Merge branch 'master' into nc_open_mem_fix

.gitignore

@@ -10,6 +10,8 @@ ctest.c
 ctest64.c
 nc_test/test_get.c
 nc_test/test_put.c
+nc_test/test_read.c
+nc_test/test_write.c
 
 #####
 # End ignored generated files.

CMakeLists.txt

@@ -7,7 +7,7 @@
 ##################################
 
 #Minimum required CMake Version
-cmake_minimum_required(VERSION 2.8.11)
+cmake_minimum_required(VERSION 3.6.1)
 
 #Project Name
 project(netCDF C)
@@ -101,10 +101,10 @@ INCLUDE(${CMAKE_ROOT}/Modules/GetPrerequisites.cmake)
 INCLUDE(CheckCCompilerFlag)
 FIND_PACKAGE(PkgConfig QUIET)
 
-# Check for Big Endian
+# A check to see if the system is big endian
 TEST_BIG_ENDIAN(BIGENDIAN)
 IF(${BIGENDIAN})
-  SET(WORDS_BIGENDIAN "1")
+ SET(WORDS_BIGENDIAN "1")
 ENDIF(${BIGENDIAN})
 
 # A macro to check if a C linker supports a particular flag.
@@ -627,6 +627,7 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
  SET(HDF5_C_LIBRARY ${HDF5_C_${NC_HDF5_LINK_TYPE_UPPER}_LIBRARY})
  SET(HDF5_C_LIBRARY_hdf5 ${HDF5_C_${NC_HDF5_LINK_TYPE_UPPER}_LIBRARY})
  SET(HDF5_HL_LIBRARY ${HDF5_HL_${NC_HDF5_LINK_TYPE_UPPER}_LIBRARY})
+
  SET(HDF5_LIBRARIES ${HDF5_C_${NC_HDF5_LINK_TYPE_UPPER}_LIBRARY} ${HDF5_HL_${NC_HDF5_LINK_TYPE_UPPER}_LIBRARY})
  ENDIF()
  ENDIF(${HDF5_VERSION} VERSION_GREATER "1.8.15")
@@ -651,12 +652,13 @@ IF(USE_HDF5 OR ENABLE_NETCDF_4)
  ENDIF()
 
  ###
- # The following options are not used in Windows.
+ # The following options are not used in Windows currently.
  ###
  IF(NOT MSVC)
  # Find out if HDF5 was built with parallel support.
  # Do that by checking for the targets H5Pget_fapl_mpiposx and
  # H5Pget_fapl_mpio in ${HDF5_LIB}.
+
  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pget_fapl_mpiposix "" HDF5_IS_PARALLEL_MPIPOSIX)
  CHECK_LIBRARY_EXISTS(${HDF5_C_LIBRARY_hdf5} H5Pget_fapl_mpio "" HDF5_IS_PARALLEL_MPIO)
  IF(HDF5_IS_PARALLEL_MPIPOSIX OR HDF5_IS_PARALLEL_MPIO)
@@ -991,22 +993,22 @@ IF(ENABLE_PNETCDF)
  FIND_LIBRARY(PNETCDF NAMES pnetcdf)
  FIND_PATH(PNETCDF_INCLUDE_DIR pnetcdf.h)
  IF(NOT PNETCDF)
- MESSAGE(STATUS "Cannot find PNetCDF library. Disabling PNetCDF support.")
+ MESSAGE(STATUS "Cannot find PnetCDF library. Disabling PnetCDF support.")
  SET(USE_PNETCDF OFF CACHE BOOL "")
  ELSE(NOT PNETCDF)
  SET(USE_PARALLEL ON CACHE BOOL "")
 
- # Check PNetCDF version. Must be >= 1.6.0
+ # Check PnetCDF version. Must be >= 1.6.0
  set(pnetcdf_h "${PNETCDF_INCLUDE_DIR}/pnetcdf.h" )
- message(STATUS "PNetCDF include file ${pnetcdf_h} will be searched for version")
+ message(STATUS "PnetCDF include file ${pnetcdf_h} will be searched for version")
  file(STRINGS "${pnetcdf_h}" pnetcdf_major_string REGEX "^#define PNETCDF_VERSION_MAJOR")
  string(REGEX REPLACE "[^0-9]" "" pnetcdf_major "${pnetcdf_major_string}")
  file(STRINGS "${pnetcdf_h}" pnetcdf_minor_string REGEX "^#define PNETCDF_VERSION_MINOR")
  string(REGEX REPLACE "[^0-9]" "" pnetcdf_minor "${pnetcdf_minor_string}")
  file(STRINGS "${pnetcdf_h}" pnetcdf_sub_string REGEX "^#define PNETCDF_VERSION_SUB")
  string(REGEX REPLACE "[^0-9]" "" pnetcdf_sub "${pnetcdf_sub_string}")
  set(pnetcdf_version "${pnetcdf_major}.${pnetcdf_minor}.${pnetcdf_sub}")
- message(STATUS "Found PNetCDF version ${pnetcdf_version}")
+ message(STATUS "Found PnetCDF version ${pnetcdf_version}")
 
  if(${pnetcdf_version} VERSION_GREATER "1.6.0")
  SET(STATUS_PNETCDF "ON")
@@ -1015,13 +1017,66 @@ IF(ENABLE_PNETCDF)
  # pnetcdf => parallel
  SET(STATUS_PARALLEL ON)
  SET(USE_PARALLEL ON)
- MESSAGE(STATUS "Using PNetCDF Library: ${PNETCDF}")
+ MESSAGE(STATUS "Using PnetCDF Library: ${PNETCDF}")
  ELSE()
- MESSAGE(WARNING "ENABLE_PNETCDF requires version 1.6.1 or later; found version ${pnetcdf_version}. PNetCDF is disabled")
+ MESSAGE(WARNING "ENABLE_PNETCDF requires version 1.6.1 or later; found version ${pnetcdf_version}. PnetCDF is disabled")
  ENDIF()
  ENDIF(NOT PNETCDF)
 ENDIF()
 
+# Options to enable use of fill values for elements casuing NC_ERANGE
+SET(STATUS_ERANGE_FILL "OFF")
+OPTION(ENABLE_ERANGE_FILL "Enable use of fill value when out-of-range type conversion causes NC_ERANGE error." OF)
+IF(ENABLE_ERANGE_FILL)
+ SET(STATUS_ERANGE_FILL "ON")
+ENDIF()
+
+# Options to use a more relaxed coordinate argument boundary check
+SET(STATUS_RELAX_COORD_BOUND "OFF")
+OPTION(ENABLE_ZERO_LENGTH_COORD_BOUND "Enable a more relaxed boundary error check NC_EINVALCOORDS to allow coordinate start argument equal to dimension size when argument count is zero." OFF)
+IF(ENABLE_ZERO_LENGTH_COORD_BOUND)
+ SET(STATUS_RELAX_COORD_BOUND "ON")
+ENDIF()
+
+# check and conform with PnetCDF settings on ERANGE_FILL and RELAX_COORD_BOUND
+IF(STATUS_PNETCDF)
+ file(STRINGS "${pnetcdf_h}" enable_erange_fill_pnetcdf REGEX "^#define PNETCDF_ERANGE_FILL")
+ string(REGEX REPLACE "[^0-9]" "" erange_fill_pnetcdf "${enable_erange_fill_pnetcdf}")
+ IF("x${erange_fill_pnetcdf}" STREQUAL "x1")
+ IF(NOT STATUS_ERANGE_FILL)
+ MESSAGE(WARNING "Enable erange-fill to conform with PnetCDF setting")
+ SET(STATUS_ERANGE_FILL "ON")
+ ENDIF()
+ ELSE()
+ IF(STATUS_ERANGE_FILL)
+ MESSAGE(WARNING "Disable erange-fill to conform with PnetCDF setting")
+ SET(STATUS_ERANGE_FILL "OFF")
+ ENDIF()
+ ENDIF()
+ file(STRINGS "${pnetcdf_h}" relax_coord_bound_pnetcdf REGEX "^#define PNETCDF_RELAX_COORD_BOUND")
+ string(REGEX REPLACE "[^0-9]" "" relax_coord_bound "${relax_coord_bound_pnetcdf}")
+ IF("x${relax_coord_bound}" STREQUAL "x1")
+ IF(NOT STATUS_RELAX_COORD_BOUND)
+ MESSAGE(WARNING "Enable relax-coord-bound to conform with PnetCDF setting")
+ SET(STATUS_RELAX_COORD_BOUND "ON")
+ ENDIF()
+ ELSE()
+ IF(STATUS_RELAX_COORD_BOUND)
+ MESSAGE(WARNING "Disable relax-coord-bound to conform with PnetCDF setting")
+ SET(STATUS_RELAX_COORD_BOUND "OFF")
+ ENDIF()
+ ENDIF()
+ENDIF()
+
+IF(STATUS_ERANGE_FILL)
+ SET(M4FLAGS "-DERANGE_FILL" CACHE STRING "")
+ENDIF()
+
+IF(STATUS_RELAX_COORD_BOUND)
+ MESSAGE(STATUS "Enabling a more relatexed check for NC_EINVALCOORDS")
+ ADD_DEFINITIONS(-DRELAX_COORD_BOUND)
+ENDIF()
+
 # Enable Parallel Tests.
 OPTION(ENABLE_PARALLEL_TESTS "Enable Parallel IO Tests. Ignored if netCDF4 is not enabled, or if there is no parallel I/O Support." ${USE_PARALLEL})
 IF(ENABLE_PARALLEL_TESTS AND USE_PARALLEL)
@@ -1155,6 +1210,9 @@ CHECK_INCLUDE_FILE("stdbool.h" HAVE_STDBOOL_H)
 CHECK_INCLUDE_FILE("locale.h" HAVE_LOCALE_H)
 CHECK_INCLUDE_FILE("stdint.h" HAVE_STDINT_H)
 CHECK_INCLUDE_FILE("stdio.h" HAVE_STDIO_H)
+IF(MSVC)
+CHECK_INCLUDE_FILE("io.h" HAVE_IO_H)
+ENDIF(MSVC)
 CHECK_INCLUDE_FILE("stdlib.h" HAVE_STDLIB_H)
 CHECK_INCLUDE_FILE("stdarg.h" HAVE_STDARG_H)
 CHECK_INCLUDE_FILE("strings.h" HAVE_STRINGS_H)
@@ -1251,9 +1309,13 @@ ENDIF(SIZEOF_PTRDIFF_T)
 
 # __int64 is used on Windows for large file support.
 CHECK_TYPE_SIZE("__int64" SIZEOF___INT_64)
-CHECK_TYPE_SIZE("uchar" SIZEOF_UCHAR)
 CHECK_TYPE_SIZE("int64_t" SIZEOF_INT64_T)
 CHECK_TYPE_SIZE("uint64_t" SIZEOF_UINT64_T)
+CHECK_TYPE_SIZE("unsigned char" SIZEOF_UCHAR)
+CHECK_TYPE_SIZE("unsigned short int" SIZEOF_UNSIGNED_SHORT_INT)
+CHECK_TYPE_SIZE("unsigned int" SIZEOF_UNSIGNED_INT)
+CHECK_TYPE_SIZE("long long" SIZEOF_LONGLONG)
+CHECK_TYPE_SIZE("unsigned long long" SIZEOF_ULONGLONG)
 
 # On windows systems, we redefine off_t as __int64
 # to enable LFS. This is true on 32 and 64 bit system.s
@@ -1348,7 +1410,7 @@ IF(HAVE_M4)
  ADD_CUSTOM_COMMAND(
  OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/${filename}.c
  COMMAND ${NC_M4}
- ARGS ${CMAKE_CURRENT_SOURCE_DIR}/${filename}.m4 > ${CMAKE_CURRENT_SOURCE_DIR}/${filename}.c
+ ARGS ${M4FLAGS} ${CMAKE_CURRENT_SOURCE_DIR}/${filename}.m4 > ${CMAKE_CURRENT_SOURCE_DIR}/${filename}.c
  VERBATIM
  )
 ENDIF(HAVE_M4)
@@ -1826,6 +1888,7 @@ is_enabled(ENABLE_DAP4 HAS_DAP4)
 is_enabled(USE_DISKLESS HAS_DISKLESS)
 is_enabled(USE_MMAP HAS_MMAP)
 is_enabled(JNA HAS_JNA)
+is_enabled(STATUS_RELAX_COORD_BOUND RELAX_COORD_BOUND)
 
 # Generate file from template.
 CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/libnetcdf.settings.in"

Makefile.am

@@ -131,6 +131,7 @@ settings_DATA=libnetcdf.settings
 ####
 
 MM4= ./nc_test/test_put ./nc_test/test_get \
+ ./nc_test/test_write ./nc_test/test_read \
  ./libsrc/netcdf ./libsrc/putget ./libsrc/ncx \
  ./libsrc/t_ncxx ./libsrc/attr
 

acinclude.m4

@@ -749,3 +749,25 @@ esac
 
 ])# AX_C_FLOAT_WORDS_BIGENDIAN
 
+dnl Find the full path of a header file
+dnl
+dnl UD_CHECK_HEADER_PATH(file, [action-if-found], [action-if-not-found])
+dnl Example:
+dnl UD_CHECK_HEADER_PATH([math.h])
+dnl AC_MSG_NOTICE([ac_cv_header_path_math_h=$ac_cv_header_path_math_h])
+dnl
+dnl
+AC_DEFUN([UD_CHECK_HEADER_PATH],
+[
+ AS_VAR_PUSHDEF([ac_Path], [ac_cv_header_path_$1])dnl
+ AC_CACHE_CHECK(
+ [for full path of header file $1], [ac_Path],
+ [AC_PREPROC_IFELSE(
+ [AC_LANG_PROGRAM([[#include <$1>]])],
+ [AS_VAR_SET([ac_Path], [`sed -n '/\.h"/s/.*"\(.*\)".*/\1/p' conftest.i | grep -m 1 $1`])],
+ [AC_MSG_RESULT([not found])]
+ )])
+ AS_VAR_SET_IF([ac_Path], [$2], [$3])
+ AS_VAR_POPDEF([ac_Path])dnl
+])
+

config.h.cmake.in

@@ -45,7 +45,9 @@ are set when opening a binary file on Windows. */
  #define fdopen _fdopen
  #define write _write
  #define strtoll _strtoi64
-#endif
+#endif /*_MSC_VER */
+
+#cmakedefine const
 
 /* Define if building universal (internal helper macro) */
 #cmakedefine AC_APPLE_UNIVERSAL_BUILD 1
@@ -456,6 +458,27 @@ are set when opening a binary file on Windows. */
 /* Define to the version of this package. */
 #cmakedefine PACKAGE_VERSION "${netCDF_VERSION}"
 
+/* The size of `ulonglong` as computed by sizeof. */
+#cmakedefine SIZEOF_ULONGLONG @SIZEOF_ULONGLONG@
+
+/* The size of `longlong` as computed by sizeof. */
+#cmakedefine SIZEOF_LONGLONG @SIZEOF_LONGLONG@
+
+/* The size of `uchar` as computed by sizeof. */
+#cmakedefine SIZEOF_UCHAR @SIZEOF_UCHAR@
+
+/* The size of `ssize_t` as computed by sizeof. */
+#cmakedefine SIZEOF_SSIZE_T @SIZEOF_SSIZE_T@
+
+/* The size of `__int64` found on Windows systems. */
+#cmakedefine SIZEOF___INT64 ${SIZEOF___INT64}
+
+/* The size of `void*` as computed by sizeof. */
+#cmakedefine SIZEOF_VOIDSTAR ${SIZEOF_VOIDSTAR}
+
+/* The size of `short` as computed by sizeof. */
+#cmakedefine SIZEOF_OFF64_T ${SIZEOF_OFF64_T}
+
 /* The size of `double', as computed by sizeof. */
 #cmakedefine SIZEOF_DOUBLE ${SIZEOF_DOUBLE}
 
@@ -607,9 +630,6 @@ are set when opening a binary file on Windows. */
 #cmakedefine __CHAR_UNSIGNED__
 #endif
 
-/* Define to empty if `const' does not conform to ANSI C. */
-#cmakedefine const
-
 /* Define to `long int' if <sys/types.h> does not define. */
 #cmakedefine off_t long int
 

configure.ac

@@ -890,6 +890,13 @@ AC_CHECK_SIZEOF(unsigned long long)
 $SLEEPCMD
 AC_CHECK_SIZEOF(unsigned long long)
 
+$SLEEPCMD
+if test "$ac_cv_type_uchar" = yes ; then
+ AC_CHECK_SIZEOF(uchar)
+else
+ AC_CHECK_SIZEOF(unsigned char)
+fi
+
 $SLEEPCMD
 if test "$ac_cv_type_ushort" = yes ; then
  AC_CHECK_SIZEOF(ushort)
@@ -1110,6 +1117,83 @@ if test "x$enable_parallel" = xyes; then
  AC_DEFINE([USE_PARALLEL], [1], [if true, pnetcdf or parallel netcdf-4 is in use])
 fi
 
+AC_ARG_ENABLE([erange_fill],
+ [AS_HELP_STRING([--enable-erange-fill],
+ [Enable use of fill value when out-of-range type
+ conversion causes NC_ERANGE error. @<:@default: disabled@:>@])],
+ [enable_erange_fill=${enableval}], [enable_erange_fill=no]
+)
+
+AC_ARG_ENABLE([zero-length-coord-bound],
+ [AS_HELP_STRING([--enable-zero-length-coord-bound],
+ [Enable a more relaxed boundary error check NC_EINVALCOORDS
+ to allow coordinate start argument equal to dimension size
+ when argument count is zero. @<:@default: disabled@:>@])],
+ [enable_zero_length_coord_bound=${enableval}], [enable_zero_length_coord_bound=no]
+)
+
+# check PnetCDF's settings on enable_erange_fill and relax_coord_bound
+if test "x$enable_pnetcdf" = xyes; then
+ UD_CHECK_HEADER_PATH([pnetcdf.h])
+
+ AC_MSG_CHECKING([if erange-fill is enabled in PnetCDF])
+ erange_fill_pnetcdf=`grep PNETCDF_ERANGE_FILL ${ac_cv_header_path_pnetcdf_h}`
+ if test "x$erange_fill_pnetcdf" = x; then
+ erange_fill_pnetcdf=no
+ else
+ erange_fill_pnetcdf=`echo ${erange_fill_pnetcdf} | cut -d' ' -f3`
+ if test "x$coord_bound_pnetcdf" = x0; then
+ enable_erange_fill_pnetcdf=no
+ else
+ enable_erange_fill_pnetcdf=yes
+ fi
+ fi
+ AC_MSG_NOTICE([$enable_erange_fill_pnetcdf])
+ if test "$enable_erange_fill" != "$enable_erange_fill_pnetcdf"; then
+ if test "$enable_erange_fill_pnetcdf" = yes; then
+ AC_MSG_WARN([Enable erange-fill to conform with PnetCDF setting])
+ else
+ AC_MSG_WARN([Disable erange-fill to conform with PnetCDF setting])
+ fi
+ enable_erange_fill=$enable_erange_fill_pnetcdf
+ fi
+
+ AC_MSG_CHECKING([if relax-coord-bound is enabled in PnetCDF])
+ relax_coord_bound_pnetcdf=`grep PNETCDF_RELAX_COORD_BOUND ${ac_cv_header_path_pnetcdf_h}`
+ if test "x$relax_coord_bound_pnetcdf" = x; then
+ elax_coord_bound_pnetcdf=no
+ else
+ coord_bound_pnetcdf=`echo ${relax_coord_bound_pnetcdf} | cut -d' ' -f3`
+ if test "x$coord_bound_pnetcdf" = x0; then
+ relax_coord_bound_pnetcdf=no
+ else
+ relax_coord_bound_pnetcdf=yes
+ fi
+ fi
+ AC_MSG_NOTICE([$relax_coord_bound_pnetcdf])
+ if test "$enable_zero_length_coord_bound" != "$relax_coord_bound_pnetcdf"; then
+ if test "$relax_coord_bound_pnetcdf" = yes; then
+ AC_MSG_WARN([Enable relax-coord-bound to conform with PnetCDF setting])
+ else
+ AC_MSG_WARN([Disable relax-coord-bound to conform with PnetCDF setting])
+ fi
+ enable_zero_length_coord_bound=$relax_coord_bound_pnetcdf
+ fi
+fi
+
+if test "x$enable_erange_fill" = xyes ; then
+ if test "x$M4FLAGS" = x ; then
+ M4FLAGS="-DERANGE_FILL"
+ else
+ M4FLAGS="$M4FLAGS -DERANGE_FILL"
+ fi
+fi
+AC_SUBST(M4FLAGS)
+
+if test "x$enable_zero_length_coord_bound" = xyes; then
+ AC_DEFINE([RELAX_COORD_BOUND], [1], [if true, NC_EINVALCOORDS check is more relaxed])
+fi
+
 # Check for downloading/building fortran via postinstall script.
 if test "x$enable_remote_fortran_bootstrap" = xyes; then
  AC_DEFINE([BUILD_FORTRAN], 1, [If true, will attempt to download and build netcdf-fortran.])
@@ -1282,6 +1366,7 @@ AC_SUBST(HAS_PARALLEL4,[$enable_parallel4])
 AC_SUBST(HAS_DISKLESS,[$enable_diskless])
 AC_SUBST(HAS_MMAP,[$enable_mmap])
 AC_SUBST(HAS_JNA,[$enable_jna])
+AC_SUBST(RELAX_COORD_BOUND,[$enable_relax_coord_bound])
 
 # Include some specifics for netcdf on windows.
 #AH_VERBATIM([_WIN32_STRICMP],

gdb-branch.txt

@@ -0,0 +1,18 @@
+set breakpoint pending yes
+break test_nc_redef
+commands
+break util.c:888 if i == 6
+end
+
+#break util.c:903 if i == 6
+#break util.c:1020
+#break util.c:1014 if i == 6 && j == 0
+#break util.c:1016 if i == 6 && j == 0
+#commands
+#break putget.c:10948
+#end
+
+#break test_write.c:216
+#commands
+#break ncx_put_int_double
+#end