Release 0.5.4

CMakeLists.txt

@@ -30,6 +30,8 @@ project(ZFP VERSION ${ZFP_VERSION})
 # Some boilerplate to setup nice output directories
 #------------------------------------------------------------------------------#
 include(GNUInstallDirs)
+set(CMAKE_INSTALL_CMAKEDIR ${CMAKE_INSTALL_LIBDIR}/cmake/zfp
+  CACHE STRING "Installation CMake subdirectory")
 
 list(INSERT CMAKE_MODULE_PATH 0 "${ZFP_SOURCE_DIR}/cmake")
 if(NOT CMAKE_RUNTIME_OUTPUT_DIRECTORY)
@@ -88,22 +90,25 @@ cmake_dependent_option(BUILD_SHARED_LIBS
 
 # PIC is always on for shared libs.  This allows it to be selectable for
 # static libs.
-if(SHARED_LIBS_SUPPORTED)
-  cmake_dependent_option(ZFP_ENABLE_PIC
-    "Build with Position Independent Code" ON
-    "NOT BUILD_SHARED_LIBS" ON)
-endif()
-if(ZFP_ENABLE_PIC)
-  set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+if(DEFINED ZFP_ENABLE_PIC)
+  set(ZFP_ENABLE_PIC_DEFAULT ${ZFP_ENABLE_PIC})
+elseif(DEFINED CMAKE_POSITION_INDEPENDENT_CODE)
+  set(ZFP_ENABLE_PIC_DEFAULT ${CMAKE_POSITION_INDEPENDENT_CODE})
+else()
+  set(ZFP_ENABLE_PIC_DEFAULT ${SHARED_LIBS_SUPPORTED})
 endif()
+cmake_dependent_option(ZFP_ENABLE_PIC
+  "Build with Position Independent Code" ${ZFP_ENABLE_PIC_DEFAULT}
+  "SHARED_LIBS_SUPPORTED" OFF)
+set(CMAKE_POSITION_INDEPENDENT_CODE ${ZFP_ENABLE_PIC})
 
 # Compile-time options.
 
 set(ZFP_BIT_STREAM_WORD_SIZE 64 CACHE STRING
   "Use smaller bit stream word type for finer rate granularity")
 set_property(CACHE ZFP_BIT_STREAM_WORD_SIZE PROPERTY STRINGS "8;16;32;64")
 
-option(ZFP_WITH_OPENMP "Enable OpenMP parallel compression" ON)
+option(ZFP_WITH_CUDA "Enable CUDA parallel compression" OFF)
 
 option(ZFP_WITH_BIT_STREAM_STRIDED
   "Enable strided access for progressive zfp streams" OFF)
@@ -129,12 +134,36 @@ if((DEFINED ZFP_UINT64) AND (DEFINED ZFP_UINT64_SUFFIX))
   list(APPEND zfp_defs ZFP_UINT64_SUFFIX=${ZFP_UINT64_SUFFIX})
 endif()
 
-if(ZFP_WITH_OPENMP)
-  find_package(OpenMP)
-  if(OPENMP_FOUND)
-    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
-    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+# This odd cmake pattern here let's the OpenMP feature be either auto-detected,
+# explicitly enabled, or explicitly disabled, instead of just on or off.
+if(DEFINED ZFP_WITH_OPENMP)
+  option(ZFP_WITH_OPENMP "Enable OpenMP parallel compression"
+    ${ZFP_WITH_OPENMP})
+  if(ZFP_WITH_OPENMP)
+    find_package(OpenMP COMPONENTS C REQUIRED)
+  endif()
+else()
+  find_package(OpenMP COMPONENTS C)
+  option(ZFP_WITH_OPENMP "Enable OpenMP parallel compression" ${OPENMP_FOUND})
+endif()
+
+# Some compilers don't use explicit libraries on the link line for OpenMP but
+# instead need to treat the OpenMP C flags as both compile and link flags
+# i.e. -fopenmp for compiling and -lgomp for linking, use -fomp for both
+# compiling and linking
+if(ZFP_WITH_OPENMP AND NOT OpenMP_C_LIBRARIES)
+  set(OpenMP_C_LIBRARIES ${OpenMP_C_FLAGS})
+endif()
+
+if(ZFP_WITH_CUDA)
+  # use CUDA_BIN_DIR hint
+  set(ENV{CUDA_BIN_PATH} ${CUDA_BIN_DIR})
+  find_package(CUDA)
+  if(NOT CUDA_FOUND)
+    message(FATAL_ERROR "ZFP_WITH_CUDA is enabled, but a CUDA installation was not found.")
+  endif()
+  if(${CUDA_VERSION_MAJOR} LESS 7)
+        message(FATAL_ERROR "zfp requires at least CUDA 7.0.")
   endif()
 endif()
 
@@ -162,11 +191,32 @@ if(ZFP_WITH_CACHE_PROFILE)
   list(APPEND zfp_defs ZFP_CACHE_PROFILE)
 endif()
 
+# Link libm only if necessary
+include(CheckCSourceCompiles)
+check_c_source_compiles("#include<math.h>\nfloat f; int main(){sqrt(f);return 0;}" HAVE_MATH)
+if(NOT HAVE_MATH)
+  set(CMAKE_REQUIRED_LIBRARIES m)
+  check_c_source_compiles("#include<math.h>\nfloat f; int main(){sqrt(f);return 0;}" HAVE_LIBM_MATH)
+  unset(CMAKE_REQUIRED_LIBRARIES)
+  if(NOT HAVE_LIBM_MATH)
+    message(FATAL_ERROR "Unable to use C math library functions (with or without -lm)")
+  endif()
+endif()
+
 #------------------------------------------------------------------------------#
 # Add source code
 #------------------------------------------------------------------------------#
+set(ZFP_LIBRARY_PREFIX "" CACHE STRING
+  "Prefix to prepend to the output library name")
+mark_as_advanced(ZFP_LIBRARY_PREFIX)
+
 add_subdirectory(src)
 
+option(BUILD_CFP "Build CFP arrays library" OFF)
+if(BUILD_CFP)
+  add_subdirectory(cfp)
+endif()
+
 option(BUILD_UTILITIES "Build command line utilities for zfp" ON)
 if(BUILD_UTILITIES)
   add_subdirectory(utils)
@@ -192,6 +242,28 @@ install(DIRECTORY array/   DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
 #------------------------------------------------------------------------------#
 # Build type: one of None, Debug, Release, RelWithDebInfo, MinSizeRel
 #------------------------------------------------------------------------------#
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Type of CMake build" FORCE)
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY VALUE Release)
 endif()
+
+#------------------------------------------------------------------------------#
+# Packaging
+#------------------------------------------------------------------------------#
+
+# Add all targets to the build-tree export set
+export(TARGETS zfp NAMESPACE zfp::
+  FILE "${PROJECT_BINARY_DIR}/zfp-targets.cmake")
+configure_file(zfp-config.cmake.in
+  "${PROJECT_BINARY_DIR}/zfp-config.cmake" @ONLY)
+configure_file(zfp-config-version.cmake.in
+  "${PROJECT_BINARY_DIR}/zfp-config-version.cmake" @ONLY)
+
+# Install the zfp-config.cmake and zfp-config-version.cmake
+install(FILES
+  "${PROJECT_BINARY_DIR}/zfp-config.cmake"
+  "${PROJECT_BINARY_DIR}/zfp-config-version.cmake"
+  DESTINATION "${CMAKE_INSTALL_CMAKEDIR}")
+
+# Install the export set for use with the install-tree
+install(EXPORT zfp-targets NAMESPACE zfp::
+  DESTINATION "${CMAKE_INSTALL_CMAKEDIR}")

Config

@@ -13,6 +13,11 @@ CXX = g++
 # common compiler options -----------------------------------------------------
 
 FLAGS = -O3 -fPIC -Wall -pedantic -I../include
+SOFLAGS =
+
+# macOS compiler options (uncomment on macOS) ---------------------------------
+
+# SOFLAGS += -undefined dynamic_lookup
 
 # OpenMP compiler options -----------------------------------------------------
 
@@ -46,6 +51,24 @@ OMPFLAGS = -fopenmp
 # count cache misses
 # DEFS += -DZFP_WITH_CACHE_PROFILE
 
+# build targets ---------------------------------------------------------------
+
+BUILD_CFP = 0
+BUILD_UTILITIES = 1
+BUILD_EXAMPLES = 0
+BUILD_TESTING = 1
+BUILD_SHARED_LIBS = 0
+
+ifneq ($(BUILD_SHARED_LIBS),0)
+  LIBRARY = shared
+  LIBZFP = libzfp.so
+  LIBCFP = libcfp.so
+else
+  LIBRARY = static
+  LIBZFP = libzfp.a
+  LIBCFP = libcfp.a
+endif
+
 # conditionals ----------------------------------------------------------------
 
 # enable OpenMP?

LICENSE

@@ -1,6 +1,6 @@
 Copyright (c) 2014-2018, Lawrence Livermore National Security, LLC.
 Produced at the Lawrence Livermore National Laboratory.
-Written by Peter Lindstrom and Markus Salasoo.
+Written by Peter Lindstrom, Markus Salasoo, and Matt Larsen.
 LLNL-CODE-663824.
 All rights reserved.
 

Makefile

@@ -1,21 +1,36 @@
 # see Config file for compile-time settings
+include Config
 
 MAKEFLAGS += --no-print-directory
 
+
+# default: build all targets enabled in Config
 all:
-	@cd src; $(MAKE) clean static
+	@echo $(LIBRARY)
+	@cd src; $(MAKE) clean $(LIBRARY)
+ifneq ($(BUILD_CFP),0)
+	@cd cfp/src; $(MAKE) clean $(LIBRARY)
+endif
+ifneq ($(BUILD_UTILITIES),0)
 	@cd utils; $(MAKE) clean all
+endif
+ifneq ($(BUILD_TESTING),0)
 	@cd tests; $(MAKE) clean all
+endif
+ifneq ($(BUILD_EXAMPLES),0)
 	@cd examples; $(MAKE) clean all
+endif
 
-shared:
-	@cd src; $(MAKE) shared
 
+# run basic regression tests
 test:
 	@cd tests; $(MAKE) test
 
+
+# clean all
 clean:
 	@cd src; $(MAKE) clean
+	@cd cfp/src; $(MAKE) clean
 	@cd utils; $(MAKE) clean
 	@cd tests; $(MAKE) clean
 	@cd examples; $(MAKE) clean

README.md

@@ -46,34 +46,37 @@ DOCUMENTATION
 -------------
 
 Full
-[documentation](http://zfp.readthedocs.io/en/release0.5.3/)
+[documentation](http://zfp.readthedocs.io/en/release0.5.4/)
 is available online via Read the Docs.  A
-[PDF](http://readthedocs.org/projects/zfp/downloads/pdf/release0.5.3/)
+[PDF](http://readthedocs.org/projects/zfp/downloads/pdf/release0.5.4/)
 version is also available.
 
 
 INSTALLATION
 ------------
 
 zfp consists of three distinct parts: a compression library written in C;
-a set of C++ header files that implement compressed arrays; and a set of
-C and C++ examples.  The main compression codec is written in C and should
-conform to both the ISO C89 and C99 standards.  The C++ array classes are
-implemented entirely in header files and can be included as is, but since
-they call the compression library, applications must link with libzfp.
+a set of C++ header files with C wrappers that implement compressed arrays;
+and a set of C and C++ examples.  The main compression codec is written in
+C and should conform to both the ISO C89 and C99 standards.  The C++ array
+classes are implemented entirely in header files and can be included as is,
+but since they call the compression library, applications must link with
+libzfp.
 
 On Linux, macOS, and MinGW, zfp is easiest compiled using gcc and gmake.
-CMake support is also available, e.g. for Windows builds.  See below for
+CMake support is also available, e.g., for Windows builds.  See below for
 instructions on GNU and CMake builds.
 
 zfp has successfully been built and tested using these compilers:
 
-    gcc versions 4.4.7, 4.7.2, 4.8.2, 4.9.2, 5.4.1, 6.3.0
-    icc versions 12.0.5, 12.1.5, 15.0.4, 16.0.1, 17.0.0, 18.0.0
-    clang version 3.6.0
-    xlc version 12.1
+    gcc versions 4.4.7, 4.9.4, 5.5.0, 6.1.0, 6.4.0, 7.1.0, 7.3.0, 8.1.0
+    icc versions 15.0.6, 16.0.4, 17.0.2, 18.0.2, 19.0.0
+    clang versions 3.9.1, 4.0.0, 5.0.0, 6.0.0 
     MinGW version 5.3.0
-    Visual Studio versions 14.0 (2015), 14.1 (2017)
+    Visual Studio versions 14 (2015), 15 (2017)
+
+zfp conforms to various language standards, including C89, C99, C++98,
+C++11, and C++14.
 
 NOTE: zfp requires 64-bit compiler and operating system support.
 
@@ -84,23 +87,8 @@ To compile zfp using gcc, type
     make
 
 from this directory.  This builds libzfp as a static library as well as
-utilities and example programs.  To optionally create a shared library,
-type
-
-    make shared
-
-and set LD_LIBRARY_PATH to point to ./lib.  To test the compressor, type
-
-    make test
-
-If the compilation or regression tests fail, it is possible that some of
-the macros in the file 'Config' have to be adjusted.  Also, the tests may
-fail due to minute differences in the computed floating-point fields
-being compressed (as indicated by checksum errors).  It is surprisingly
-difficult to portably generate a floating-point array that agrees
-bit-for-bit across platforms.  If most tests succeed and the failures
-result in byte sizes and error values reasonably close to the expected
-values, then it is likely that the compressor is working correctly.
+utilities and example programs.  See documentation for complete build
+instructions.
 
 ## CMake builds
 
@@ -115,13 +103,32 @@ To also build the examples, replace the cmake line with
 
     cmake -DBUILD_EXAMPLES=ON ..
 
-To build zfp using Visual Studio on Windows, start an MSBuild shell and type
+To build zfp using Visual Studio on Windows, start a DOS shell, cd to the
+top-level zfp directory, and type
 
     mkdir build
     cd build
     cmake ..
-    msbuild /p:Configuration=Release zfp.sln
-    msbuild /p:Configuration=Debug   zfp.sln
+    cmake --build . --config Release
+
+This builds zfp in release mode.  Replace 'Release' with 'Debug' to build
+zfp in debug mode.  See the instructions for Linux on how to change the
+cmake line to also build the example programs.
+
+## Testing
+
+To test that zfp is working properly, type
+
+    make test
+
+or using CMake
+
+    ctest
 
-This builds zfp in both debug and release mode.  See the instructions for
-Linux on how to change the cmake line to also build the example programs.
+If the compilation or regression tests fail, it is possible that some of the
+macros in the file 'Config' have to be adjusted.  Also, the tests may fail
+due to minute differences in the computed floating-point fields being
+compressed, which will be indicated by checksum errors.  If most tests
+succeed and the failures result in byte sizes and error values reasonably
+close to the expected values, then it is likely that the compressor is
+working correctly.

VERSIONS.md

@@ -1,5 +1,28 @@
 # zfp Release Notes
 
+## 0.5.4 (October 1, 2018)
+
+- Added support for CUDA fixed-rate compression and decompression.
+
+- Added views into compressed arrays for thread safety, nested array
+  indexing, slicing, and array subsetting.
+
+- Added C language bindings for compressed arrays.
+
+- Added support for compressing and decompressing 4D data.
+
+- Changes:
+  - Execution policy now applies to both compression and decompression.
+  - Compressed array accessors now return Scalar type instead of
+    const Scalar& to avoid stale references to evicted cache lines.
+
+- Bug fixes:
+  - Handling of negative strides.
+  - Command line tool handling of arrays with more than 2^32 elements.
+  - bitstream C++ compatibility.  
+  - Respect minimum cache size request.
+
+
 ## 0.5.3 (March 28, 2018)
 
 - Added support for OpenMP multithreaded compression (but not decompression).