diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
new file mode 100644
index 0000000000000000000000000000000000000000..a70b45abe2f7bd9b20e4e347f42d811721b98c05
--- /dev/null
+++ b/.gitlab-ci.yml
@@ -0,0 +1,59 @@
+centos_build:
+ stage: build
+ tags:
+ - centos
+ artifacts:
+ paths:
+ - ./openfpm_io/build/src/io
+ - ./openfpm_io/test_data
+ script:
+ - ./build.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
+
+centos_run:
+ stage: test
+ tags:
+ - centos
+ dependencies:
+ - centos_build
+ script:
+ - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
+
+mac_build:
+ stage: build
+ tags:
+ - mac
+ artifacts:
+ paths:
+ - ./openfpm_io/build/src/io
+ - ./openfpm_io/test_data
+ script:
+ - ./build.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
+
+mac_run:
+ stage: test
+ tags:
+ - mac
+ dependencies:
+ - mac_build
+ script:
+ - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
+
+ubuntu_build:
+ stage: build
+ tags:
+ - ubuntu
+ artifacts:
+ paths:
+ - ./openfpm_io/build/src/io
+ - ./openfpm_io/test_data
+ script:
+ - ./build.sh $CI_PROJECT_DIR $CI_RUNNER_EXECUTABLE_TAGS NO $CI_COMMIT_REF_NAME
+
+ubuntu_run:
+ stage: test
+ tags:
+ - ubuntu
+ dependencies:
+ - ubuntu_build
+ script:
+ - ./run.sh $CI_PROJECT_DIR $CI_RUNNER_TAGS NO $CI_COMMIT_REF_NAME
diff --git a/CMakeLists.txt b/CMakeLists.txt
index ee92db08f5acf185f18eddde6ff2d44d2cbdf901..d2530cc7992bbdba69149f6d619e3fb5e80ed9b0 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,9 +1,16 @@
cmake_minimum_required(VERSION 3.8 FATAL_ERROR)
project(openfpm_pdata LANGUAGES C CXX)
+if (POLICY CMP0074)
+ cmake_policy(SET CMP0074 OLD)
+endif ()
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR}/cmake_modules/)
+if (POLICY CMP0074)
+ cmake_policy(SET CMP0074 NEW)
+endif()
+
set(BOOST_INCLUDE ${Boost_INCLUDE_DIR} CACHE PATH "Include directory for BOOST")
set(HDF5_ROOT CACHE PATH "HDF5 root path")
set(SE_CLASS1 CACHE BOOL "Activate compilation with SE_CLASS1")
@@ -11,6 +18,9 @@ set(SE_CLASS2 CACHE BOOL "Activate compilation with SE_CLASS2")
set(SE_CLASS3 CACHE BOOL "Activate compilation with SE_CLASS3")
set(ENV{HDF5_ROOT} ${HDF5_ROOT})
set(OPENFPM_PDATA_DIR CACHE PATH "OpenFPM_pdata dirs")
+set(PETSC_ROOT CACHE PATH "If compiling with linear algebra indicate the PETSC root directory")
+set(ENV{PETSC_DIR} ${PETSC_ROOT})
+
set (CMAKE_CXX_STANDARD 11)
set (CMAKE_CUDA_STANDARD 11)
@@ -25,12 +35,26 @@ set(HDF5_PREFER_PARALLEL TRUE)
if(ENABLE_GPU)
enable_language(CUDA)
find_package(CUDA)
+
+ if (CUDA_VERSION_MAJOR EQUAL 9 AND CUDA_VERSION_MINOR EQUAL 2)
+ message("CUDA is compatible")
+ set(WARNING_SUPPRESSION_AND_OPTION_NVCC -Xcudafe "--display_error_number --diag_suppress=611 --diag_suppress=2885 --diag_suppress=2886 --diag_suppress=2887 --diag_suppress=2888 --diag_suppress=186 --diag_suppress=111 " --expt-extended-lambda)
+ elseif ( CUDA_VERSION_MAJOR EQUAL 10 AND CUDA_VERSION_MINOR EQUAL 1 )
+ message("CUDA is compatible")
+ set(WARNING_SUPPRESSION_AND_OPTION_NVCC -Xcudafe "--display_error_number --diag_suppress=2915 --diag_suppress=2912 --diag_suppress=2913 --diag_suppress=111 --diag_suppress=186 --diag_suppress=611 " --expt-extended-lambda)
+ elseif ( CUDA_VERSION_MAJOR EQUAL 10 AND CUDA_VERSION_MINOR EQUAL 2 )
+ message("CUDA is compatible")
+ set(WARNING_SUPPRESSION_AND_OPTION_NVCC -Xcudafe "--display_error_number --diag_suppress=2977 --diag_suppress=2976 --diag_suppress=2979 --diag_suppress=186" --expt-extended-lambda)
+ else()
+ message(FATAL_ERROR "CUDA is incompatible, version 9.2 10.1 and 10.2 is only supported")
+ endif()
endif()
find_package(Boost 1.66.0 REQUIRED COMPONENTS unit_test_framework iostreams program_options)
find_package(MPI REQUIRED)
find_package(HDF5 REQUIRED)
-find_package(TinyObjLoader )
+find_package(TinyObjLoader)
+find_package(PETSc)
if(CUDA_FOUND)
set(OPENFPM_INIT_FILE "initialize/initialize_wrapper_cuda.cu")
@@ -62,6 +86,10 @@ else()
message( FATAL_ERROR "MPI is required in order to install OpenFPM" )
endif()
+if(PETSC_FOUND)
+ set(DEFINE_HAVE_PETSC "#define HAVE_PETSC")
+endif()
+
if (Boost_FOUND)
set(DEFINE_HAVE_BOOST "#define HAVE_BOOST")
set(DEFINE_HAVE_BOOST_IOSTREAMS "#define HAVE_BOOST_IOSTREAMS")
diff --git a/build.sh b/build.sh
index cc7256a86c889ffe07a5fad66cef3cc8f9c262ca..b2e14c5a9dea7c1153ace40a724e90fcd9e321bf 100755
--- a/build.sh
+++ b/build.sh
@@ -19,13 +19,19 @@ mv /tmp/openfpm_io openfpm_io
git clone git@git.mpi-cbg.de:openfpm/openfpm_devices.git openfpm_devices
cd openfpm_devices
+git checkout master
cd ..
git clone git@git.mpi-cbg.de:openfpm/openfpm_data.git openfpm_data
cd openfpm_data
+git checkout master
cd ..
git clone git@git.mpi-cbg.de:openfpm/openfpm_pdata.git openfpm_pdata
+cd openfpm_pdata
+git checkout master
+cd ..
git clone git@git.mpi-cbg.de:openfpm/openfpm_vcluster.git openfpm_vcluster
cd openfpm_vcluster
+git checkout master
cd ..
cd "$1/openfpm_io"
diff --git a/cmake_modules/CorrectWindowsPaths.cmake b/cmake_modules/CorrectWindowsPaths.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..09bcdd67dcd04fd001d2b7acbd904b5014ebe42b
--- /dev/null
+++ b/cmake_modules/CorrectWindowsPaths.cmake
@@ -0,0 +1,14 @@
+# CorrectWindowsPaths - this module defines one macro
+#
+# CONVERT_CYGWIN_PATH( PATH )
+# This uses the command cygpath (provided by cygwin) to convert
+# unix-style paths into paths useable by cmake on windows
+
+macro (CONVERT_CYGWIN_PATH _path)
+ if (WIN32)
+ EXECUTE_PROCESS(COMMAND cygpath.exe -m ${${_path}}
+ OUTPUT_VARIABLE ${_path})
+ string (STRIP ${${_path}} ${_path})
+ endif (WIN32)
+endmacro (CONVERT_CYGWIN_PATH)
+
diff --git a/cmake_modules/FindPETSc.cmake b/cmake_modules/FindPETSc.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..f8ea15b67fbb5a237169411fe37fa5227e6b7aee
--- /dev/null
+++ b/cmake_modules/FindPETSc.cmake
@@ -0,0 +1,349 @@
+# - Try to find PETSc
+# Once done this will define
+#
+# PETSC_FOUND - system has PETSc
+# PETSC_INCLUDES - the PETSc include directories
+# PETSC_LIBRARIES - Link these to use PETSc
+# PETSC_COMPILER - Compiler used by PETSc, helpful to find a compatible MPI
+# PETSC_DEFINITIONS - Compiler switches for using PETSc
+# PETSC_MPIEXEC - Executable for running MPI programs
+# PETSC_VERSION - Version string (MAJOR.MINOR.SUBMINOR)
+#
+# Usage:
+# find_package(PETSc COMPONENTS CXX) - required if build --with-clanguage=C++ --with-c-support=0
+# find_package(PETSc COMPONENTS C) - standard behavior of checking build using a C compiler
+# find_package(PETSc) - same as above
+#
+# Setting these changes the behavior of the search
+# PETSC_DIR - directory in which PETSc resides
+# PETSC_ARCH - build architecture
+#
+# Redistribution and use is allowed according to the terms of the BSD license.
+# For details see the accompanying COPYING-CMAKE-SCRIPTS file.
+#
+
+cmake_policy(VERSION 3.3)
+
+set(PETSC_VALID_COMPONENTS
+ C
+ CXX)
+
+if(NOT PETSc_FIND_COMPONENTS)
+ get_property (_enabled_langs GLOBAL PROPERTY ENABLED_LANGUAGES)
+ if ("C" IN_LIST _enabled_langs)
+ set(PETSC_LANGUAGE_BINDINGS "C")
+ else ()
+ set(PETSC_LANGUAGE_BINDINGS "CXX")
+ endif ()
+else()
+ # Right now, this is designed for compatability with the --with-clanguage option, so
+ # only allow one item in the components list.
+ list(LENGTH ${PETSc_FIND_COMPONENTS} components_length)
+ if(${components_length} GREATER 1)
+ message(FATAL_ERROR "Only one component for PETSc is allowed to be specified")
+ endif()
+ # This is a stub for allowing multiple components should that time ever come. Perhaps
+ # to also test Fortran bindings?
+ foreach(component ${PETSc_FIND_COMPONENTS})
+ list(FIND PETSC_VALID_COMPONENTS ${component} component_location)
+ if(${component_location} EQUAL -1)
+ message(FATAL_ERROR "\"${component}\" is not a valid PETSc component.")
+ else()
+ list(APPEND PETSC_LANGUAGE_BINDINGS ${component})
+ endif()
+ endforeach()
+endif()
+
+function (petsc_get_version)
+ if (EXISTS "${PETSC_DIR}/include/petscversion.h")
+ file (STRINGS "${PETSC_DIR}/include/petscversion.h" vstrings REGEX "#define PETSC_VERSION_(RELEASE|MAJOR|MINOR|SUBMINOR|PATCH) ")
+ foreach (line ${vstrings})
+ string (REGEX REPLACE " +" ";" fields ${line}) # break line into three fields (the first is always "#define")
+ list (GET fields 1 var)
+ list (GET fields 2 val)
+ set (${var} ${val} PARENT_SCOPE)
+ set (${var} ${val}) # Also in local scope so we have access below
+ endforeach ()
+ if (PETSC_VERSION_RELEASE)
+ if ($(PETSC_VERSION_PATCH) GREATER 0)
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}p${PETSC_VERSION_PATCH}" CACHE INTERNAL "PETSc version")
+ else ()
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}" CACHE INTERNAL "PETSc version")
+ endif ()
+ else ()
+ # make dev version compare higher than any patch level of a released version
+ set (PETSC_VERSION "${PETSC_VERSION_MAJOR}.${PETSC_VERSION_MINOR}.${PETSC_VERSION_SUBMINOR}.99" CACHE INTERNAL "PETSc version")
+ endif ()
+ else ()
+ message (SEND_ERROR "PETSC_DIR can not be used, ${PETSC_DIR}/include/petscversion.h does not exist")
+ endif ()
+endfunction ()
+
+# Debian uses versioned paths e.g /usr/lib/petscdir/3.5/
+file (GLOB DEB_PATHS "/usr/lib/petscdir/*")
+
+find_path (PETSC_DIR include/petsc.h
+ HINTS ENV PETSC_DIR
+ PATHS
+ /usr/lib/petsc
+ # Debian paths
+ ${DEB_PATHS}
+ # Arch Linux path
+ /opt/petsc/linux-c-opt
+ # MacPorts path
+ /opt/local/lib/petsc
+ $ENV{HOME}/petsc
+ DOC "PETSc Directory")
+
+find_program (MAKE_EXECUTABLE NAMES make gmake)
+
+if (PETSC_DIR AND NOT PETSC_ARCH)
+ set (_petsc_arches
+ $ENV{PETSC_ARCH} # If set, use environment variable first
+ linux-gnu-c-debug linux-gnu-c-opt # Debian defaults
+ x86_64-unknown-linux-gnu i386-unknown-linux-gnu)
+ set (petscconf "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+ foreach (arch ${_petsc_arches})
+ if (NOT PETSC_ARCH)
+ find_path (petscconf petscconf.h
+ HINTS ${PETSC_DIR}
+ PATH_SUFFIXES ${arch}/include bmake/${arch}
+ NO_DEFAULT_PATH)
+ if (petscconf)
+ set (PETSC_ARCH "${arch}" CACHE STRING "PETSc build architecture")
+ endif (petscconf)
+ endif (NOT PETSC_ARCH)
+ endforeach (arch)
+ set (petscconf "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+endif (PETSC_DIR AND NOT PETSC_ARCH)
+
+set (petsc_slaves LIBRARIES_SYS LIBRARIES_VEC LIBRARIES_MAT LIBRARIES_DM LIBRARIES_KSP LIBRARIES_SNES LIBRARIES_TS
+ INCLUDE_DIR INCLUDE_CONF)
+include (FindPackageMultipass)
+find_package_multipass (PETSc petsc_config_current
+ STATES DIR ARCH
+ DEPENDENTS INCLUDES LIBRARIES COMPILER MPIEXEC ${petsc_slaves})
+
+# Determine whether the PETSc layout is old-style (through 2.3.3) or
+# new-style (>= 3.0.0)
+if (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/petscvariables") # > 3.5
+ set (petsc_conf_rules "${PETSC_DIR}/lib/petsc/conf/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/lib/petsc/conf/variables")
+elseif (EXISTS "${PETSC_DIR}/${PETSC_ARCH}/include/petscconf.h") # > 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/conf/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/conf/variables")
+elseif (EXISTS "${PETSC_DIR}/bmake/${PETSC_ARCH}/petscconf.h") # <= 2.3.3
+ set (petsc_conf_rules "${PETSC_DIR}/bmake/common/rules")
+ set (petsc_conf_variables "${PETSC_DIR}/bmake/common/variables")
+elseif (PETSC_DIR)
+ message (SEND_ERROR "The pair PETSC_DIR=${PETSC_DIR} PETSC_ARCH=${PETSC_ARCH} do not specify a valid PETSc installation")
+endif ()
+
+if (petsc_conf_rules AND petsc_conf_variables AND NOT petsc_config_current)
+ petsc_get_version()
+
+ # Put variables into environment since they are needed to get
+ # configuration (petscvariables) in the PETSc makefile
+ set (ENV{PETSC_DIR} "${PETSC_DIR}")
+ set (ENV{PETSC_ARCH} "${PETSC_ARCH}")
+
+ # A temporary makefile to probe the PETSc configuration
+ set (petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
+ file (WRITE "${petsc_config_makefile}"
+"## This file was autogenerated by FindPETSc.cmake
+# PETSC_DIR = ${PETSC_DIR}
+# PETSC_ARCH = ${PETSC_ARCH}
+include ${petsc_conf_rules}
+include ${petsc_conf_variables}
+show :
+\t-@echo -n \${\${VARIABLE}}
+")
+
+ macro (PETSC_GET_VARIABLE name var)
+ set (${var} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} show VARIABLE=${name}
+ OUTPUT_VARIABLE ${var}
+ RESULT_VARIABLE petsc_return)
+ endmacro (PETSC_GET_VARIABLE)
+ petsc_get_variable (PETSC_LIB_DIR petsc_lib_dir)
+ petsc_get_variable (PETSC_EXTERNAL_LIB_BASIC petsc_libs_external)
+ petsc_get_variable (PETSC_CCPPFLAGS petsc_cpp_line)
+ petsc_get_variable (PETSC_INCLUDE petsc_include)
+ petsc_get_variable (PCC petsc_cc)
+ petsc_get_variable (PCC_FLAGS petsc_cc_flags)
+ petsc_get_variable (MPIEXEC petsc_mpiexec)
+ # We are done with the temporary Makefile, calling PETSC_GET_VARIABLE after this point is invalid!
+ file (REMOVE ${petsc_config_makefile})
+
+ execute_process(COMMAND ${MPI_C_COMPILER} --showme:compile OUTPUT_VARIABLE mpi_compile_options ERROR_VARIABLE mpi_compile_error)
+ set(petsc_cpp_line ${petsc_cpp_line} ${mpi_compile_options})
+
+ include (ResolveCompilerPaths)
+ # Extract include paths and libraries from compile command line
+ resolve_includes (petsc_includes_all "${petsc_cpp_line}")
+
+ #on windows we need to make sure we're linking against the right
+ #runtime library
+ if (WIN32)
+ if (petsc_cc_flags MATCHES "-MT")
+ set(using_md False)
+ foreach(flag_var
+ CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
+ CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO
+ CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
+ CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO)
+ if(${flag_var} MATCHES "/MD")
+ set(using_md True)
+ endif(${flag_var} MATCHES "/MD")
+ endforeach(flag_var)
+ if(${using_md} MATCHES "True")
+ message(WARNING "PETSc was built with /MT, but /MD is currently set.
+ See http://www.cmake.org/Wiki/CMake_FAQ#How_can_I_build_my_MSVC_application_with_a_static_runtime.3F")
+ endif(${using_md} MATCHES "True")
+ endif (petsc_cc_flags MATCHES "-MT")
+ endif (WIN32)
+
+ include (CorrectWindowsPaths)
+ convert_cygwin_path(petsc_lib_dir)
+ message (STATUS "petsc_lib_dir ${petsc_lib_dir}")
+
+ macro (PETSC_FIND_LIBRARY suffix name)
+ set (PETSC_LIBRARY_${suffix} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # Clear any stale value, if we got here, we need to find it again
+ if (WIN32)
+ set (libname lib${name}) #windows expects "libfoo", linux expects "foo"
+ else (WIN32)
+ set (libname ${name})
+ endif (WIN32)
+ find_library (PETSC_LIBRARY_${suffix} NAMES ${libname} HINTS ${petsc_lib_dir} NO_DEFAULT_PATH)
+ set (PETSC_LIBRARIES_${suffix} "${PETSC_LIBRARY_${suffix}}")
+ mark_as_advanced (PETSC_LIBRARY_${suffix})
+ endmacro (PETSC_FIND_LIBRARY suffix name)
+
+ # Look for petscvec first, if it doesn't exist, we must be using single-library
+ petsc_find_library (VEC petscvec)
+ if (PETSC_LIBRARY_VEC)
+ petsc_find_library (SYS "petscsys;petsc") # libpetscsys is called libpetsc prior to 3.1 (when single-library was introduced)
+ petsc_find_library (MAT petscmat)
+ petsc_find_library (DM petscdm)
+ petsc_find_library (KSP petscksp)
+ petsc_find_library (SNES petscsnes)
+ petsc_find_library (TS petscts)
+ macro (PETSC_JOIN libs deps)
+ list (APPEND PETSC_LIBRARIES_${libs} ${PETSC_LIBRARIES_${deps}})
+ endmacro (PETSC_JOIN libs deps)
+ petsc_join (VEC SYS)
+ petsc_join (MAT VEC)
+ petsc_join (DM MAT)
+ petsc_join (KSP DM)
+ petsc_join (SNES KSP)
+ petsc_join (TS SNES)
+ petsc_join (ALL TS)
+ else ()
+ set (PETSC_LIBRARY_VEC "NOTFOUND" CACHE INTERNAL "Cleared" FORCE) # There is no libpetscvec
+ petsc_find_library (SINGLE petsc)
+ # Debian 9/Ubuntu 16.04 uses _real and _complex extensions when using libraries in /usr/lib/petsc.
+ if (NOT PETSC_LIBRARY_SINGLE)
+ petsc_find_library (SINGLE petsc_real)
+ endif()
+ if (NOT PETSC_LIBRARY_SINGLE)
+ petsc_find_library (SINGLE petsc_complex)
+ endif()
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ set (PETSC_LIBRARIES_${pkg} "${PETSC_LIBRARY_SINGLE}")
+ endforeach ()
+ endif ()
+ if (PETSC_LIBRARY_TS)
+ message (STATUS "Recognized PETSc install with separate libraries for each package")
+ else ()
+ message (STATUS "Recognized PETSc install with single library for all packages")
+ endif ()
+
+ include(Check${PETSC_LANGUAGE_BINDINGS}SourceRuns)
+ macro (PETSC_TEST_RUNS includes libraries runs)
+ if (PETSC_VERSION VERSION_GREATER 3.1)
+ set (_PETSC_TSDestroy "TSDestroy(&ts)")
+ else ()
+ set (_PETSC_TSDestroy "TSDestroy(ts)")
+ endif ()
+
+ set(_PETSC_TEST_SOURCE "
+static const char help[] = \"PETSc test program.\";
+#include <petscts.h>
+int main(int argc,char *argv[]) {
+ PetscErrorCode ierr;
+ TS ts;
+
+ ierr = PetscInitialize(&argc,&argv,0,help);CHKERRQ(ierr);
+ ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
+ ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
+ ierr = ${_PETSC_TSDestroy};CHKERRQ(ierr);
+ ierr = PetscFinalize();CHKERRQ(ierr);
+ return 0;
+}
+")
+ multipass_source_runs ("${includes}" "${libraries}" "${_PETSC_TEST_SOURCE}" ${runs} "${PETSC_LANGUAGE_BINDINGS}")
+ if (${${runs}})
+ set (PETSC_EXECUTABLE_RUNS "YES" CACHE BOOL
+ "Can the system successfully run a PETSc executable? This variable can be manually set to \"YES\" to force CMake to accept a given PETSc configuration, but this will almost always result in a broken build. If you change PETSC_DIR, PETSC_ARCH, or PETSC_CURRENT you would have to reset this variable." FORCE)
+ endif (${${runs}})
+ endmacro (PETSC_TEST_RUNS)
+
+
+ find_path (PETSC_INCLUDE_DIR petscts.h HINTS "${PETSC_DIR}" PATH_SUFFIXES include NO_DEFAULT_PATH)
+ find_path (PETSC_INCLUDE_CONF petscconf.h HINTS "${PETSC_DIR}" PATH_SUFFIXES "${PETSC_ARCH}/include" "bmake/${PETSC_ARCH}" NO_DEFAULT_PATH)
+ mark_as_advanced (PETSC_INCLUDE_DIR PETSC_INCLUDE_CONF)
+ set (petsc_includes_minimal ${PETSC_INCLUDE_CONF} ${PETSC_INCLUDE_DIR})
+
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_minimal)
+ if (petsc_works_minimal)
+ message (STATUS "Minimal PETSc includes and libraries work. This probably means we are building with shared libs.")
+ set (petsc_includes_needed "${petsc_includes_minimal}")
+ else (petsc_works_minimal) # Minimal includes fail, see if just adding full includes fixes it
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_allincludes)
+ if (petsc_works_allincludes) # It does, we just need all the includes (
+ message (STATUS "PETSc requires extra include paths, but links correctly with only interface libraries. This is an unexpected configuration (but it seems to work fine).")
+ set (petsc_includes_needed ${petsc_includes_all})
+ else (petsc_works_allincludes) # We are going to need to link the external libs explicitly
+ resolve_libraries (petsc_libraries_external "${petsc_libs_external}")
+ foreach (pkg SYS VEC MAT DM KSP SNES TS ALL)
+ list (APPEND PETSC_LIBRARIES_${pkg} ${petsc_libraries_external})
+ endforeach (pkg)
+ petsc_test_runs ("${petsc_includes_minimal}" "${PETSC_LIBRARIES_TS}" petsc_works_alllibraries)
+ if (petsc_works_alllibraries)
+ message (STATUS "PETSc only need minimal includes, but requires explicit linking to all dependencies. This is expected when PETSc is built with static libraries.")
+ set (petsc_includes_needed ${petsc_includes_minimal})
+ else (petsc_works_alllibraries)
+ # It looks like we really need everything, should have listened to Matt
+ set (petsc_includes_needed ${petsc_includes_all})
+ petsc_test_runs ("${petsc_includes_all}" "${PETSC_LIBRARIES_TS}" petsc_works_all)
+ if (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc requires extra include paths and explicit linking to all dependencies. This probably means you have static libraries and something unexpected in PETSc headers.")
+ else (petsc_works_all) # We fail anyways
+ message (STATUS "PETSc could not be used, maybe the install is broken.")
+ endif (petsc_works_all)
+ endif (petsc_works_alllibraries)
+ endif (petsc_works_allincludes)
+ endif (petsc_works_minimal)
+
+ # We do an out-of-source build so __FILE__ will be an absolute path, hence __INSDIR__ is superfluous
+ if (${PETSC_VERSION} VERSION_LESS 3.1)
+ set (PETSC_DEFINITIONS "-D__SDIR__=\"\"" CACHE STRING "PETSc definitions" FORCE)
+ else ()
+ set (PETSC_DEFINITIONS "-D__INSDIR__=" CACHE STRING "PETSc definitions" FORCE)
+ endif ()
+ # Sometimes this can be used to assist FindMPI.cmake
+ set (PETSC_MPIEXEC ${petsc_mpiexec} CACHE FILEPATH "Executable for running PETSc MPI programs" FORCE)
+ set (PETSC_INCLUDES ${petsc_includes_needed} CACHE STRING "PETSc include path" FORCE)
+ set (PETSC_LIBRARIES ${PETSC_LIBRARIES_ALL} CACHE STRING "PETSc libraries" FORCE)
+ set (PETSC_COMPILER ${petsc_cc} CACHE FILEPATH "PETSc compiler" FORCE)
+ # Note that we have forced values for all these choices. If you
+ # change these, you are telling the system to trust you that they
+ # work. It is likely that you will end up with a broken build.
+ mark_as_advanced (PETSC_INCLUDES PETSC_LIBRARIES PETSC_COMPILER PETSC_DEFINITIONS PETSC_MPIEXEC PETSC_EXECUTABLE_RUNS)
+endif ()
+
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PETSc
+ REQUIRED_VARS PETSC_INCLUDES PETSC_LIBRARIES PETSC_EXECUTABLE_RUNS
+ VERSION_VAR PETSC_VERSION
+ FAIL_MESSAGE "PETSc could not be found. Be sure to set PETSC_DIR and PETSC_ARCH.")
diff --git a/cmake_modules/FindPackageMultipass.cmake b/cmake_modules/FindPackageMultipass.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..fbf06a7f0fc3aa20a0387f091eac4f74e7ffdab2
--- /dev/null
+++ b/cmake_modules/FindPackageMultipass.cmake
@@ -0,0 +1,106 @@
+# PackageMultipass - this module defines two macros
+#
+# FIND_PACKAGE_MULTIPASS (Name CURRENT
+# STATES VAR0 VAR1 ...
+# DEPENDENTS DEP0 DEP1 ...)
+#
+# This function creates a cache entry <UPPERCASED-Name>_CURRENT which
+# the user can set to "NO" to trigger a reconfiguration of the package.
+# The first time this function is called, the values of
+# <UPPERCASED-Name>_VAR0, ... are saved. If <UPPERCASED-Name>_CURRENT
+# is false or if any STATE has changed since the last time
+# FIND_PACKAGE_MULTIPASS() was called, then CURRENT will be set to "NO",
+# otherwise CURRENT will be "YES". IF not CURRENT, then
+# <UPPERCASED-Name>_DEP0, ... will be FORCED to NOTFOUND.
+# Example:
+# find_path (FOO_DIR include/foo.h)
+# FIND_PACKAGE_MULTIPASS (Foo foo_current
+# STATES DIR
+# DEPENDENTS INCLUDES LIBRARIES)
+# if (NOT foo_current)
+# # Make temporary files, run programs, etc, to determine FOO_INCLUDES and FOO_LIBRARIES
+# endif (NOT foo_current)
+#
+# MULTIPASS_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS LANGUAGE)
+# Always runs the given test, use this when you need to re-run tests
+# because parent variables have made old cache entries stale. The LANGUAGE
+# variable is either C or CXX indicating which compiler the test should
+# use.
+# MULTIPASS_C_SOURCE_RUNS (Name INCLUDES LIBRARIES SOURCE RUNS)
+# DEPRECATED! This is only included for backwards compatability. Use
+# the more general MULTIPASS_SOURCE_RUNS instead.
+# Always runs the given test, use this when you need to re-run tests
+# because parent variables have made old cache entries stale.
+
+macro (FIND_PACKAGE_MULTIPASS _name _current)
+ string (TOUPPER ${_name} _NAME)
+ set (_args ${ARGV})
+ list (REMOVE_AT _args 0 1)
+
+ set (_states_current "YES")
+ list (GET _args 0 _cmd)
+ if (_cmd STREQUAL "STATES")
+ list (REMOVE_AT _args 0)
+ list (GET _args 0 _state)
+ while (_state AND NOT _state STREQUAL "DEPENDENTS")
+ # The name of the stored value for the given state
+ set (_stored_var PACKAGE_MULTIPASS_${_NAME}_${_state})
+ if (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+ set (_states_current "NO")
+ endif (NOT "${${_stored_var}}" STREQUAL "${${_NAME}_${_state}}")
+ set (${_stored_var} "${${_NAME}_${_state}}" CACHE INTERNAL "Stored state for ${_name}." FORCE)
+ list (REMOVE_AT _args 0)
+ list (GET _args 0 _state)
+ endwhile (_state AND NOT _state STREQUAL "DEPENDENTS")
+ endif (_cmd STREQUAL "STATES")
+
+ set (_stored ${_NAME}_CURRENT)
+ if (NOT ${_stored})
+ set (${_stored} "YES" CACHE BOOL "Is the configuration for ${_name} current? Set to \"NO\" to reconfigure." FORCE)
+ set (_states_current "NO")
+ endif (NOT ${_stored})
+
+ set (${_current} ${_states_current})
+ if (NOT ${_current} AND PACKAGE_MULTIPASS_${_name}_CALLED)
+ message (STATUS "Clearing ${_name} dependent variables")
+ # Clear all the dependent variables so that the module can reset them
+ list (GET _args 0 _cmd)
+ if (_cmd STREQUAL "DEPENDENTS")
+ list (REMOVE_AT _args 0)
+ foreach (dep ${_args})
+ set (${_NAME}_${dep} "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ endforeach (dep)
+ endif (_cmd STREQUAL "DEPENDENTS")
+ set (${_NAME}_FOUND "NOTFOUND" CACHE INTERNAL "Cleared" FORCE)
+ endif ()
+ set (PACKAGE_MULTIPASS_${name}_CALLED YES CACHE INTERNAL "Private" FORCE)
+endmacro (FIND_PACKAGE_MULTIPASS)
+
+
+macro (MULTIPASS_SOURCE_RUNS includes libraries source runs language)
+ include (Check${language}SourceRuns)
+ # This is a ridiculous hack. CHECK_${language}_SOURCE_* thinks that if the
+ # *name* of the return variable doesn't change, then the test does
+ # not need to be re-run. We keep an internal count which we
+ # increment to guarantee that every test name is unique. If we've
+ # gotten here, then the configuration has changed enough that the
+ # test *needs* to be rerun.
+ if (NOT MULTIPASS_TEST_COUNT)
+ set (MULTIPASS_TEST_COUNT 00)
+ endif (NOT MULTIPASS_TEST_COUNT)
+ math (EXPR _tmp "${MULTIPASS_TEST_COUNT} + 1") # Why can't I add to a cache variable?
+ set (MULTIPASS_TEST_COUNT ${_tmp} CACHE INTERNAL "Unique test ID")
+ set (testname MULTIPASS_TEST_${MULTIPASS_TEST_COUNT}_${runs})
+ set (CMAKE_REQUIRED_INCLUDES ${includes})
+ set (CMAKE_REQUIRED_LIBRARIES ${libraries})
+ if(${language} STREQUAL "C")
+ check_c_source_runs ("${source}" ${testname})
+ elseif(${language} STREQUAL "CXX")
+ check_cxx_source_runs ("${source}" ${testname})
+ endif()
+ set (${runs} "${${testname}}")
+endmacro (MULTIPASS_SOURCE_RUNS)
+
+macro (MULTIPASS_C_SOURCE_RUNS includes libraries source runs)
+ multipass_source_runs("${includes}" "${libraries}" "${source}" ${runs} "C")
+endmacro (MULTIPASS_C_SOURCE_RUNS)
diff --git a/cmake_modules/FindTinyObjLoader.cmake b/cmake_modules/FindTinyObjLoader.cmake
index 98bdae4d34b20e541c783cda224c40881694d974..3410fb89255b171376592f8a3aa4ccaf0a8bc9e9 100644
--- a/cmake_modules/FindTinyObjLoader.cmake
+++ b/cmake_modules/FindTinyObjLoader.cmake
@@ -1,10 +1,10 @@
# - Try to find LibHilbert
# Once done this will define
#
-# TINYOBJLOADER_FOUND - system has LibHilbert
-# TINYOBJLOADER_INCLUDE_DIRS - include directories for PETSc
-# TINYOBJLOADER_LIBRARY_DIRS - library directories for PETSc
-# TINYOBJLOADER_LIBRARIES - libraries for PETSc
+# TINYOBJLOADER_FOUND - system has TinyObjLoader
+# TINYOBJLOADER_INCLUDE_DIRS - include directories for TinyObjLoader
+# TINYOBJLOADER_LIBRARY_DIRS - library directories for TinyObjLoader
+# TINYOBJLOADER_LIBRARIES - libraries for TinyObjLoader
#
#=============================================================================
# Copyright (C) 2010-2016 Pietro Incardona
diff --git a/cmake_modules/ResolveCompilerPaths.cmake b/cmake_modules/ResolveCompilerPaths.cmake
new file mode 100644
index 0000000000000000000000000000000000000000..54787fa38ffa50136414e6c788c50fb3c63746b8
--- /dev/null
+++ b/cmake_modules/ResolveCompilerPaths.cmake
@@ -0,0 +1,105 @@
+# ResolveCompilerPaths - this module defines two macros
+#
+# RESOLVE_LIBRARIES (XXX_LIBRARIES LINK_LINE)
+# This macro is intended to be used by FindXXX.cmake modules.
+# It parses a compiler link line and resolves all libraries
+# (-lfoo) using the library path contexts (-L/path) in scope.
+# The result in XXX_LIBRARIES is the list of fully resolved libs.
+# Example:
+#
+# RESOLVE_LIBRARIES (FOO_LIBRARIES "-L/A -la -L/B -lb -lc -ld")
+#
+# will be resolved to
+#
+# FOO_LIBRARIES:STRING="/A/liba.so;/B/libb.so;/A/libc.so;/usr/lib/libd.so"
+#
+# if the filesystem looks like
+#
+# /A: liba.so libc.so
+# /B: liba.so libb.so
+# /usr/lib: liba.so libb.so libc.so libd.so
+#
+# and /usr/lib is a system directory.
+#
+# Note: If RESOLVE_LIBRARIES() resolves a link line differently from
+# the native linker, there is a bug in this macro (please report it).
+#
+# RESOLVE_INCLUDES (XXX_INCLUDES INCLUDE_LINE)
+# This macro is intended to be used by FindXXX.cmake modules.
+# It parses a compile line and resolves all includes
+# (-I/path/to/include) to a list of directories. Other flags are ignored.
+# Example:
+#
+# RESOLVE_INCLUDES (FOO_INCLUDES "-I/A -DBAR='\"irrelevant -I/string here\"' -I/B")
+#
+# will be resolved to
+#
+# FOO_INCLUDES:STRING="/A;/B"
+#
+# assuming both directories exist.
+# Note: as currently implemented, the -I/string will be picked up mistakenly (cry, cry)
+include (CorrectWindowsPaths)
+
+macro (RESOLVE_LIBRARIES LIBS LINK_LINE)
+ string (REGEX MATCHALL "((-L|-l|-Wl)([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))" _all_tokens "${LINK_LINE}")
+ set (_libs_found "")
+ set (_directory_list "")
+ foreach (token ${_all_tokens})
+ if (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+ # If it's a library path, add it to the list
+ string (REGEX REPLACE "^-L" "" token ${token})
+ string (REGEX REPLACE "//" "/" token ${token})
+ convert_cygwin_path(token)
+ list (APPEND _directory_list ${token})
+ elseif (token MATCHES "^(-l([^\" ]+|\"[^\"]+\")|[^\" ]+\\.(a|so|dll|lib))")
+ # It's a library, resolve the path by looking in the list and then (by default) in system directories
+ if (WIN32) #windows expects "libfoo", linux expects "foo"
+ string (REGEX REPLACE "^-l" "lib" token ${token})
+ else (WIN32)
+ string (REGEX REPLACE "^-l" "" token ${token})
+ endif (WIN32)
+ set (_root "")
+ if (token MATCHES "^/") # We have an absolute path
+ #separate into a path and a library name:
+ string (REGEX MATCH "[^/]*\\.(a|so|dll|lib)$" libname ${token})
+ string (REGEX MATCH ".*[^${libname}$]" libpath ${token})
+ convert_cygwin_path(libpath)
+ set (_directory_list ${_directory_list} ${libpath})
+ set (token ${libname})
+ endif (token MATCHES "^/")
+ set (_lib "NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
+ find_library (_lib ${token} HINTS ${_directory_list} ${_root})
+ if (_lib)
+ string (REPLACE "//" "/" _lib ${_lib})
+ list (APPEND _libs_found ${_lib})
+ else (_lib)
+ message (STATUS "Unable to find library ${token}")
+ endif (_lib)
+ endif (token MATCHES "-L([^\" ]+|\"[^\"]+\")")
+ endforeach (token)
+ set (_lib "NOTFOUND" CACHE INTERNAL "Scratch variable" FORCE)
+ # only the LAST occurence of each library is required since there should be no circular dependencies
+ if (_libs_found)
+ list (REVERSE _libs_found)
+ list (REMOVE_DUPLICATES _libs_found)
+ list (REVERSE _libs_found)
+ endif (_libs_found)
+ set (${LIBS} "${_libs_found}")
+endmacro (RESOLVE_LIBRARIES)
+
+macro (RESOLVE_INCLUDES INCS COMPILE_LINE)
+ string (REGEX MATCHALL "-I([^\" ]+|\"[^\"]+\")" _all_tokens "${COMPILE_LINE}")
+ set (_incs_found "")
+ foreach (token ${_all_tokens})
+ string (REGEX REPLACE "^-I" "" token ${token})
+ string (REGEX REPLACE "//" "/" token ${token})
+ convert_cygwin_path(token)
+ if (EXISTS ${token})
+ list (APPEND _incs_found ${token})
+ else (EXISTS ${token})
+ message (STATUS "Include directory ${token} does not exist")
+ endif (EXISTS ${token})
+ endforeach (token)
+ list (REMOVE_DUPLICATES _incs_found)
+ set (${INCS} "${_incs_found}")
+endmacro (RESOLVE_INCLUDES)
diff --git a/run.sh b/run.sh
index c820dd3c9fcbdaa34d4fa0974fb6a0b2b422c71e..0af9464b804cbfcf3cc08226342d8b99a0b009cd 100755
--- a/run.sh
+++ b/run.sh
@@ -5,15 +5,11 @@ branch=$3
# Make a directory in /tmp/openfpm_data
-cd "$1/openfpm_io"
-
-if [ "$2" == "gin" ]
-then
- module load gcc/4.9.2
- module load boost/1.54.0
-fi
+cd "openfpm_io"
+echo "CHECKING MACHINE"
if [ x"$hostname" == x"cifarm-centos-node.mpi-cbg.de" ]; then
+ echo "CENTOS"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
fi
@@ -24,14 +20,13 @@ if [ x"$hostname" == x"cifarm-ubuntu-node" ]; then
fi
if [ x"$hostname" == x"cifarm-mac-node.mpi-cbg.de" ]; then
+ echo "MACOS X"
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/HDF5/lib"
export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$HOME/openfpm_dependencies/openfpm_io/$branch/BOOST/lib"
fi
+pwd
+
./build/src/io
-if [ $? -ne 0 ]; then
- curl -X POST --data "payload={\"icon_emoji\": \":jenkins:\", \"username\": \"jenkins\" , \"attachments\":[{ \"title\":\"Error:\", \"color\": \"#FF0000\", \"text\":\"$2 failed to complete the openfpm_io test \" }] }" https://hooks.slack.com/services/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
- exit 1 ;
-fi
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 8f05ae1eb490035ed55574e236dcac0ad8e12636..87dafed2448824d29b617e398601b3c855f883a6 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -22,10 +22,15 @@ endif()
###########################
if (CUDA_FOUND)
- target_compile_options(io PUBLIC $<$<COMPILE_LANGUAGE:CUDA>:-Xcudafe "--display_error_number --diag_suppress=611 --diag_suppress=2885 --diag_suppress=2886 --diag_suppress=2887 --diag_suppress=2888 --diag_suppress=186 --diag_suppress=111" --expt-extended-lambda>)
+ target_compile_options(io PUBLIC $<$<COMPILE_LANGUAGE:CUDA>: ${WARNING_SUPPRESSION_AND_OPTION_NVCC} >)
target_include_directories (io PUBLIC ${MPI_C_INCLUDE_DIRS})
+
+ if( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0 )
+ add_compile_options( "-fabi-version=6" )
+ endif()
+
if (TEST_COVERAGE)
- target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fprofile-arcs -ftest-coverage">)
+ target_compile_options(io PRIVATE $<$<COMPILE_LANGUAGE:CUDA>: -Xcompiler "-fprofile-arcs -ftest-coverage" >)
endif()
endif()
@@ -46,8 +51,8 @@ if (PETSC_FOUND)
endif()
target_link_libraries(io ${Boost_LIBRARIES})
-target_link_libraries(io -L${HDF5_ROOT}/lib hdf5 hdf5_hl)
-target_link_libraries(io -L${TINYOBJLOADER_LIBRARY_DIRS} -ltinyobjloader )
+target_link_libraries(io ${HDF5_LIBRARIES})
+target_link_libraries(io ${TINYOBJLOADER_LIBRARIES} )
if (PETSC_FOUND)
target_link_libraries(io ${PETSC_LIBRARIES})
endif()
diff --git a/src/CSVWriter/CSVWriter.hpp b/src/CSVWriter/CSVWriter.hpp
index cd50cd221ac9f577c0ceae797e471b5c7979ff92..c7abc933923e4115cf88a2e057ff287cc6279924 100644
--- a/src/CSVWriter/CSVWriter.hpp
+++ b/src/CSVWriter/CSVWriter.hpp
@@ -14,7 +14,7 @@
#include <fstream>
#include "util/common.hpp"
#include <boost/mpl/range_c.hpp>
-#include <boost/mpl/for_each.hpp>
+#include "util/for_each_ref_host.hpp"
#include "csv_multiarray.hpp"
#include "util/util.hpp"
#include "is_csv_writable.hpp"
@@ -56,12 +56,12 @@ struct csv_prp
template<typename T>
void operator()(T& t)
{
- // This is the type of the csv column
- typedef decltype(obj.template get<T::value>()) col_type;
+ // This is the type of the csv column
+ typedef typename boost::mpl::at<typename Tobj::type,T>::type col_type;
- // Remove the reference from the column type
- typedef typename boost::remove_reference<col_type>::type col_rtype;
- typedef typename std::remove_all_extents<col_rtype>::type base_col_rtype;
+ // Remove the reference from the column type
+ typedef typename boost::remove_reference<col_type>::type col_rtype;
+ typedef typename std::remove_all_extents<col_rtype>::type base_col_rtype;
csv_value_str<col_rtype, is_csv_writable<base_col_rtype>::value >(obj.template get<T::value>(),str);
}
@@ -183,7 +183,7 @@ class CSVWriter
csv_col<typename v_prp::value_type,has_attributes<typename v_prp::value_type>::value> col(str);
// Iterate through all the vertex and create the vertex list
- boost::mpl::for_each< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(col);
+ boost::mpl::for_each_ref_host< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(col);
str << "\n";
@@ -225,7 +225,7 @@ class CSVWriter
csv_prp<decltype(obj)> c_prp(str,obj);
// write the properties to the stream string
- boost::mpl::for_each< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(c_prp);
+ boost::mpl::for_each_ref_host< boost::mpl::range_c<int,0,v_prp::value_type::max_prop> >(c_prp);
str << "\n";
}
diff --git a/src/CSVWriter/csv_multiarray.hpp b/src/CSVWriter/csv_multiarray.hpp
index f8ff9f815d4b67998115e7e71aa73494b3383a92..6d91899f626798730a0dc77fed1a953ee44c2e78 100644
--- a/src/CSVWriter/csv_multiarray.hpp
+++ b/src/CSVWriter/csv_multiarray.hpp
@@ -137,7 +137,8 @@ struct csv_value_str
template<typename T,size_t N1, bool is_writable>
struct csv_value_str<T[N1], is_writable>
{
- inline csv_value_str(const T v[N1], std::stringstream & str)
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
{
for (size_t i = 0 ; i < N1 ; i++)
str << "," << v[i];
@@ -148,7 +149,8 @@ struct csv_value_str<T[N1], is_writable>
template<typename T,size_t N1,size_t N2, bool is_writable>
struct csv_value_str<T[N1][N2], is_writable>
{
- inline csv_value_str(const T v[N1][N2], std::stringstream & str)
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
@@ -164,7 +166,8 @@ struct csv_value_str<T[N1][N2], is_writable>
template<typename T,size_t N1,size_t N2,size_t N3, bool is_writable>
struct csv_value_str<T[N1][N2][N3], is_writable>
{
- inline csv_value_str(const T v[N1][N2][N3], std::stringstream & str)
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
@@ -183,7 +186,8 @@ struct csv_value_str<T[N1][N2][N3], is_writable>
template<typename T,size_t N1,size_t N2,size_t N3,size_t N4, bool is_writable>
struct csv_value_str<T[N1][N2][N3][N4],is_writable>
{
- inline csv_value_str(const T v[N1][N2][N3][N4], std::stringstream & str)
+ template<typename ArrObject>
+ inline csv_value_str(const ArrObject v, std::stringstream & str)
{
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
diff --git a/src/CSVWriter/is_csv_writable.hpp b/src/CSVWriter/is_csv_writable.hpp
index b7268b09d9cb62b3f9671c146d06147f1f4cd25a..48beba760ab6169b962bc252a6ba38f615d57e05 100644
--- a/src/CSVWriter/is_csv_writable.hpp
+++ b/src/CSVWriter/is_csv_writable.hpp
@@ -141,5 +141,37 @@ struct is_csv_writable<bool>
};
};
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1>
+struct is_csv_writable<T[N1]>
+{
+ //! bool is writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1, unsigned int N2>
+struct is_csv_writable<T[N1][N2]>
+{
+ //! bool is writable
+ enum
+ {
+ value = true
+ };
+};
+
+//! Indicate if the property T is writable in CSV
+template<typename T, unsigned int N1, unsigned int N2, unsigned int N3>
+struct is_csv_writable<T[N1][N2][N3]>
+{
+ //! bool is writable
+ enum
+ {
+ value = true
+ };
+};
#endif /* OPENFPM_IO_SRC_CSVWRITER_IS_CSV_WRITABLE_HPP_ */
diff --git a/src/GraphMLWriter/GraphMLWriter.hpp b/src/GraphMLWriter/GraphMLWriter.hpp
index b4f76c7737ee169c178d589f2f9f94ba321427ab..d34504e9220116119f086da98002418a606b61ed 100644
--- a/src/GraphMLWriter/GraphMLWriter.hpp
+++ b/src/GraphMLWriter/GraphMLWriter.hpp
@@ -125,17 +125,17 @@ struct vertex_prop
{cnt++; return ;}
// Create a property string based on the type of the property
- if (typeid(T) == typeid(float))
+ if (std::is_same<T,float>::value)
v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"float\"/>\n";
- else if (typeid(T) == typeid(double))
+ else if (std::is_same<T,double>::value)
v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"double\"/>\n";
- else if (typeid(T) == typeid(int))
+ else if (std::is_same<T,int>::value)
v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"int\"/>\n";
- else if (typeid(T) == typeid(long int))
+ else if (std::is_same<T,long int>::value)
v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"long\"/>\n";
- else if (typeid(T) == typeid(bool))
+ else if (std::is_same<T,bool>::value)
v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"boolean\"/>\n";
- else if (typeid(T) == typeid(std::string))
+ else if (std::is_same<T,std::string>::value)
v_prop += "<key id=\"vk" + std::to_string(cnt) + "\" for=\"node\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"string\"/>\n";
}
@@ -278,18 +278,20 @@ struct vertex_node
//! Create an entry for the attribute
if (T::value < n_attr)
{
+ typedef typename std::remove_reference<decltype(vo.template get<T::value>())>::type type_get;
+
// Create a property string based on the type of the property
- if (typeid(decltype(vo.template get<T::value>())) == typeid(float))
+ if (std::is_same<type_get,float>::value)
v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(double))
+ else if (std::is_same<type_get,double>::value)
v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(int))
+ else if (std::is_same<type_get,int>::value )
v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(long int))
+ else if (std::is_same<type_get,long int>::value)
v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(bool))
+ else if (std::is_same<type_get,bool>::value)
v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(std::string))
+ else if (std::is_same<type_get,std::string>::value)
v_node += " <data key=\"vk" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
}
@@ -379,17 +381,17 @@ struct edge_prop
if (cnt < n_attr)
{
// Create a property string based on the type of the property
- if (typeid(T) == typeid(float))
+ if (std::is_same<T,float>::value)
e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"float\"/>\n";
- else if (typeid(T) == typeid(double))
+ else if (std::is_same<T,double>::value)
e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"double\"/>\n";
- else if (typeid(T) == typeid(int))
+ else if (std::is_same<T,int>::value)
e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"int\"/>\n";
- else if (typeid(T) == typeid(long int))
+ else if (std::is_same<T,long int>::value)
e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"long\"/>\n";
- else if (typeid(T) == typeid(bool))
+ else if (std::is_same<T,bool>::value)
e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"boolean\"/>\n";
- else if (typeid(T) == typeid(std::string))
+ else if (std::is_same<T,std::string>::value)
e_prop += "<key id=\"ek" + std::to_string(cnt) + "\" for=\"edge\" attr.name=\"" + attributes_names[cnt] + "\" attr.type=\"string\"/>\n";
}
@@ -510,18 +512,20 @@ struct edge_node
//! Create an entry for the attribute
if (T::value < n_attr)
{
+ typedef typename std::remove_reference<decltype(vo.template get<T::value>())>::type type_get;
+
// Create a property string based on the type of the property
- if (typeid(decltype(vo.template get<T::value>())) == typeid(float))
+ if (std::is_same<type_get,float>::value)
e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(double))
+ else if (std::is_same<type_get,double>::value)
e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(int))
+ else if (std::is_same<type_get,int>::value)
e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(long int))
+ else if (std::is_same<type_get,long int>::value)
e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(bool))
+ else if (std::is_same<type_get,bool>::value)
e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
- else if (typeid(decltype(vo.template get<T::value>())) == typeid(std::string))
+ else if (std::is_same<type_get,std::string>::value)
e_node += " <data key=\"ek" + std::to_string(cnt) + "\">" + std::to_string(vo.template get<T::value>()) + "</data>\n";
}
diff --git a/src/HDF5_wr/HDF5_reader_gd.hpp b/src/HDF5_wr/HDF5_reader_gd.hpp
index 7da37708d2acfe39cb5f415a51e46bb07f9b0abc..500f9715b3cdb76a685f1c4eb49243b950bdeb3e 100644
--- a/src/HDF5_wr/HDF5_reader_gd.hpp
+++ b/src/HDF5_wr/HDF5_reader_gd.hpp
@@ -19,7 +19,7 @@ class HDF5_reader<GRID_DIST>
{
template<typename device_grid> void load_block(long int bid,
hssize_t mpi_size_old,
- int * metadata_out,
+ long int * metadata_out,
openfpm::vector<size_t> & metadata_accum,
hid_t plist_id,
hid_t dataset_2,
@@ -42,24 +42,47 @@ class HDF5_reader<GRID_DIST>
hsize_t count[1] = {1};
+ // allocate the memory
+ HeapMemory pmem;
+ //pmem.allocate(req);
+ ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
+ mem.incRef();
+
//Select file dataspace
hid_t file_dataspace_id_2 = H5Dget_space(dataset_2);
- H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset, NULL, count, block);
+ size_t to_read = block[0];
+ size_t coffset = 0;
- hsize_t mdim_2[1] = {block[0]};
+ auto & v_cl = create_vcluster();
- //Create data space in memory
- hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+ int read_test = (to_read != 0);
+ v_cl.max(read_test);
+ v_cl.execute();
- // allocate the memory
- HeapMemory pmem;
- //pmem.allocate(req);
- ExtPreAlloc<HeapMemory> & mem = *(new ExtPreAlloc<HeapMemory>(block[0],pmem));
- mem.incRef();
+ while (read_test)
+ {
+ hsize_t block_c[1];
+ block_c[0] = std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
- // Read the dataset.
- H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer());
+ hsize_t offset_c[1] = {offset[0] + coffset};
+ H5Sselect_hyperslab(file_dataspace_id_2, H5S_SELECT_SET, offset_c, NULL, count, block_c);
+
+ hsize_t mdim_2[1] = {block_c[0]};
+
+ //Create data space in memory
+ hid_t mem_dataspace_id_2 = H5Screate_simple(1, mdim_2, NULL);
+
+ // Read the dataset.
+ H5Dread(dataset_2, H5T_NATIVE_CHAR, mem_dataspace_id_2, file_dataspace_id_2, plist_id, (char *)mem.getPointer() + coffset);
+
+ coffset += std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
+ to_read -= std::min((size_t)(to_read),(size_t)0x7FFFFFFF);
+
+ read_test = (to_read != 0);
+ v_cl.max(read_test);
+ v_cl.execute();
+ }
mem.allocate(pmem.size());
@@ -72,7 +95,10 @@ class HDF5_reader<GRID_DIST>
Unpacker<typename std::remove_reference<decltype(gdb_ext_old)>::type,HeapMemory>::unpack(mem,gdb_ext_old_unp,ps,1);
for (size_t i = 0; i < loc_grid_old_unp.size(); i++)
- loc_grid_old.add(loc_grid_old_unp.get(i));
+ {
+ loc_grid_old.add();
+ loc_grid_old.last().swap(loc_grid_old_unp.get(i));
+ }
for (size_t i = 0; i < gdb_ext_old_unp.size(); i++)
gdb_ext_old.add(gdb_ext_old_unp.get(i));
@@ -120,7 +146,7 @@ public:
//printf ("\nOld MPI size: %llu\n", mpi_size_old);
//Where to read metadata
- int metadata_out[mpi_size_old];
+ long int metadata_out[mpi_size_old];
for (int i = 0; i < mpi_size_old; i++)
{
@@ -133,30 +159,9 @@ public:
//Create data space in memory
hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
-/*
- if (mpi_rank == 0)
- {
- hssize_t size;
-
- size = H5Sget_select_npoints (mem_dataspace_id);
- printf ("\nmemspace_id size: %llu\n", size);
- size = H5Sget_select_npoints (file_dataspace_id);
- printf ("dataspace_id size: %llu\n", size);
- }
-*/
// Read the dataset.
- H5Dread(dataset, H5T_NATIVE_INT, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
-/*
- if (mpi_rank == 0)
- {
- std::cout << "Metadata_out[]: ";
- for (int i = 0; i < mpi_size_old; i++)
- {
- std::cout << metadata_out[i] << " ";
- }
- std::cout << " " << std::endl;
- }
-*/
+ H5Dread(dataset, H5T_NATIVE_LLONG, mem_dataspace_id, file_dataspace_id, plist_id, metadata_out);
+
openfpm::vector<size_t> metadata_accum;
metadata_accum.resize(mpi_size_old);
@@ -183,12 +188,6 @@ public:
size_t rest_block = mpi_size_old % v_cl.getProcessingUnits();
- // std::cout << "MPI size old: " << mpi_size_old << std::endl;
- //std::cout << "MPI size: " << v_cl.getProcessingUnits() << std::endl;
-
-
- // std::cout << "Rest block: " << rest_block << std::endl;
-
size_t max_block;
if (rest_block != 0)
diff --git a/src/HDF5_wr/HDF5_writer.hpp b/src/HDF5_wr/HDF5_writer.hpp
index 95b686cf9a4867d49d3110dddfef79ba492670c1..d0c2b673ddaf6efaddc1efe063f9bebe92f3fefc 100644
--- a/src/HDF5_wr/HDF5_writer.hpp
+++ b/src/HDF5_wr/HDF5_writer.hpp
@@ -10,7 +10,7 @@
#include "VCluster/VCluster.hpp"
-#include <hdf5.h>
+#include "hdf5.h"
template <unsigned int type>
class HDF5_writer
diff --git a/src/HDF5_wr/HDF5_writer_gd.hpp b/src/HDF5_wr/HDF5_writer_gd.hpp
index 89ea004827824fc2b0dac30fed254a03dd1d3740..8a1b98e78d433c6975940e2373287c893e0f30c1 100644
--- a/src/HDF5_wr/HDF5_writer_gd.hpp
+++ b/src/HDF5_wr/HDF5_writer_gd.hpp
@@ -92,12 +92,6 @@ public:
//Create data space in file
hid_t file_dataspace_id_2 = H5Screate_simple(1, fdim2, NULL);
- //Size for data space in memory
- hsize_t mdim[1] = {pmem.size()};
-
- //Create data space in memory
- hid_t mem_dataspace_id = H5Screate_simple(1, mdim, NULL);
-
//if (mpi_rank == 0)
//std::cout << "Total object size: " << sum << std::endl;
@@ -105,7 +99,7 @@ public:
hid_t file_dataset = H5Dcreate (file, "grid_dist", H5T_NATIVE_CHAR, file_dataspace_id, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//Create data set 2 in file
- hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_INT, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ hid_t file_dataset_2 = H5Dcreate (file, "metadata", H5T_NATIVE_LLONG, file_dataspace_id_2, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
//H5Pclose(plist_id);
H5Sclose(file_dataspace_id);
@@ -132,45 +126,51 @@ public:
// std::cout << "MPI rank: " << mpi_rank << ", MPI size: " << mpi_size << ", Offset: " << offset[0] << ", Block: " << block[0] << std::endl;
- int metadata[mpi_size];
+ long int metadata[mpi_size];
for (int i = 0; i < mpi_size; i++)
metadata[i] = sz_others.get(i);
//Select hyperslab in the file.
file_dataspace_id = H5Dget_space(file_dataset);
- H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset, NULL, count, block);
- file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+ //Create property list for collective dataset write.
+ plist_id = H5Pcreate(H5P_DATASET_XFER);
+ H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+ // We slipt the write in chunk of 2GB maximum
+ size_t to_write = block[0];
+ size_t coffset = 0;
+ while (to_write)
+ {
+ hsize_t block_c[1];
+ block_c[0] = std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
- //Create property list for collective dataset write.
- plist_id = H5Pcreate(H5P_DATASET_XFER);
- H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_COLLECTIVE);
+ //Create data space in memory
+ hid_t mem_dataspace_id = H5Screate_simple(1, block_c, NULL);
- //Write a data set to a file
- H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer());
+ hsize_t offset_c[1] = {offset[0] + coffset};
+ H5Sselect_hyperslab(file_dataspace_id, H5S_SELECT_SET, offset_c, NULL, count, block_c);
- //Write a data set 2 to a file
- H5Dwrite(file_dataset_2, H5T_NATIVE_INT, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
-/*
- for (size_t i = 0; i < gdb_ext.size(); i++)
- {
- Box<dim,long int> box = gdb_ext.get(i).Dbox;
- std::cout << "Dboxes saved: (" << box.getLow(0) << "; " << box.getLow(1) << "); (" << box.getHigh(0) << "; " << box.getHigh(1) << ")" << std::endl;
- }
-
- for (size_t i = 0; i < loc_grid.size(); i++)
- {
- std::cout << "loc_grids saved: (" << loc_grid.get(i).getGrid().getBox().getLow(0) << "; " << loc_grid.get(i).getGrid().getBox().getLow(1) << "); (" << loc_grid.get(i).getGrid().getBox().getHigh(0) << "; " << loc_grid.get(i).getGrid().getBox().getHigh(1) << ")" << std::endl;
- }
-*/
+ //Write a data set to a file
+ H5Dwrite(file_dataset, H5T_NATIVE_CHAR, mem_dataspace_id, file_dataspace_id, plist_id, (const char *)pmem.getPointer() + coffset);
+
+ coffset += std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
+ to_write -= std::min((size_t)(to_write),(size_t)0x7FFFFFFF);
+
+ H5Sclose(mem_dataspace_id);
+ }
+
+ file_dataspace_id_2 = H5Dget_space(file_dataset_2);
+
+ //Write a data set 2 to a file
+ H5Dwrite(file_dataset_2, H5T_NATIVE_LLONG, H5S_ALL, file_dataspace_id_2, plist_id, metadata);
+
//Close/release resources.
H5Dclose(file_dataset);
H5Sclose(file_dataspace_id);
H5Dclose(file_dataset_2);
H5Sclose(file_dataspace_id_2);
- H5Sclose(mem_dataspace_id);
H5Pclose(plist_id);
H5Fclose(file);
}
diff --git a/src/Plot/GoogleChart.hpp b/src/Plot/GoogleChart.hpp
index 136e7b228c4ae2c7d9412616079a209d346f2353..b35bab5476911010cf5eb4a9e712899df3d5e639 100644
--- a/src/Plot/GoogleChart.hpp
+++ b/src/Plot/GoogleChart.hpp
@@ -10,6 +10,7 @@
#include <fstream>
#include "Vector/map_vector.hpp"
+#include <cmath>
#define GGRAPH_COLUMS 1
#define GGRAPH_POINTS 2
@@ -153,6 +154,33 @@ const std::string saving_javascript = "function save(i)\n\
var e = document.getElementById('chart_')\n\
e.getElementsByTagName('svg')[0].parentNode.innerHTML";
+template<typename T>
+struct check_nan
+{
+ static bool check(const T & n)
+ {
+ return false;
+ }
+};
+
+template<>
+struct check_nan<float>
+{
+ static bool check(const float & n)
+ {
+ return std::isnan(n);
+ }
+};
+
+template<>
+struct check_nan<double>
+{
+ static bool check(const double & n)
+ {
+ return std::isnan(n);
+ }
+};
+
/////////////////////////////////////////////////////////////////////
/*! \brief Small class to produce graph with Google chart in HTML
@@ -186,12 +214,213 @@ const std::string saving_javascript = "function save(i)\n\
*/
class GoogleChart
{
+ template<typename arg_0, typename ... args>
+ struct get_value_type
+ {
+ typedef typename arg_0::value_type type;
+ };
+
//! set of graphs
openfpm::vector<GGraph> set_of_graphs;
//! set inject HTML;
openfpm::vector<std::string> injectHTML;
+ //! Data has holes
+ bool holes = false;
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename X, typename ... Xs>
+ void recursive_sort(X & x,X & y,Xs& ... xy)
+ {
+ struct srt_xy
+ {
+ typename X::value_type x;
+ unsigned int id;
+
+ bool operator<(const srt_xy & tmp) const
+ {
+ return x < tmp.x;
+ }
+ };
+
+ openfpm::vector<srt_xy> reord;
+ X y_tmp;
+
+ reord.resize(x.size());
+ y_tmp.resize(x.size());
+
+ for (size_t i = 0 ; i < x.size() ; i++)
+ {
+ reord.get(i).x = x.get(i);
+ reord.get(i).id = i;
+ }
+
+ reord.sort();
+
+ // reorder x and y
+
+ for (size_t i = 0 ; i < x.size() ; i++)
+ {
+ x.get(i) = reord.get(i).x;
+ y_tmp.get(i) = y.get(reord.get(i).id);
+ }
+
+ y_tmp.swap(y);
+
+ // sort x
+
+ recursive_sort(xy ...);
+ }
+
+ //! terminator for recursive sort
+ void recursive_sort()
+ {}
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename X, typename ... Xs>
+ bool isNext(size_t * counters,X & x,X & y,Xs& ... xy)
+ {
+ if (counters[0] < x.size())
+ {
+ return true;
+ }
+ return isNext(&counters[1],xy ...);
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ *
+ */
+ bool isNext(size_t * counters)
+ {
+ return false;
+ }
+
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename T, typename X, typename ... Xs>
+ T get_low(size_t * counters,X & x,X & y,Xs& ... xy)
+ {
+ if (sizeof...(Xs) != 0)
+ {
+ T low1;
+ if (counters[0] >= x.size())
+ {low1 = std::numeric_limits<typename X::value_type>::infinity();}
+ else
+ {low1 = x.get(counters[0]);}
+
+ T low2 = get_low<T>(&counters[1],xy ...);
+ return (low1 < low2)?low1:low2;
+ }
+
+ if (counters[0] >= x.size())
+ {return std::numeric_limits<typename X::value_type>::infinity();}
+ return x.get(counters[0]);
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param counters indexes
+ *
+ */
+ template<typename T>
+ T get_low(size_t * counters)
+ {
+ return 0.0;
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename X, typename ... Xs>
+ void get_point(typename X::value_type low,
+ typename X::value_type * point,
+ size_t * counters,
+ X & x,
+ X & y,
+ Xs& ... xy)
+ {
+ if (low == x.get(counters[0]))
+ {
+ point[0] = y.get(counters[0]);
+ counters[0]++;
+ }
+ else
+ {
+ point[0] = std::numeric_limits<typename X::value_type>::quiet_NaN();
+ }
+
+ get_point(low,&point[1],&counters[1],xy...);
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename T>
+ void get_point(T low,
+ T * point,
+ size_t * counters)
+ {
+ return;
+ }
+
+ /*! \brief Recursively sort variadic template of vectors
+ *
+ * \param x vector with x
+ * \param y vector with y
+ * \param xy all the other vectors
+ *
+ */
+ template<typename ... Xs>
+ bool get_v(typename get_value_type<Xs...>::type & x,
+ typename get_value_type<Xs...>::type * point,
+ size_t * counters,
+ Xs& ... xy)
+ {
+ // if exist the next element
+ if (isNext(counters,xy...) == false)
+ {return false;}
+
+ // get lowest x
+ typename get_value_type<Xs...>::type low = get_low<typename get_value_type<Xs...>::type>(counters,xy...);
+
+ x = low;
+
+ get_point(low,point,counters,xy...);
+
+ return true;
+ }
+
/*! \brief Given X and Y vector return the string representing the data section of the Google Chart
*
* \tparam X type for the X coordinates
@@ -215,7 +444,7 @@ class GoogleChart
// we require that the number of x elements are the same as y elements
if (x.size() != y.size())
- std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " vector x and the vector y must have the same number of elements " << x.size() << "!=" << y.size() << "\n";
+ {std::cerr << "Error: " << __FILE__ << ":" << __LINE__ << " vector x and the vector y must have the same number of elements " << x.size() << "!=" << y.size() << "\n";}
// Google chart visualization
data << "var data" << i << " = new google.visualization.DataTable();\n";
@@ -250,7 +479,17 @@ class GoogleChart
data << "[" << x.get(i);
}
else
- data << "," << y.get(i).get(j-1);
+ {
+ if (check_nan<typename Y::value_type>::check(y.get(i).get(j-1)) == false)
+ {
+ data << "," << y.get(i).get(j-1);
+ }
+ else
+ {
+ holes = true;
+ data << "," << "null";
+ }
+ }
}
data << "],\n";
}
@@ -351,6 +590,8 @@ class GoogleChart
of << "var options";
of << i;
of << "= {\n";
+ if (holes == true)
+ {of << "interpolateNulls : true,\n";}
of << opt;
of << "};\n";
}
@@ -513,16 +754,69 @@ public:
set_of_graphs.last().opt = opt;
}
+
/*! \brief Add lines graph
*
- * \param y A vector of vectors of values. each vector is a graph of points
+ * \param xy list of vectors like openfpm::vector<float> or openfpm::vector<double>. Suppose you have a dataset of points x1,y1
+ * and a dataset x2,y2 and you want to display all these points in one graph. Than you call this function with
+ * AddLines(x1,y1,x2,y2,opt)
*
- * \param x Give a name or number to each x value, so can be a string or a number
+ * \param opt Graph options
+ *
+ */
+ template<typename ... X> void AddLines(const openfpm::vector<std::string> & yn,
+ const GCoptions & opt,
+ X ... xy)
+ {
+ // first we sort the vectors
+ recursive_sort(xy ... );
+
+ size_t counters[sizeof...(X)];
+ memset(&counters,0,sizeof(counters));
+
+ typename get_value_type<X...>::type point[sizeof...(X)];
+ typename get_value_type<X...>::type xe;
+
+ openfpm::vector<typename get_value_type<X...>::type> x;
+
+ openfpm::vector<openfpm::vector<typename get_value_type<X...>::type>> y;
+
+
+ while (get_v(xe,point,counters,xy...))
+ {
+ y.add();
+ x.add(xe);
+
+ for (size_t i = 0 ; i < sizeof...(X)/2 ; i++)
+ {
+ y.last().add(point[i]);
+ }
+ }
+
+ AddLinesGraph(x,y,yn,opt);
+ }
+
+ /*! \brief Add lines graph
+ *
+ * If the x vector contain 0.0,0.1,0.2,0.3,0.4 and you want to draw two lines you specifying two y values for each of the x points
+ * you create an openfpm::vector<openfpm::vector<float>> y such that
+ *
+ * \verbatim
+ ------ j ------- |
+ y.get(i).get(j) = 3.2 3.4 5.4 1.3 2.3 i
+ 1.4 5.3 3.2 2.1 1.1 |
+
+ \endverbatim
+ *
+ * \param y A vector of vectors of values. each vector contain the graph points, compared to AddLinesGraph the points are stored
+ *
+ *
+ * \param x axis values
*
* \param opt Graph options
*
*/
- template<typename X, typename Y> void AddLines(openfpm::vector<X> & x, openfpm::vector<Y> & y , const GCoptions & opt)
+ template<typename X, typename Y> void AddLinesGraphT(openfpm::vector<X> & x, openfpm::vector<Y> & y , const GCoptions & opt)
{
openfpm::vector<std::string> yn;
@@ -568,6 +862,18 @@ public:
/*! \brief Add a simple lines graph
*
+ * If the x vector contain 0.0,0.1,0.2,0.3,0.4 and you want to draw two lines you specifying two y values for each of the x points
+ * you create an openfpm::vector<openfpm::vector<float>> y such that
+ *
+ * \verbatim
+ -- j --
+ y.get(i).get(j) = 3.2 3.4
+ 1.4 5.3 |
+ 5.4 3.2 i
+ 1.3 2.2 |
+ 2.3 1.1
+ \endverbatim
+ *
* \param y A vector of vectors of values. The size of y indicate how many x values
* we have, while the internal vector can store multiple value of the same point,
* for example error bar
diff --git a/src/Plot/Plot_unit_tests.hpp b/src/Plot/Plot_unit_tests.hpp
index ddb4350e5dce1fdc39abf6a7ba198951906b1a2a..37a742f4dfde5ab96a73c051099fa06b3d06283e 100644
--- a/src/Plot/Plot_unit_tests.hpp
+++ b/src/Plot/Plot_unit_tests.hpp
@@ -124,7 +124,7 @@ BOOST_AUTO_TEST_CASE( google_chart )
//! [Producing an Histogram graph]
- bool test = compare("gc_out.html","gc_out_test.html");
+ bool test = compare("gc_out.html","test_data/gc_out_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -173,7 +173,7 @@ BOOST_AUTO_TEST_CASE( google_chart2 )
cg.AddHistGraph(x,y,yn,options);
cg.write("gc_out2.html");
- bool test = compare("gc_out2.html","gc_out2_test.html");
+ bool test = compare("gc_out2.html","test_data/gc_out2_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -221,7 +221,7 @@ BOOST_AUTO_TEST_CASE( google_chart3 )
cg.AddHistGraph(x,y,yn,options);
cg.write("gc_out3.html");
- bool test = compare("gc_out3.html","gc_out3_test.html");
+ bool test = compare("gc_out3.html","test_data/gc_out3_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -262,7 +262,7 @@ BOOST_AUTO_TEST_CASE( google_chart4 )
cg.AddHistGraph(x,y,yn);
cg.write("gc_out4.html");
- bool test = compare("gc_out4.html","gc_out4_test.html");
+ bool test = compare("gc_out4.html","test_data/gc_out4_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -295,7 +295,7 @@ BOOST_AUTO_TEST_CASE( google_chart5 )
cg.AddHistGraph(x,y);
cg.write("gc_out5.html");
- bool test = compare("gc_out5.html","gc_out5_test.html");
+ bool test = compare("gc_out5.html","test_data/gc_out5_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -320,7 +320,7 @@ BOOST_AUTO_TEST_CASE( google_chart6 )
cg.AddHistGraph(y);
cg.write("gc_out6.html");
- bool test = compare("gc_out6.html","gc_out6_test.html");
+ bool test = compare("gc_out6.html","test_data/gc_out6_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -383,7 +383,127 @@ BOOST_AUTO_TEST_CASE( google_chart_with_inject_HTML )
//! [Producing a set of histograms graphs]
- bool test = compare("gc_out7.html","gc_out7_test.html");
+ bool test = compare("gc_out7.html","test_data/gc_out7_test.html");
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart_number )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+ //! [Producing a set of histograms graphs]
+
+ openfpm::vector<float> x;
+ openfpm::vector<openfpm::vector<size_t>> y;
+ openfpm::vector<std::string> yn;
+
+ x.add(0.1);
+ x.add(0.2);
+ x.add(0.3);
+ x.add(0.4);
+ x.add(0.5);
+ x.add(0.6);
+
+ // Each colum can have multiple data set (in this case 4 dataset)
+ // Each dataset can have a name
+ yn.add("dataset1");
+ yn.add("dataset2");
+ yn.add("dataset3");
+ yn.add("dataset4");
+
+ // Each colums can have multiple data-set
+ y.add({2,3,5,6});
+ y.add({5,6,1,6});
+ y.add({2,1,6,9});
+ y.add({1,6,3,2});
+ y.add({3,3,0,6});
+ y.add({2,1,4,6});
+
+ // Google charts options
+ GCoptions options;
+
+ options.title = std::string("Example");
+ options.yAxis = std::string("Y Axis");
+ options.xAxis = std::string("X Axis");
+ options.stype = std::string("line");
+
+ GoogleChart cg;
+ //
+ cg.AddLinesGraph(x,y,yn,options);
+ cg.write("gc_num_plot.html");
+
+ //! [Producing a set of histograms graphs]
+
+ bool test = compare("gc_num_plot.html","test_data/gc_num_plot_test.html");
+ BOOST_REQUIRE_EQUAL(true,test);
+}
+
+BOOST_AUTO_TEST_CASE( google_chart_number_lines_different_x )
+{
+ Vcluster<> & v_cl = create_vcluster();
+
+ if (v_cl.getProcessUnitID() != 0)
+ return;
+
+ //! [Producing a set of histograms graphs]
+
+ openfpm::vector<float> x1;
+ openfpm::vector<float> y1;
+ openfpm::vector<float> x2;
+ openfpm::vector<float> y2;
+ openfpm::vector<float> x3;
+ openfpm::vector<float> y3;
+ openfpm::vector<std::string> yn;
+
+ x1.add(0.1); y1.add(4.5);
+ x1.add(0.2); y1.add(3.0);
+ x1.add(0.3); y1.add(5.5);
+ x1.add(0.4); y1.add(3.3);
+ x1.add(0.5); y1.add(1.0);
+ x1.add(0.6); y1.add(7.0);
+
+ x2.add(0.15); y2.add(1.5);
+ x2.add(0.2); y2.add(4.5);
+ x2.add(0.35); y2.add(2.5);
+ x2.add(0.45); y2.add(6.5);
+
+ x3.add(0.1); y3.add(3.5);
+ x3.add(0.2); y3.add(6.5);
+ x3.add(0.63); y3.add(1.5);
+ x3.add(0.37); y3.add(1.5);
+ x3.add(0.7); y3.add(3.5);
+ x3.add(0.82); y3.add(2.5);
+ x3.add(0.4); y3.add(2.5);
+ x3.add(1.0); y3.add(1.5);
+ x3.add(0.5); y3.add(7.5);
+ x3.add(0.91); y3.add(5.5);
+
+ // Each colum can have multiple data set (in this case 4 dataset)
+ // Each dataset can have a name
+ yn.add("dataset1");
+ yn.add("dataset2");
+ yn.add("dataset3");
+
+
+ // Google charts options
+ GCoptions options;
+
+ options.title = std::string("Example");
+ options.yAxis = std::string("Y Axis");
+ options.xAxis = std::string("X Axis");
+ options.stype = std::string("line");
+
+ GoogleChart cg;
+
+ cg.AddLines(yn,options,x1,y1,x2,y2,x3,y3);
+ cg.write("gc_num_ydif_plot.html");
+
+ //! [Producing a set of histograms graphs]
+
+ bool test = compare("gc_num_ydif_plot.html","test_data/gc_num_ydif_plot_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -450,7 +570,7 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot )
//! [Producing lines graph with style]
- bool test = compare("gc_plot_out.html","gc_plot_out_test.html");
+ bool test = compare("gc_plot_out.html","test_data/gc_plot_out_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
@@ -499,7 +619,7 @@ BOOST_AUTO_TEST_CASE( google_chart_linear_plot2 )
//! [Producing lines]
- bool test = compare("gc_plot2_out.html","gc_plot2_out_test.html");
+ bool test = compare("gc_plot2_out.html","test_data/gc_plot2_out_test.html");
BOOST_REQUIRE_EQUAL(true,test);
}
diff --git a/src/VTKWriter/VTKWriter.hpp b/src/VTKWriter/VTKWriter.hpp
index d8fa3e328e45c5aa2358c101ed563d00d20ec8dc..16f5a1c9daa2c38aa6aaae6bb42cc4e11c39585e 100644
--- a/src/VTKWriter/VTKWriter.hpp
+++ b/src/VTKWriter/VTKWriter.hpp
@@ -24,27 +24,27 @@
template <typename T> std::string getType()
{
// Create a property string based on the type of the property
- if (typeid(T) == typeid(float))
+ if (std::is_same<T,float>::value)
return "float";
- else if (typeid(T) == typeid(double))
+ else if (std::is_same<T,double>::value)
return "double";
- else if (typeid(T) == typeid(char))
+ else if (std::is_same<T,char>::value)
return "char";
- else if (typeid(T) == typeid(unsigned char))
+ else if (std::is_same<T,unsigned char>::value)
return "unsigned_char";
- else if (typeid(T) == typeid(short))
+ else if (std::is_same<T,short>::value)
return "short";
- else if (typeid(T) == typeid(unsigned short))
+ else if (std::is_same<T,unsigned short>::value)
return "unsigned_short";
- else if (typeid(T) == typeid(int))
+ else if (std::is_same<T,int>::value)
return "int";
- else if (typeid(T) == typeid(unsigned int))
+ else if (std::is_same<T,unsigned int>::value)
return "unsigned_int";
- else if (typeid(T) == typeid(long int))
+ else if (std::is_same<T,long int>::value)
return "int";
- else if (typeid(T) == typeid(unsigned long int))
+ else if (std::is_same<T,unsigned long int>::value )
return "unsigned_int";
- else if (typeid(T) == typeid(bool))
+ else if (std::is_same<T,bool>::value )
return "bit";
return "";
@@ -103,6 +103,7 @@ enum file_type
#define VTK_WRITER 0x10000
#define FORMAT_ASCII 0x0
#define FORMAT_BINARY 0x10000000
+#define PRINT_GHOST 1
template <typename Object, unsigned int imp>
class VTKWriter
@@ -121,7 +122,6 @@ class VTKWriter
#include "VTKWriter_dist_graph.hpp"
#endif
-
#include "VTKWriter_point_set.hpp"
#endif /* VTKWRITER_HPP_ */
diff --git a/src/VTKWriter/VTKWriter_graph.hpp b/src/VTKWriter/VTKWriter_graph.hpp
index 18d4667808aea9f99c298d72dcadecb16bc78728..bb5be70cdf655d27b9a5913904e43f5ba80589fb 100644
--- a/src/VTKWriter/VTKWriter_graph.hpp
+++ b/src/VTKWriter/VTKWriter_graph.hpp
@@ -65,14 +65,13 @@ struct vtk_vertex_node_array_scalar_selector<true>
static inline void move(typename G::V_container &vo, s_type (&x)[3], bool &z_set)
{
if (G::V_type::attributes::name[T::value] != "x")
- return;
+ {return;}
if (std::extent<ele_v>::value == 3)
- z_set = true;
+ {z_set = true;}
for (size_t i = 0; i < std::extent<ele_v>::value; i++)
- x[i] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>()[i])>::type>::template to<s_type>(vo.template get<T::value>()[i]);
-
+ {x[i] = convert<typename boost::remove_reference<decltype(vo.template get<T::value>()[i])>::type>::template to<s_type>(vo.template get<T::value>()[i]);}
}
};
diff --git a/src/VTKWriter/VTKWriter_grids.hpp b/src/VTKWriter/VTKWriter_grids.hpp
index 46059296bd512cab4ce3d72bd4458ae231b583dc..21c1848560b07903c3af325c309b9747ab3683bd 100644
--- a/src/VTKWriter/VTKWriter_grids.hpp
+++ b/src/VTKWriter/VTKWriter_grids.hpp
@@ -117,10 +117,36 @@ struct prop_out_g
// if there is the next element
while (it.isNext())
{
- if (vg.get(k).dom.isInside(it.get().toPoint()) == true)
- v_out += "1.0\n";
+ if (ft == file_type::ASCII)
+ {
+ if (vg.get(k).dom.isInside(it.get().toPoint()) == true)
+ {
+ float flag = 1.0;
+ flag += vg.get(k).g.getFlag(it.get()) * 2;
+ v_out += std::to_string(flag) + "\n";
+ }
+ else
+ {
+ float flag = 0.0;
+ flag += vg.get(k).g.getFlag(it.get()) * 2;
+ v_out += std::to_string(flag) + "\n";
+ }
+ }
else
- v_out += "0.0\n";
+ {
+ if (vg.get(k).dom.isInside(it.get().toPoint()) == true)
+ {
+ float flag = 1.0;
+ flag = swap_endian_lt(flag);
+ v_out.append((const char *)&flag,sizeof(flag));
+ }
+ else
+ {
+ float flag = 0.0;
+ flag = swap_endian_lt(flag);
+ v_out.append((const char *)&flag,sizeof(flag));
+ }
+ }
// increment the iterator and counter
++it;
@@ -142,8 +168,8 @@ template <typename pair>
class VTKWriter<pair,VECTOR_GRIDS>
{
//! Vector of grids
- openfpm::vector< ele_g<typename pair::first,typename pair::second> > vg;
+ openfpm::vector< ele_g<typename pair::first,typename pair::second> > vg;
/*! \brief Get the total number of points
*
* \return the total number
@@ -380,9 +406,9 @@ public:
prop_out_g< ele_g<typename pair::first,typename pair::second>, typename pair::second > pp(point_data, vg, prop_names, ft);
if (prp == -1)
- boost::mpl::for_each< boost::mpl::range_c<int,0, pair::first::value_type::max_prop> >(pp);
+ {boost::mpl::for_each< boost::mpl::range_c<int,0, pair::first::value_type::max_prop> >(pp);}
else
- boost::mpl::for_each< boost::mpl::range_c<int,prp, prp> >(pp);
+ {boost::mpl::for_each< boost::mpl::range_c<int,prp, prp> >(pp);}
// Add the last property
pp.lastProp();
diff --git a/src/VTKWriter/VTKWriter_grids_st.hpp b/src/VTKWriter/VTKWriter_grids_st.hpp
index 43b4167318ba3bdad75185e2a1523fb08706919f..b6b523a83e1f843f00aca92d44c541237e75f25d 100644
--- a/src/VTKWriter/VTKWriter_grids_st.hpp
+++ b/src/VTKWriter/VTKWriter_grids_st.hpp
@@ -371,7 +371,9 @@ class VTKWriter<pair,VECTOR_ST_GRIDS>
// if the type is not supported return
if (type.size() == 0)
{
+#ifndef DISABLE_ALL_RTTI
std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " the type " << demangle(typeid(ctype).name()) << " is not supported by vtk\n";
+#endif
return "";
}
diff --git a/src/VTKWriter/VTKWriter_grids_util.hpp b/src/VTKWriter/VTKWriter_grids_util.hpp
index 8adc6e2e7d4a7a2e76e90c69a44eb0d1f146ec59..2e05b26defb337db772b3d97514ec0dfd5abe41d 100644
--- a/src/VTKWriter/VTKWriter_grids_util.hpp
+++ b/src/VTKWriter/VTKWriter_grids_util.hpp
@@ -89,7 +89,9 @@ template<unsigned int i, typename ele_g, bool has_attributes> std::string get_po
// if the type is not supported skip-it
if (type.size() == 0)
{
+#ifndef DISABLE_ALL_RTTI
std::cerr << "Error " << __FILE__ << ":" << __LINE__ << " the type " << demangle(typeid(ctype).name()) << " is not supported by vtk\n";
+#endif
return "";
}
@@ -200,17 +202,17 @@ public:
*/
template<typename vector, typename iterator, typename I> static void write(std::string & v_out, vector & vg, size_t k, iterator & it, file_type ft)
{
- typedef decltype(vg.get(k).g.get_o(it.get()).template get<I::value>()) ctype_;
- typedef typename std::remove_reference<ctype_>::type ctype;
+ typedef decltype(vg.get(k).g.template get<I::value>(it.get())) ctype_;
+ typedef typename std::remove_const<typename std::remove_reference<ctype_>::type>::type ctype;
if (ft == file_type::ASCII)
{
// Print the property
- v_out += std::to_string(vg.get(k).g.get_o(it.get()).template get<I::value>()) + "\n";
+ v_out += std::to_string(vg.get(k).g.template get<I::value>(it.get())) + "\n";
}
else
{
- typename is_vtk_writable<ctype>::base tmp = vg.get(k).g.get_o(it.get()).template get<I::value>();
+ typename is_vtk_writable<ctype>::base tmp = vg.get(k).g.template get<I::value>(it.get());
tmp = swap_endian_lt(tmp);
v_out.append((const char *)&tmp,sizeof(tmp));
}
@@ -309,10 +311,10 @@ struct meta_prop<I, ele_g,St,T[N1],is_writable>
{
// Print the properties
for (size_t i1 = 0 ; i1 < N1 ; i1++)
- {v_out += std::to_string(vg.get(k).g.get_o(it.get()).template get<I::value>()[i1]) + " ";}
+ {v_out += std::to_string(vg.get(k).g.template get<I::value>(it.get())[i1]) + " ";}
if (N1 == 2)
- {v_out += "0.0";}
+ {v_out += std::to_string((decltype(vg.get(k).g.template get<I::value>(it.get())[0])) 0);}
v_out += "\n";
}
@@ -323,7 +325,7 @@ struct meta_prop<I, ele_g,St,T[N1],is_writable>
// Print the properties
for (size_t i1 = 0 ; i1 < N1 ; i1++)
{
- tmp = vg.get(k).g.get_o(it.get()).template get<I::value>()[i1];
+ tmp = vg.get(k).g.template get<I::value>(it.get())[i1];
tmp = swap_endian_lt(tmp);
v_out.append((const char *)&tmp,sizeof(T));
}
@@ -388,11 +390,11 @@ struct meta_prop<I, ele_g,St, T[N1][N2],is_writable>
if (ft == file_type::ASCII)
{
// Print the property
- v_out += std::to_string(vg.get(k).g.get_o(it.get()).template get<I::value>()[i1][i2]) + "\n";
+ v_out += std::to_string(vg.get(k).g.template get<I::value>(it.get())[i1][i2]) + "\n";
}
else
{
- tmp = vg.get(k).g.get_o(it.get()).template get<I::value>()[i1][i2];
+ tmp = vg.get(k).g.template get<I::value>(it.get())[i1][i2];
tmp = swap_endian_lt(tmp);
v_out.append((const char *)&tmp,sizeof(tmp));
}
diff --git a/src/VTKWriter/VTKWriter_point_set.hpp b/src/VTKWriter/VTKWriter_point_set.hpp
index ce920abdbae5bd71972416b427f98c67daadf626..b3060663d3327338b556fa092863ac83a5412cdd 100644
--- a/src/VTKWriter/VTKWriter_point_set.hpp
+++ b/src/VTKWriter/VTKWriter_point_set.hpp
@@ -343,7 +343,7 @@ class VTKWriter<pair,VECTOR_POINTS>
* \param meta_data string with the meta-data to add
*
*/
- std::string add_meta_data(std::string & meta_data)
+ std::string add_meta_data(std::string & meta_data, file_type & opt)
{
std::string meta_string;
@@ -362,7 +362,13 @@ class VTKWriter<pair,VECTOR_POINTS>
{
meta_string += "FIELD FieldData 1\n";
meta_string += "TIME 1 1 double\n";
- meta_string += std::to_string(time);
+ if (opt == file_type::ASCII)
+ {meta_string += std::to_string(time);}
+ else
+ {
+ time = swap_endian_lt(time);
+ meta_string.append((const char *)&time,sizeof(double));
+ }
meta_string += "\n";
}
@@ -446,7 +452,7 @@ public:
// Data type for graph is DATASET POLYDATA
vtk_header += "DATASET POLYDATA\n";
- vtk_header += add_meta_data(meta_data);
+ vtk_header += add_meta_data(meta_data,ft);
// point properties header
point_prop_header = get_point_properties_list(ft);
diff --git a/src/VTKWriter/VTKWriter_unit_tests.hpp b/src/VTKWriter/VTKWriter_unit_tests.hpp
index de10b80628d954d9552138fbb1e0ff91df6b3d3b..b123d40c8730a1598af01adc4e4aaba110c5786b 100644
--- a/src/VTKWriter/VTKWriter_unit_tests.hpp
+++ b/src/VTKWriter/VTKWriter_unit_tests.hpp
@@ -1049,6 +1049,9 @@ BOOST_AUTO_TEST_CASE( vtk_writer_use_point_set )
vtk_v3.write("vtk_points_pp_header.vtk",prp_names,"points","time=5.123");
+ // We try binary
+ vtk_v3.write("vtk_points_pp_header_bin.vtk",prp_names,"points","time=5.123",file_type::BINARY);
+
#ifndef SE_CLASS3
// Check that match
diff --git a/src/util/GBoxes.hpp b/src/util/GBoxes.hpp
index 4f4304c454bb18d2c9c06a960b2c1ee5e66cbc42..8ece35653eded808bbf8aa4911b8f0bb30fafc85 100644
--- a/src/util/GBoxes.hpp
+++ b/src/util/GBoxes.hpp
@@ -45,6 +45,10 @@ struct GBoxes
//! origin of GDbox in global grid coordinates
Point<dim,long int> origin;
+ //! In case the grid is not defined everywhere but is defined by a set of boxes
+ //! indicate from which box it come from
+ size_t k;
+
/*! \brief Indicate that this structure has no pointers inside
*
* \return true
diff --git a/test_data/gc_num_plot_test.html b/test_data/gc_num_plot_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..455f7c46e1ee67ad0c4a5a38faad543bd4917c38
--- /dev/null
+++ b/test_data/gc_num_plot_test.html
@@ -0,0 +1,50 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('number','X Axis');
+data0.addColumn('number','dataset1');
+data0.addColumn('number','dataset2');
+data0.addColumn('number','dataset3');
+data0.addColumn('number','dataset4');
+data0.addRows([
+[0.1,2,3,5,6],
+[0.2,5,6,1,6],
+[0.3,2,1,6,9],
+[0.4,1,6,3,2],
+[0.5,3,3,0,6],
+[0.6,2,1,4,6],
+]);
+var options0= {
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+curveType: 'function',
+lineWidth: 4,
+intervals: { 'style':'area' }};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/test_data/gc_num_ydif_plot_test.html b/test_data/gc_num_ydif_plot_test.html
new file mode 100644
index 0000000000000000000000000000000000000000..0a54032227398f1544586ea733e28cf5c22cd276
--- /dev/null
+++ b/test_data/gc_num_ydif_plot_test.html
@@ -0,0 +1,59 @@
+<html>
+ <head>
+ <script type="text/javascript" src="https://www.gstatic.com/charts/loader.js"></script>
+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.4/jquery.min.js"></script>
+ <script type="text/javascript">
+ google.charts.load('current', {'packages':['corechart']});
+ google.charts.setOnLoadCallback(drawVisualization);
+
+function exportToSVG(i)
+{
+var e = document.getElementById('chart_div'+i);
+var svg = e.getElementsByTagName('svg')[0].parentNode.innerHTML;
+var pos = svg.lastIndexOf("</svg>");
+pos += 6;
+svg = svg.substring(0,4) + " xmlns='http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink' " + svg.substring(4,pos);
+svgData = 'data:image/svg+xml;charset=utf-8,' + encodeURIComponent(svg);
+$(this).attr({'href': svgData,'target': '_blank'});
+}
+
+ function drawVisualization() {
+var data0 = new google.visualization.DataTable();
+data0.addColumn('number','X Axis');
+data0.addColumn('number','dataset1');
+data0.addColumn('number','dataset2');
+data0.addColumn('number','dataset3');
+data0.addRows([
+[0.1,4.5,null,3.5],
+[0.15,null,1.5,null],
+[0.2,3,4.5,6.5],
+[0.3,5.5,null,null],
+[0.35,null,2.5,null],
+[0.37,null,null,1.5],
+[0.4,3.3,null,2.5],
+[0.45,null,6.5,null],
+[0.5,1,null,7.5],
+[0.6,7,null,null],
+[0.63,null,null,1.5],
+[0.7,null,null,3.5],
+[0.82,null,null,2.5],
+[0.91,null,null,5.5],
+[1,null,null,1.5],
+]);
+var options0= {
+interpolateNulls : true,
+title : 'Example',
+vAxis: {title: 'Y Axis'},
+hAxis: {title: 'X Axis'},
+curveType: 'function',
+lineWidth: 4,
+intervals: { 'style':'area' }};
+$("#export_svg0").on("click", function (event) {exportToSVG.apply(this,[0]);});
+var chart = new google.visualization.ComboChart(document.getElementById('chart_div0'));
+chart.draw(data0, options0);
+}</script>
+</head>
+<body>
+<a href="#" download="graph1.svg" id="export_svg0"><button>Export data into svg</button></a><div id="chart_div0" style="width: 900px; height: 500px;"></div>
+</body>
+</html>
diff --git a/gc_out2_test.html b/test_data/gc_out2_test.html
similarity index 100%
rename from gc_out2_test.html
rename to test_data/gc_out2_test.html
diff --git a/gc_out3_test.html b/test_data/gc_out3_test.html
similarity index 100%
rename from gc_out3_test.html
rename to test_data/gc_out3_test.html
diff --git a/gc_out4_test.html b/test_data/gc_out4_test.html
similarity index 100%
rename from gc_out4_test.html
rename to test_data/gc_out4_test.html
diff --git a/gc_out5_test.html b/test_data/gc_out5_test.html
similarity index 100%
rename from gc_out5_test.html
rename to test_data/gc_out5_test.html
diff --git a/gc_out6_test.html b/test_data/gc_out6_test.html
similarity index 100%
rename from gc_out6_test.html
rename to test_data/gc_out6_test.html
diff --git a/gc_out7_test.html b/test_data/gc_out7_test.html
similarity index 100%
rename from gc_out7_test.html
rename to test_data/gc_out7_test.html
diff --git a/gc_out_test.html b/test_data/gc_out_test.html
similarity index 100%
rename from gc_out_test.html
rename to test_data/gc_out_test.html
diff --git a/gc_plot2_out_test.html b/test_data/gc_plot2_out_test.html
similarity index 100%
rename from gc_plot2_out_test.html
rename to test_data/gc_plot2_out_test.html
diff --git a/gc_plot_out_test.html b/test_data/gc_plot_out_test.html
similarity index 100%
rename from gc_plot_out_test.html
rename to test_data/gc_plot_out_test.html
diff --git a/test_data/vtk_grids_prp_test.vtk b/test_data/vtk_grids_prp_test.vtk
index 600c2207429792f3c196a4c075e1c42e79dde1ee..f861b08723489bcc41f4c16cc5b792344b364fa9 100644
--- a/test_data/vtk_grids_prp_test.vtk
+++ b/test_data/vtk_grids_prp_test.vtk
@@ -6159,1027 +6159,1027 @@ LOOKUP_TABLE default
1.000000
SCALARS domain float
LOOKUP_TABLE default
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diff --git a/test_data/vtk_grids_test.vtk b/test_data/vtk_grids_test.vtk
index 5e292278af14dc4d2f5993d5492aa0e25e427016..bfb0de82b7e03a0f4f14026be4327f5d77beffc3 100644
--- a/test_data/vtk_grids_test.vtk
+++ b/test_data/vtk_grids_test.vtk
@@ -16418,1027 +16418,1027 @@ LOOKUP_TABLE default
255.000000
SCALARS domain float
LOOKUP_TABLE default
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diff --git a/test_data/vtk_grids_test_1d.vtk b/test_data/vtk_grids_test_1d.vtk
index 67aae8b5ba98195378710e35d6619f0847694e7f..76e6973b75c2f3fb6620405e1d1bf3997369840c 100644
--- a/test_data/vtk_grids_test_1d.vtk
+++ b/test_data/vtk_grids_test_1d.vtk
@@ -1058,67 +1058,67 @@ LOOKUP_TABLE default
15.000000
SCALARS domain float
LOOKUP_TABLE default
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