Fix szip handling

This commit is contained in:
Dennis Heimbigner 2022-04-30 19:06:01 -06:00
parent e667afad36
commit f897b458ea
11 changed files with 95 additions and 220 deletions

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@ -7,7 +7,7 @@
name: Run macOS-based netCDF Tests
on: [pull_request]
on: [pull_request,push]
jobs:

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@ -4,7 +4,7 @@
name: Run Ubuntu/Linux netCDF Tests
on: [pull_request]
on: [pull_request,push]
jobs:

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@ -7,7 +7,7 @@
name: Run MSYS2, MinGW64-based Tests
on: [pull_request]
on: [pull_request,push]
jobs:

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@ -623,26 +623,6 @@ ENDIF(ENABLE_STRICT_NULL_BYTE_HEADER_PADDING)
# 3. is nczarr enabled?
# We need separate flags for cases 1 and 2
# We need to determine if libsz is available both for HDF5 and NCZarr
# If user has specified the `SZIP_LIBRARY`, use it; otherwise try to find...
IF(NOT SZIP_LIBRARY)
FIND_LIBRARY(SZIP PATH NAMES szip sz sz2)
IF(SZIP)
SET(SZIP_LIBRARY ${SZIP})
ELSE()
UNSET(SZIP_LIBRARY)
UNSET(SZIP)
ENDIF()
ENDIF()
IF(SZIP_LIBRARY)
SET(SZIP_FOUND yes)
SET(HAVE_SZ yes)
ELSE()
SET(SZIP_FOUND no)
SET(HAVE_SZ no)
ENDIF()
##
# Option to Enable HDF5
#
@ -905,15 +885,6 @@ IF(USE_HDF5)
int x = 1;}" USE_HDF5_SZIP)
IF(USE_HDF5_SZIP)
SET(HAVE_H5Z_SZIP yes)
# If user has specified the `SZIP_LIBRARY`, use it; otherwise try to find...
IF(SZIP_FOUND)
SET(CMAKE_REQUIRED_LIBRARIES ${SZIP_LIBRARY} ${CMAKE_REQUIRED_LIBRARIES})
MESSAGE(STATUS "HDF5 has szip.")
ELSE()
MESSAGE(FATAL_ERROR "HDF5 Requires SZIP, but cannot find libszip or libsz.")
ENDIF()
ELSE()
SET(HAVE_H5Z_SZIP no)
ENDIF()
####
@ -1124,13 +1095,15 @@ ENDIF()
endmacro(set_std_filter)
# Locate some compressors
FIND_PACKAGE(Szip)
FIND_PACKAGE(Bz2)
FIND_PACKAGE(Blosc)
FIND_PACKAGE(Zstd)
# Accumulate standard filters
set(STD_FILTERS "deflate") # Always have deflate*/
set_std_filter(SZIP)
set_std_filter(Szip)
SET(HAVE_SZ ${Szip_FOUND})
set_std_filter(Blosc)
set_std_filter(Zstd)
IF(Bz2_FOUND)
@ -1143,6 +1116,7 @@ ELSE()
set(STD_FILTERS "${STD_FILTERS} bz2")
ENDIF()
# If user wants, then install selected plugins
SET(PLUGIN_INSTALL_DIR "" CACHE STRING "Whether and where we should install plugins")
SET(ENABLE_PLUGIN_INSTALL OFF)

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@ -1,179 +0,0 @@
# - Find SZIP library
# - Derived from the FindTiff.cmake that is included with cmake
# Find the native SZIP includes and library
# This module defines
# SZIP_INCLUDE_DIRS, where to find tiff.h, etc.
# SZIP_LIBRARIES, libraries to link against to use SZIP.
# SZIP_FOUND, If false, do not try to use SZIP.
# also defined, but not for general use are
# SZIP_LIBRARY, where to find the SZIP library.
# SZIP_LIBRARY_DEBUG - Debug version of SZIP library
# SZIP_LIBRARY_RELEASE - Release Version of SZIP library
# MESSAGE (STATUS "Finding SZIP library and headers..." )
############################################
#
# Check the existence of the libraries.
#
############################################
# This macro was taken directly from the FindQt4.cmake file that is included
# with the CMake distribution. This is NOT my work. All work was done by the
# original authors of the FindQt4.cmake file. Only minor modifications were
# made to remove references to Qt and make this file more generally applicable
#########################################################################
MACRO (SZIP_ADJUST_LIB_VARS basename)
IF (${basename}_INCLUDE_DIR)
# if only the release version was found, set the debug variable also to the release version
IF (${basename}_LIBRARY_RELEASE AND NOT ${basename}_LIBRARY_DEBUG)
SET (${basename}_LIBRARY_DEBUG ${${basename}_LIBRARY_RELEASE})
SET (${basename}_LIBRARY ${${basename}_LIBRARY_RELEASE})
SET (${basename}_LIBRARIES ${${basename}_LIBRARY_RELEASE})
ENDIF (${basename}_LIBRARY_RELEASE AND NOT ${basename}_LIBRARY_DEBUG)
# if only the debug version was found, set the release variable also to the debug version
IF (${basename}_LIBRARY_DEBUG AND NOT ${basename}_LIBRARY_RELEASE)
SET (${basename}_LIBRARY_RELEASE ${${basename}_LIBRARY_DEBUG})
SET (${basename}_LIBRARY ${${basename}_LIBRARY_DEBUG})
SET (${basename}_LIBRARIES ${${basename}_LIBRARY_DEBUG})
ENDIF (${basename}_LIBRARY_DEBUG AND NOT ${basename}_LIBRARY_RELEASE)
IF (${basename}_LIBRARY_DEBUG AND ${basename}_LIBRARY_RELEASE)
# if the generator supports configuration types then set
# optimized and debug libraries, or if the CMAKE_BUILD_TYPE has a value
IF (CMAKE_CONFIGURATION_TYPES OR CMAKE_BUILD_TYPE)
SET (${basename}_LIBRARY optimized ${${basename}_LIBRARY_RELEASE} debug ${${basename}_LIBRARY_DEBUG})
ELSE(CMAKE_CONFIGURATION_TYPES OR CMAKE_BUILD_TYPE)
# if there are no configuration types and CMAKE_BUILD_TYPE has no value
# then just use the release libraries
SET (${basename}_LIBRARY ${${basename}_LIBRARY_RELEASE} )
ENDIF (CMAKE_CONFIGURATION_TYPES OR CMAKE_BUILD_TYPE)
SET (${basename}_LIBRARIES optimized ${${basename}_LIBRARY_RELEASE} debug ${${basename}_LIBRARY_DEBUG})
ENDIF (${basename}_LIBRARY_DEBUG AND ${basename}_LIBRARY_RELEASE)
SET (${basename}_LIBRARY ${${basename}_LIBRARY} CACHE FILEPATH "The ${basename} library")
IF (${basename}_LIBRARY)
SET (${basename}_FOUND 1)
ENDIF (${basename}_LIBRARY)
ENDIF (${basename}_INCLUDE_DIR )
# Make variables changeble to the advanced user
MARK_AS_ADVANCED (${basename}_LIBRARY ${basename}_LIBRARY_RELEASE ${basename}_LIBRARY_DEBUG ${basename}_INCLUDE_DIR )
ENDMACRO (SZIP_ADJUST_LIB_VARS)
# Look for the header file.
SET (SZIP_INCLUDE_SEARCH_DIRS
$ENV{SZIP_INSTALL}/include
$ENV{SZIP_INSTALL}/include/szip
/usr/include
/usr/include/szip
)
SET (SZIP_LIB_SEARCH_DIRS
$ENV{SZIP_INSTALL}/lib
/usr/lib
)
SET (SZIP_BIN_SEARCH_DIRS
$ENV{SZIP_INSTALL}/bin
/usr/bin
)
FIND_PATH (SZIP_INCLUDE_DIR
NAMES szlib.h
PATHS ${SZIP_INCLUDE_SEARCH_DIRS}
NO_DEFAULT_PATH
)
IF (WIN32 AND NOT MINGW)
SET (SZIP_SEARCH_DEBUG_NAMES "sz_d;libsz_d")
SET (SZIP_SEARCH_RELEASE_NAMES "sz;libsz;szip")
ELSE (WIN32 AND NOT MINGW)
SET (SZIP_SEARCH_DEBUG_NAMES "sz_d")
SET (SZIP_SEARCH_RELEASE_NAMES "sz")
ENDIF (WIN32 AND NOT MINGW)
# Look for the library.
FIND_LIBRARY (SZIP_LIBRARY_DEBUG
NAMES ${SZIP_SEARCH_DEBUG_NAMES}
PATHS ${SZIP_LIB_SEARCH_DIRS}
NO_DEFAULT_PATH
)
FIND_LIBRARY (SZIP_LIBRARY_RELEASE
NAMES ${SZIP_SEARCH_RELEASE_NAMES}
PATHS ${SZIP_LIB_SEARCH_DIRS}
NO_DEFAULT_PATH
)
SZIP_ADJUST_LIB_VARS (SZIP)
IF (SZIP_INCLUDE_DIR AND SZIP_LIBRARY)
SET (SZIP_FOUND 1)
SET (SZIP_LIBRARIES ${SZIP_LIBRARY})
SET (SZIP_INCLUDE_DIRS ${SZIP_INCLUDE_DIR})
IF (SZIP_LIBRARY_DEBUG)
GET_FILENAME_COMPONENT (SZIP_LIBRARY_PATH ${SZIP_LIBRARY_DEBUG} PATH)
SET (SZIP_LIB_DIR ${SZIP_LIBRARY_PATH})
ELSEIF (SZIP_LIBRARY_RELEASE)
GET_FILENAME_COMPONENT (SZIP_LIBRARY_PATH ${SZIP_LIBRARY_RELEASE} PATH)
SET (SZIP_LIB_DIR ${SZIP_LIBRARY_PATH})
ENDIF (SZIP_LIBRARY_DEBUG)
ELSE (SZIP_INCLUDE_DIR AND SZIP_LIBRARY)
SET (SZIP_FOUND 0)
SET (SZIP_LIBRARIES)
SET (SZIP_INCLUDE_DIRS)
ENDIF (SZIP_INCLUDE_DIR AND SZIP_LIBRARY)
# Report the results.
IF (NOT SZIP_FOUND)
SET (SZIP_DIR_MESSAGE
"SZip was not found. Make sure SZIP_LIBRARY and SZIP_INCLUDE_DIR are set or set the SZIP_INSTALL environment variable."
)
IF (NOT SZIP_FIND_QUIETLY)
MESSAGE (STATUS "${SZIP_DIR_MESSAGE}")
ELSE (NOT SZIP_FIND_QUIETLY)
IF (SZIP_FIND_REQUIRED)
MESSAGE (FATAL_ERROR "SZip was NOT found and is Required by this project")
ENDIF (SZIP_FIND_REQUIRED)
ENDIF (NOT SZIP_FIND_QUIETLY)
ENDIF (NOT SZIP_FOUND)
IF (SZIP_FOUND)
INCLUDE (CheckSymbolExists)
#############################################
# Find out if SZIP was build using dll's
#############################################
# Save required variable
SET (CMAKE_REQUIRED_INCLUDES_SAVE ${CMAKE_REQUIRED_INCLUDES})
SET (CMAKE_REQUIRED_FLAGS_SAVE ${CMAKE_REQUIRED_FLAGS})
# Add SZIP_INCLUDE_DIR to CMAKE_REQUIRED_INCLUDES
SET (CMAKE_REQUIRED_INCLUDES "${CMAKE_REQUIRED_INCLUDES};${SZIP_INCLUDE_DIRS}")
CHECK_SYMBOL_EXISTS (SZIP_BUILT_AS_DYNAMIC_LIB "SZconfig.h" HAVE_SZIP_DLL)
IF (HAVE_SZIP_DLL STREQUAL "TRUE")
SET (HAVE_SZIP_DLL "1")
ENDIF (HAVE_SZIP_DLL STREQUAL "TRUE")
# Restore CMAKE_REQUIRED_INCLUDES and CMAKE_REQUIRED_FLAGS variables
SET (CMAKE_REQUIRED_INCLUDES ${CMAKE_REQUIRED_INCLUDES_SAVE})
SET (CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE})
#
#############################################
ENDIF (SZIP_FOUND)
IF (FIND_SZIP_DEBUG)
MESSAGE (STATUS "SZIP_INCLUDE_DIR: ${SZIP_INCLUDE_DIR}")
MESSAGE (STATUS "SZIP_INCLUDE_DIRS: ${SZIP_INCLUDE_DIRS}")
MESSAGE (STATUS "SZIP_LIBRARY_DEBUG: ${SZIP_LIBRARY_DEBUG}")
MESSAGE (STATUS "SZIP_LIBRARY_RELEASE: ${SZIP_LIBRARY_RELEASE}")
MESSAGE (STATUS "HAVE_SZIP_DLL: ${HAVE_SZIP_DLL}")
MESSAGE (STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
ENDIF (FIND_SZIP_DEBUG)

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@ -0,0 +1,64 @@
# Searches for an installation of the szip library. On success, it sets the following variables:
#
# Szip_FOUND Set to true to indicate the szip library was found
# Szip_INCLUDE_DIRS The directory containing the header file szip/szip.h
# Szip_LIBRARIES The libraries needed to use the szip library
#
# To specify an additional directory to search, set Szip_ROOT.
#
# Author: Siddhartha Chaudhuri, 2009
#
# Look for the header, first in the user-specified location and then in the system locations
SET(Szip_INCLUDE_DOC "The directory containing the header file szip.h")
FIND_PATH(Szip_INCLUDE_DIRS NAMES szlib.h szip.h szip/szip.h PATHS ${Szip_ROOT} ${Szip_ROOT}/include DOC ${Szip_INCLUDE_DOC} NO_DEFAULT_PATH)
IF(NOT Szip_INCLUDE_DIRS) # now look in system locations
FIND_PATH(Szip_INCLUDE_DIRS NAMES szlib.h szip.h szip/szip.h DOC ${Szip_INCLUDE_DOC})
ENDIF(NOT Szip_INCLUDE_DIRS)
SET(Szip_FOUND FALSE)
IF(Szip_INCLUDE_DIRS)
SET(Szip_LIBRARY_DIRS ${Szip_INCLUDE_DIRS})
IF("${Szip_LIBRARY_DIRS}" MATCHES "/include$")
# Strip off the trailing "/include" in the path.
GET_FILENAME_COMPONENT(Szip_LIBRARY_DIRS ${Szip_LIBRARY_DIRS} PATH)
ENDIF("${Szip_LIBRARY_DIRS}" MATCHES "/include$")
IF(EXISTS "${Szip_LIBRARY_DIRS}/lib")
SET(Szip_LIBRARY_DIRS ${Szip_LIBRARY_DIRS}/lib)
ENDIF(EXISTS "${Szip_LIBRARY_DIRS}/lib")
# Find Szip libraries
FIND_LIBRARY(Szip_DEBUG_LIBRARY NAMES szipd szip_d libszipd libszip_d szip libszip sz2 libsz2
PATH_SUFFIXES Debug ${CMAKE_LIBRARY_ARCHITECTURE} ${CMAKE_LIBRARY_ARCHITECTURE}/Debug
PATHS ${Szip_LIBRARY_DIRS} NO_DEFAULT_PATH)
FIND_LIBRARY(Szip_RELEASE_LIBRARY NAMES szip libszip sz libsz sz2 libsz2
PATH_SUFFIXES Release ${CMAKE_LIBRARY_ARCHITECTURE} ${CMAKE_LIBRARY_ARCHITECTURE}/Release
PATHS ${Szip_LIBRARY_DIRS} NO_DEFAULT_PATH)
SET(Szip_LIBRARIES )
IF(Szip_DEBUG_LIBRARY AND Szip_RELEASE_LIBRARY)
SET(Szip_LIBRARIES debug ${Szip_DEBUG_LIBRARY} optimized ${Szip_RELEASE_LIBRARY})
ELSEIF(Szip_DEBUG_LIBRARY)
SET(Szip_LIBRARIES ${Szip_DEBUG_LIBRARY})
ELSEIF(Szip_RELEASE_LIBRARY)
SET(Szip_LIBRARIES ${Szip_RELEASE_LIBRARY})
ENDIF(Szip_DEBUG_LIBRARY AND Szip_RELEASE_LIBRARY)
IF(Szip_LIBRARIES)
SET(Szip_FOUND TRUE)
ENDIF(Szip_LIBRARIES)
ENDIF(Szip_INCLUDE_DIRS)
IF(Szip_FOUND)
# IF(NOT Szip_FIND_QUIETLY)
MESSAGE(STATUS "Found Szip: headers at ${Szip_INCLUDE_DIRS}, libraries at ${Szip_LIBRARY_DIRS}")
MESSAGE(STATUS " library is ${Szip_LIBRARIES}")
# ENDIF(NOT Szip_FIND_QUIETLY)
ELSE(Szip_FOUND)
IF(Szip_FIND_REQUIRED)
MESSAGE(FATAL_ERROR "Szip library not found")
ENDIF(Szip_FIND_REQUIRED)
ENDIF(Szip_FOUND)

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@ -935,10 +935,16 @@ This is for internal use only.
As part of the overall build process, a number of filters are built as shared libraries in the "plugins" directory
— in that directory or the "plugins/.libs" subdirectory.
An option exists to allow some of those filters to be installed into a user-specified directory.
Presumably this directory is part of the value of the HDF5_PLUGIN_PATH environment variable.
The ./configure option is ````--with-plugin-dir=<absolute-directory-path>````.
The corresponding CMake option is ````-DPLUGIN_INSTALL_DIR=<absolute-directory-path>````.
An option exists to allow some of those filters to be installed into a user-specified directory. The relevant options are as follows:
````
./configure: --with-plugin-dir=<absolute-directory-path>
cmake: -DPLUGIN_INSTALL_DIR=<absolute-directory-path>
````
If the value of the environment variable "HDF5_PLUGIN_PATH" is a single directory, then
a good value for the install directory is "$HDF5_PLUGIN_PATH", so for example:
````
./configure ... --with-plugin-dir="$HDF5_PLUGIN_DIR"
````
If this option is specified, then as part of the "install" build action,
a specified set of filter shared libraries will be copied into the specified directory.

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@ -8,6 +8,7 @@
if test "x$srcdir" = x ; then srcdir=`pwd`; fi
. ../test_common.sh
set -x
set -e
if test "x$TESTNCZARR" = x1 ; then
@ -96,6 +97,12 @@ rm -f $file
fi
setfilter $zfilt ref_any.cdl "tmp_filt_${zfilt}.cdl" "$zparams" "$zcodec"
if test "x$TESTNCZARR" = x1 ; then
if test "x$zfilt" = xszip ; then
echo "@@@"
find /usr -name 'libsz*'
find ${HDF5_PLUGIN_DIR} -name '*sz*.so'
ldd ${HDF5_PLUGIN_DIR}/libh5szip.so
fi
${NCGEN} -4 -lb -o $fileurl "tmp_filt_${zfilt}.cdl"
${NCDUMP} -n $zfilt -sF $fileurl > "tmp_filt_${zfilt}.tmp"
else

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@ -8,7 +8,9 @@
if test "x$srcdir" = x ; then srcdir=`pwd`; fi
. ../test_common.sh
set -x
set -e
echo ""
# get some config.h parameters

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@ -4,6 +4,7 @@ if test "x$srcdir" = x ; then srcdir=`pwd`; fi
. ../test_common.sh
# This shell script tests the output from several previous tests.
set -x
set -e
echo ""

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@ -10,10 +10,10 @@ TESTS_ENVIRONMENT =
#TEST_EXTENSIONS = .sh
#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
#TESTS_ENVIRONMENT += export SETX=1;
SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
TESTS_ENVIRONMENT += export SETX=1;
AM_CPPFLAGS += -I${top_srcdir} -I${top_srcdir}/libnczarr
AM_LDFLAGS += ${top_builddir}/liblib/libnetcdf.la