Merge commit '40e3ee35ad7c5158b2184aed925ac7c9f1b293bc' as 'src/SZ'

src/SZ/.dockerignore

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+build.*

src/SZ/.e4s/e4s.yaml

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+- e4s_product: SZ
+  version: 1.2.12
+  type: Compression
+  website: https://szcompressor.org
+  docs: [README.md]
+  subrepo_urls: ["https://github.com/szcompressor/SZ", "https://github.com/szcompressor/SZ3", "https://github.com/szcompressor/SZx", "https://github.com/szcompressor/cuSZ", "https://github.com/szcompressor/SZauto", "https://github.com/szcompressor/MMD-SZ"]

src/SZ/.gitignore

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+build
+compile_commands.json
+tags
+CMakeCache.txt
+cmake-build-debug/
+CMakeFiles/

src/SZ/.travis.yml

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+sudo: false
+
+language: c
+
+before_install:
+- cd test/travis-ci && ./getData.sh && cd -
+
+matrix:
+  include:
+    - dist: xenial
+      os: linux
+      addons:
+        apt:
+          sources:
+            - ubuntu-toolchain-r-test     # For gcc 4.9, 5 and 7
+          packages:
+            - gcc-7
+            - gfortran-7
+            - zstd
+            - libzstd1-dev
+            - exuberant-ctags
+            - libcunit1-dev 
+            - libnetcdf-dev 
+    - osx_image: xcode11
+      os: osx
+      env: PATH=/usr/local/bin:$PATH
+install:
+    - mkdir build
+    - cd build
+    - |
+      if [[ "${TRAVIS_OS_NAME}" != "linux" ]]; then
+        brew install ctags
+        brew install cunit
+        brew upgrade pkg-config
+      fi
+    - cmake -DCMAKE_INSTALL_PREFIX=$HOME -DBUILD_TESTS=ON -DBUILD_INTEGRATION_TESTS=ON ..
+    - make 
+    - make install
+    - make test
+
+script:
+- cd ..
+- ./configure && make
+- cd example && ./test.sh && cd -
+- cd test/travis-ci && ./test.sh && cd -

src/SZ/CMakeLists.txt

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+cmake_minimum_required (VERSION 3.10.2)
+
+#disable in-source builds
+set (CMAKE_DISABLE_SOURCE_CHANGES ON)
+set (CMAKE_DISABLE_IN_SOURCE_BUILD ON)
+
+#define the project
+project (sz 
+  VERSION 2.1.6.2
+  DESCRIPTION "SZ Error Bounded Lossy Compressor"
+  LANGUAGES C CXX
+  )
+enable_testing()
+
+#correct was to set a default build type
+# https://blog.kitware.com/cmake-and-the-default-build-type/
+set(default_build_type "Release")
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "No build type was set. Setting build type to ${default_build_type}.")
+  set(CMAKE_BUILD_TYPE ${default_build_type} CACHE 
+    STRING "Choose the type to build" FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
+    "MinSizeRel" "RelWithDebInfo")
+endif()
+
+#set the Compiler ID for clang on macOS to AppleClang
+if (POLICY CMP0025)
+  cmake_policy (SET CMP0025 NEW)
+endif()
+
+#compile with C-99 and standard C++14
+set(CMAKE_C_STANDARD 99)
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
+#  Check for the existence of certain header files
+include (CheckIncludeFiles)
+include (CheckFunctionExists)
+CHECK_INCLUDE_FILES ("unistd.h"        HAVE_UNISTD_H)
+CHECK_INCLUDE_FILES ("sys/time.h"      HAVE_SYS_TIME_H)
+
+if (WINDOWS)
+  set (HAVE_GETTIMEOFDAY 1)
+endif ()
+
+if (MINGW OR NOT WINDOWS)
+  CHECK_FUNCTION_EXISTS (gettimeofday           HAVE_GETTIMEOFDAY)
+  CHECK_FUNCTION_EXISTS (clock_gettime          HAVE_CLOCK_GETTIME)
+endif ()
+
+# Generate the config.h file containing user settings needed by compilation
+configure_file (config.h.cmake ${CMAKE_BINARY_DIR}/config.h @ONLY)
+
+#generate tags for the project if tags exist
+option(BUILD_CTAGS "enable ctags generation target" OFF)
+if(BUILD_CTAGS)
+  find_program(TAGS ctags)
+  if(TAGS)
+    add_custom_target(tags ALL
+      COMMAND ${TAGS} --exclude=${CMAKE_BINARY_DIR} -f ${CMAKE_BINARY_DIR}/tags --c++-kinds=+p --fields=+iaS -R
+      COMMENT Generating Tag files
+      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+      )
+  endif()
+endif()
+
+option(BUILD_SHARED_LIBS "build shared libraries over static libraries" ON)
+
+#find dependencies
+option(SZ_FIND_DEPS "find dependent libraries or build ext libraries" ON)
+include(GNUInstallDirs)
+if(SZ_FIND_DEPS)
+  find_package(PkgConfig)
+  pkg_search_module(ZSTD  IMPORTED_TARGET libzstd)
+
+  #by default pass no 3rd party exports
+  set(thirdparty_export "")
+
+  if(ZSTD_FOUND)
+    set(ZSTD_dep PkgConfig::ZSTD)
+  else()
+    add_subdirectory(zstd)
+    set(ZSTD_dep zstd)
+    list(APPEND thirdparty_export "zstd")
+  endif()
+
+  find_package(ZLIB)
+  if(ZLIB_FOUND)
+    set(ZLIB_dep ZLIB::ZLIB)
+  else()
+    add_subdirectory(zlib)
+    set(ZLIB_dep ZLIB)
+    list(APPEND thirdparty_export "ZLIB")
+  endif()
+else()
+    add_subdirectory(zstd)
+    set(ZSTD_dep zstd)
+    list(APPEND thirdparty_export "zstd")
+    add_subdirectory(zlib)
+    set(ZLIB_dep ZLIB)
+    list(APPEND thirdparty_export "ZLIB")
+endif()
+
+find_package(OpenMP)
+
+add_subdirectory(sz)
+option(BUILD_SZ_EXAMPLES "build sz example" OFF)
+if(BUILD_SZ_EXAMPLES)
+  add_subdirectory(example)
+endif()
+
+option(BUILD_PYTHON_WRAPPER "build python wrapper" OFF)
+if(BUILD_PYTHON_WRAPPER)
+  message(WARNING "The python bindings for SZ are deprecated.  "
+                  "Please consider using the Python bindings for "
+                  "[LibPressio](https://github.com/codarcode/libpressio#python)"
+                  " to use SZ from python instead.")
+  add_subdirectory(swig)
+endif()
+
+option(BUILD_TESTS "build test cases" OFF)
+if(BUILD_TESTS)
+  add_subdirectory(test)
+endif()
+
+option(BUILD_NETCDF_READER "build the NetCDF reader" OFF)
+if(BUILD_NETCDF_READER)
+  add_subdirectory(NetCDFReader)
+endif()
+
+option(BUILD_HDF5_FILTER "build the HDF5 filter" OFF)
+if(BUILD_HDF5_FILTER)
+  add_subdirectory(hdf5-filter/H5Z-SZ/)
+endif()
+
+option(BUILD_PASTRI "build the pastri code" OFF)
+option(BUILD_TIMECMPR "build the time based compression code" OFF)
+option(BUILD_RANDOMACCESS "build the random access code" OFF)
+option(BUILD_DOCKER_CONTAINERS "build docker containers for testing" OFF)
+option(BUILD_FORTRAN "build the fortran interface" OFF)
+option(BUILD_STATS "record statistics for prediction" OFF)
+option(BUILD_OPENMP "build OpenMP support" OFF)
+if(BUILD_DOCKER_CONTAINERS)
+
+  foreach(CONTAINER Centos Fedora Ubuntu Travis CentosPackaged)
+    set(BuildSentinel ${CMAKE_BINARY_DIR}/${CONTAINER}-built)
+    set(Dockerfile docker/Dockerfile-${CONTAINER})
+    string(TOLOWER "sz${CONTAINER}" CONTAINER_TAG)
+    add_custom_command(OUTPUT ${BuildSentinel}
+      COMMAND sudo docker build -t ${CONTAINER_TAG} -f ${Dockerfile} .
+      COMMAND touch ${BuildSentinel}
+      MAIN_DEPENDENCY ${Dockerfile}
+      DEPENDS SZ
+      WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+      COMMENT "DOCKER ${Dockerfile}"
+      )
+    list(APPEND DOCKER_CONTAINERS ${BuildSentinel})
+  endforeach()
+  add_custom_target(docker DEPENDS ${DOCKER_CONTAINERS} COMMENT "building docker containers")
+endif()
+
+configure_file(
+  ${CMAKE_CURRENT_SOURCE_DIR}/sz.pc.in
+  ${CMAKE_BINARY_DIR}/sz.pc
+  @ONLY
+)
+install(FILES ${CMAKE_BINARY_DIR}/sz.pc DESTINATION ${CMAKE_INSTALL_PREFIX}/share/pkgconfig)
+

src/SZ/Makefile.am

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+AUTOMAKE_OPTIONS=foreign
+SUBDIRS = zlib zstd sz example