME/lib/splash:$CMAKE_PREFIX_PATH``
+  - ``export LD_LIBRARY_PATH=$HOME/lib/splash/lib:$LD_LIBRARY_PATH``
 
 HDF5
 """"
diff --git a/buildsystem/CompileSuite/autoTests/new_commits.sh b/buildsystem/CompileSuite/autoTests/new_commits.sh
@@ -94,7 +94,7 @@ touch "$thisDir"runGuard
             #export PIC_COMPILE_SUITE_CMAKE="-DPIC_ENABLE_PNG=OFF -DALPAKA_CUDA_ARCH=35"
             export PIC_BACKEND="cuda"
             . /etc/profile
-            module load gcc/4.9.4 boost/1.62.0 cmake/3.7.0 cuda/8.0.44 openmpi/1.10.4
+            module load gcc/4.9.4 boost/1.62.0 cmake/3.10.0 cuda/8.0.44 openmpi/1.10.4
             module load libSplash/1.6.0 adios/1.10.0
             module load pngwriter/0.7.0 rivlib/1.0.2
             module load libjpeg-turbo/1.5.1 icet/2.1.1 jansson/2.9 isaac/1.1.0
diff --git a/etc/picongpu/draco-mpcdf/picongpu.profile.example b/etc/picongpu/draco-mpcdf/picongpu.profile.example
@@ -19,7 +19,7 @@ module purge
 
 module load git/2.14
 module load gcc/6.3
-module load cmake/3.7
+module load cmake/3.10.1
 module load boost/gcc/1.64
 module load impi/2017.3
 module load hdf5-mpi/gcc/1.8.18
@@ -28,7 +28,7 @@ module load hdf5-mpi/gcc/1.8.18
 #
 # needs to be compiled by the user
 export PNGWRITER_ROOT=$HOME/lib/pngwriter-0.7.0
-export SPLASH_ROOT=$HOME/lib/splash-1.6.0
+export SPLASH_ROOT=$HOME/lib/splash-1.7.0
 
 export LD_LIBRARY_PATH=$PNGWRITER_ROOT/lib:$LD_LIBRARY_PATH
 export LD_LIBRARY_PATH=$SPLASH_ROOT/lib:$LD_LIBRARY_PATH
diff --git a/etc/picongpu/hydra-hzdr/default_picongpu.profile.example b/etc/picongpu/hydra-hzdr/default_picongpu.profile.example
@@ -22,14 +22,14 @@ then
 
         # Core Dependencies
         module load gcc/5.3.0
-        module load cmake/3.7.2
+        module load cmake/3.10.1
         module load boost/1.62.0
         module load openmpi/1.8.6
         module load numactl
 
         # Plugins (optional)
         module load pngwriter/0.7.0
-        module load hdf5-parallel/1.8.15 libsplash/1.6.0
+        module load hdf5-parallel/1.8.15 libsplash/1.7.0
 
         # either use libSplash or ADIOS for file I/O
         #module load adios/1.10.0
diff --git a/etc/picongpu/hypnos-hzdr/k20_picongpu.profile.example b/etc/picongpu/hypnos-hzdr/k20_picongpu.profile.example
@@ -22,14 +22,14 @@ then
 
         # Core Dependencies
         module load gcc/4.9.2
-        module load cmake/3.7.2
+        module load cmake/3.10.1
         module load boost/1.62.0
         module load cuda/8.0
         module load openmpi/2.1.2.kepler.cuda80
 
         # Plugins (optional)
         module load pngwriter/0.7.0
-        module load hdf5-parallel/1.8.20 libsplash/1.6.0
+        module load hdf5-parallel/1.8.20 libsplash/1.7.0
 
         # either use libSplash or ADIOS for file I/O
         #module load adios/1.10.0
diff --git a/etc/picongpu/hypnos-hzdr/k80_picongpu.profile.example b/etc/picongpu/hypnos-hzdr/k80_picongpu.profile.example
@@ -22,14 +22,14 @@ then
 
         # Core Dependencies
         module load gcc/4.9.2
-        module load cmake/3.7.2
+        module load cmake/3.10.1
         module load boost/1.62.0
         module load cuda/8.0
         module load openmpi/2.1.2.kepler.cuda80
 
         # Plugins (optional)
         module load pngwriter/0.7.0
-        module load hdf5-parallel/1.8.20 libsplash/1.6.0
+        module load hdf5-parallel/1.8.20 libsplash/1.7.0
 
         # either use libSplash or ADIOS for file I/O
         #module load adios/1.10.0
diff --git a/etc/picongpu/hypnos-hzdr/laser_picongpu.profile.example b/etc/picongpu/hypnos-hzdr/laser_picongpu.profile.example
@@ -22,14 +22,14 @@ then
 
         # Core Dependencies
         module load gcc/4.9.2
-        module load cmake/3.7.2
+        module load cmake/3.10.1
         module load boost/1.62.0
         module load openmpi/1.8.6
         module load numactl
 
         # Plugins (optional)
         module load pngwriter/0.7.0
-        module load hdf5-parallel/1.8.15 libsplash/1.6.0
+        module load hdf5-parallel/1.8.15 libsplash/1.7.0
 
         # either use libSplash or ADIOS for file I/O
         #module load adios/1.10.0
diff --git a/etc/picongpu/pizdaint-cscs/picongpu.profile.example b/etc/picongpu/pizdaint-cscs/picongpu.profile.example
@@ -44,7 +44,7 @@ export PNG_ROOT=$SCRATCH/lib/libpng-1.6.34
 export BLOSC_ROOT=$SCRATCH/lib/blosc-1.12.1
 export PNGWRITER_ROOT=$SCRATCH/lib/pngwriter-0.7.0
 export ADIOS_ROOT=$SCRATCH/lib/adios-1.13.0
-export SPLASH_ROOT=$SCRATCH/lib/splash-1.6.0
+export SPLASH_ROOT=$SCRATCH/lib/splash-1.7.0
 
 export LD_LIBRARY_PATH=$CMAKE_ROOT/lib:$LD_LIBRARY_PATH
 export LD_LIBRARY_PATH=$BOOST_ROOT/lib:$LD_LIBRARY_PATH
diff --git a/etc/picongpu/taurus-tud/k20x_picongpu.profile.example b/etc/picongpu/taurus-tud/k20x_picongpu.profile.example
@@ -17,7 +17,7 @@ export MY_NAME="$(whoami) <$MY_MAIL>"
 #
 module purge
 module load oscar-modules
-module load cmake/3.9.0
+module load cmake/3.10.1
 module load git
 module load cuda/8.0.61 # gcc <= 5, intel 15-16
 module load bullxmpi
diff --git a/etc/picongpu/taurus-tud/k80_picongpu.profile.example b/etc/picongpu/taurus-tud/k80_picongpu.profile.example
@@ -17,7 +17,7 @@ export MY_NAME="$(whoami) <$MY_MAIL>"
 #
 module purge
 module load oscar-modules
-module load cmake/3.9.0
+module load cmake/3.10.1
 module load git
 module load cuda/8.0.61 # gcc <= 5, intel 15-16
 module load bullxmpi
diff --git a/etc/picongpu/taurus-tud/knl_picongpu.profile.example b/etc/picongpu/taurus-tud/knl_picongpu.profile.example
@@ -16,7 +16,7 @@ export MY_NAME="$(whoami) <$MY_MAIL>"
 # General modules #############################################################
 #
 module purge
-module load cmake/3.9.0
+module load cmake/3.10.1
 module load git
 module load intelmpi/2017.2.174
 
diff --git a/etc/picongpu/titan-ornl/picongpu.profile.example b/etc/picongpu/titan-ornl/picongpu.profile.example
@@ -37,7 +37,7 @@ export FC=$(which ftn)
 
 # required tools and libs
 module load git
-module load cmake3/3.9.0
+module load cmake3/3.10.0  # missing
 module load cudatoolkit  # 7.5.18
 # might fail to link with missing symbols:
 #   C++11 module rebuild pending [CCS #366279]
diff --git a/include/mpiInfo/CMakeLists.txt b/include/mpiInfo/CMakeLists.txt
@@ -22,7 +22,7 @@
 # Required cmake version
 ################################################################################
 
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 
 
 ################################################################################
diff --git a/include/picongpu/CMakeLists.txt b/include/picongpu/CMakeLists.txt
@@ -22,7 +22,7 @@
 # Required cmake version
 ################################################################################
 
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 
 
 ################################################################################
@@ -279,17 +279,16 @@ endif()
 # libSplash (+ hdf5 due to required headers)
 ################################################################################
 
-# 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 1.7.0 CONFIG COMPONENTS PARALLEL)
 
-if(Splash_FOUND)
-    include_directories(SYSTEM ${Splash_INCLUDE_DIRS})
-    list(APPEND Splash_DEFINITIONS "-DENABLE_HDF5=1")
-    add_definitions(${Splash_DEFINITIONS})
-    set(LIBS ${LIBS} ${Splash_LIBRARIES})
-endif(Splash_FOUND)
+if(TARGET Splash::Splash)
+    add_definitions(-DENABLE_HDF5=1)
+    set(LIBS ${LIBS} Splash::Splash)
+    message(STATUS "Found Splash: ${Splash_DIR}")
+else()
+    message(STATUS "Could NOT find Splash - "
+                   "set Splash_DIR or check your CMAKE_PREFIX_PATH")
+endif()
 
 
 ################################################################################
@@ -302,6 +301,10 @@ find_package(PNGwriter 0.7.0 CONFIG)
 if(PNGwriter_FOUND)
     set(LIBS ${LIBS} PNGwriter::PNGwriter)
     add_definitions(-DPIC_ENABLE_PNG=1)
+    message(STATUS "Found PNGwriter: ${PNGwriter_DIR}")
+else()
+    message(STATUS "Could NOT find PNGwriter - "
+                   "set PNGwriter_DIR or check your CMAKE_PREFIX_PATH")
 endif(PNGwriter_FOUND)
 
 
diff --git a/include/picongpu/plugins/hdf5/HDF5Writer.hpp b/include/picongpu/plugins/hdf5/HDF5Writer.hpp
@@ -448,7 +448,7 @@ class HDF5Writer :
 
         /* load number of slides to initialize MovingWindow */
         uint32_t slides = 0;
-        mThreadParams.dataCollector->readAttribute(restartStep, nullptr, "sim_slides", &slides);
+        mThreadParams.dataCollector->readAttributeInfo(restartStep, nullptr, "sim_slides").read(&slides, sizeof(slides));
 
         /* apply slides to set gpus to last/written configuration */
         log<picLog::INPUT_OUTPUT > ("HDF5 setting slide count for moving window to %1%") % slides;
diff --git a/include/picongpu/plugins/hdf5/NDScalars.hpp b/include/picongpu/plugins/hdf5/NDScalars.hpp
@@ -120,7 +120,7 @@ struct ReadNDScalars
         if(!attrName.empty())
         {
             log<picLog::INPUT_OUTPUT>("HDF5: read attribute %1% for scalars: %2%") % attrName % name;
-            params.dataCollector->readAttribute(params.currentStep, name.c_str(), attrName.c_str(), attribute);
+            params.dataCollector->readAttributeInfo(params.currentStep, name.c_str(), attrName.c_str()).read(attribute, sizeof(T_Attribute));
             log<picLog::INPUT_OUTPUT>("HDF5: attribute %1% = %2%") % attrName % *attribute;
         }
     }
diff --git a/include/pmacc/CMakeLists.txt b/include/pmacc/CMakeLists.txt
@@ -24,7 +24,7 @@
 # PMacc tests
 ################################################################################
 
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 project(PMaccTest)
 
 # set helper pathes to find libraries and packages
diff --git a/include/pmacc/PMaccConfig.cmake b/include/pmacc/PMaccConfig.cmake
@@ -29,7 +29,7 @@
 ###############################################################################
 # PMacc
 ###############################################################################
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 
 # set helper pathes to find libraries and packages
 # Add specific hints
diff --git a/include/pmacc/test/random/CMakeLists.txt b/include/pmacc/test/random/CMakeLists.txt
@@ -19,7 +19,7 @@
 # If not, see <http://www.gnu.org/licenses/>.
 #
 
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 project("TestRandomGenerators")
 
 set(CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/../..")
diff --git a/share/pmacc/examples/gameOfLife2D/CMakeLists.txt b/share/pmacc/examples/gameOfLife2D/CMakeLists.txt
@@ -23,7 +23,7 @@
 # Required cmake version
 ################################################################################
 
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 
 
 ################################################################################
diff --git a/src/tools/png2gas/CMakeLists.txt b/src/tools/png2gas/CMakeLists.txt
@@ -22,7 +22,7 @@
 # Required cmake version
 ################################################################################
 
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 
 
 ################################################################################
@@ -96,16 +96,10 @@ 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 REQUIRED COMPONENTS PARALLEL)
+find_package(Splash 1.7.0 REQUIRED CONFIG COMPONENTS PARALLEL)
 
-if(Splash_FOUND)
-    include_directories(SYSTEM ${Splash_INCLUDE_DIRS})
-    list(APPEND Splash_DEFINITIONS "-DENABLE_HDF5=1")
-    add_definitions(${Splash_DEFINITIONS})
-    set(LIBS ${LIBS} ${Splash_LIBRARIES})
-endif(Splash_FOUND)
+add_definitions(-DENABLE_HDF5=1)
+message(STATUS "Found Splash: ${Splash_DIR}")
 
 
 ################################################################################
@@ -115,9 +109,7 @@ endif(Splash_FOUND)
 # find PNGwriter installation
 find_package(PNGwriter 0.7.0 REQUIRED CONFIG)
 
-if(PNGwriter_FOUND)
-    set(LIBS ${LIBS} PNGwriter::PNGwriter)
-endif(PNGwriter_FOUND)
+set(LIBS ${LIBS} PNGwriter::PNGwriter)
 
 
 ################################################################################
diff --git a/src/tools/splash2txt/CMakeLists.txt b/src/tools/splash2txt/CMakeLists.txt
@@ -1,4 +1,3 @@
-#
 # Copyright 2013-2018 Felix Schmitt, Axel Huebl, Rene Widera
 #
 # This file is part of splash2txt.
@@ -23,7 +22,7 @@
 # Required cmake version
 ################################################################################
 
-cmake_minimum_required(VERSION 3.7.0)
+cmake_minimum_required(VERSION 3.10.0)
 
 
 ################################################################################
@@ -100,17 +99,10 @@ endif(MPI_CXX_FOUND)
 ################################################################################
 
 # 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 REQUIRED COMPONENTS PARALLEL)
+find_package(Splash 1.7.0 REQUIRED CONFIG COMPONENTS PARALLEL)
 
-if(Splash_FOUND)
-    include_directories(SYSTEM ${Splash_INCLUDE_DIRS})
-    list(APPEND Splash_DEFINITIONS "-DENABLE_HDF5=1")
-    add_definitions(${Splash_DEFINITIONS})
-    message(STATUS "libSplash compiler definitions: ${Splash_DEFINITIONS}")
-    set(LIBS ${LIBS} ${Splash_LIBRARIES})
-endif(Splash_FOUND)
+add_definitions(-DENABLE_HDF5=1)
+message(STATUS "Found Splash: ${Splash_DIR}")
 
 
 ################################################################################
@@ -148,9 +140,7 @@ endif()
 
 set(SRCFILES "splash2txt.cpp")
 
-if(Splash_FOUND)
-    list(APPEND SRCFILES "tools_splash_parallel.cpp")
-endif(Splash_FOUND)
+list(APPEND SRCFILES "tools_splash_parallel.cpp")
 if(ADIOS_FOUND)
     list(APPEND SRCFILES "tools_adios_parallel.cpp")
 endif(ADIOS_FOUND)
diff --git a/src/tools/splash2txt/tools_splash_parallel.cpp b/src/tools/splash2txt/tools_splash_parallel.cpp
diff --git a/thirdParty/cmake-modules/FindSplash.cmake b/thirdParty/cmake-modules/FindSplash.cmake

Original file line number	Diff line number	Diff line change
`@@ -17,7 +17,7 @@ export MY_NAME="$(whoami) <$MY_MAIL>"`
`17`	`17`	`#`
`18`	`18`	`module purge`
`19`	`19`	`module load oscar-modules`
`20`		`-module load cmake/3.9.0`
	`20`	`+module load cmake/3.10.1`
`21`	`21`	`module load git`
`22`	`22`	`module load cuda/8.0.61 # gcc <= 5, intel 15-16`
`23`	`23`	`module load bullxmpi`