patch related to Issue258

.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

@@ -984,22 +984,22 @@ 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")
@@ -1008,13 +1008,66 @@ 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 "ON")
+OPTION(ENABLE_ERANGE_FILL "Enable use of fill value when out-of-range type conversion causes NC_ERANGE error." ON)
+IF(NOT ENABLE_ERANGE_FILL)
+  SET(STATUS_ERANGE_FILL "OFF")
+ENDIF()
+
+# Options to use a more relaxed coordinate argument boundary check
+SET(STATUS_RELAX_COORD_BOUND "OFF")
+OPTION(ENABLE_RELAX_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_RELAX_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)
@@ -1242,9 +1295,13 @@ 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_USHORT)
+CHECK_TYPE_SIZE("unsigned int"       SIZEOF_UINT)
+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
@@ -1338,7 +1395,7 @@ 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)
@@ -1806,6 +1863,7 @@ is_enabled(USE_DAP HAS_DAP)
 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

@@ -128,6 +128,7 @@ 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
+])
+

configure.ac

@@ -858,6 +858,13 @@ AC_CHECK_SIZEOF(size_t)
 $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)
@@ -1079,6 +1086,83 @@ 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([--disable-erange-fill],
+                   [Disable use of fill value when out-of-range type
+                    conversion causes NC_ERANGE error. @<:@default: enabled@:>@])],
+   [enable_erange_fill=${enableval}], [enable_erange_fill=yes]
+)
+
+AC_ARG_ENABLE([relax-coord-bound],
+   [AS_HELP_STRING([--enable-relax-coord-bound],
+                   [Enable a more relaxed boundary error check NC_EINVALCOORDS
+                    to allow coordinate start argument equal to dimension size
+                    when argument count is zero. @<:@default: disabled@:>@])],
+   [enable_relax_coord_bound=${enableval}], [enable_relax_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
+      relax_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_relax_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_relax_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$enable_relax_coord_bound" = xyes; then
+   AC_DEFINE([RELAX_COORD_BOUND], [1], [if true, NC_EINVALCOORDS check is more relaxed])
+fi
+
 # Check for downloading/building fortran via postinstall script.
 if test "x$enable_remote_fortran_bootstrap" = xyes; then
    AC_DEFINE([BUILD_FORTRAN], 1, [If true, will attempt to download and build netcdf-fortran.])
@@ -1246,6 +1330,7 @@ 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],

include/nc.h

@@ -38,11 +38,7 @@ typedef struct NC {
 typedef struct {
 	/* all xdr'd */
 	size_t nchars;
-#ifdef __arm__
-  signed char *cp;
-#else
   char *cp;
-#endif
 
 } NC_string;
 
@@ -55,17 +51,10 @@ free_NC_string(NC_string *ncstrp);
 extern int
 NC_check_name(const char *name);
 
-#ifdef __arm__
-extern NC_string *
-new_NC_string(size_t slen, const signed char *str);
-extern int
-set_NC_string(NC_string *ncstrp, const signed char *str);
-#else
 extern NC_string *
 new_NC_string(size_t slen, const char *str);
 extern int
 set_NC_string(NC_string *ncstrp, const char *str);
-#endif
 
 
 /* End defined in string.c */

include/nc3internal.h

@@ -389,6 +389,12 @@ NC_sync(NC3_INFO* ncp);
 extern int
 NC_calcsize(const NC3_INFO* ncp, off_t *filesizep);
 
+extern int
+NC3_inq_default_fill_value(int xtype, void *fillp);
+
+extern int
+NC3_inq_var_fill(const NC_var *varp, void *fill_value);
+
 /* End defined in nc.c */
 /* Begin defined in v1hpg.c */
 

libdispatch/dstring.c

@@ -228,13 +228,8 @@ NC_check_name(const char *name)
 NC_new_string(count, str)
  */
 
-#ifdef __arm__
-NC_string *
-new_NC_string(size_t slen, const signed char *str)
-#else
 NC_string *
 new_NC_string(size_t slen, const char *str)
-#endif
 {
 	NC_string *ncstrp;
 	size_t sz = M_RNDUP(sizeof(NC_string)) + slen + 1;
@@ -269,13 +264,8 @@ new_NC_string(size_t slen, const char *str)
 NC_re_string()
  */
 
-#ifdef __arm__
- int
-   set_NC_string(NC_string *ncstrp, const signed char *str)
-#else
  int
    set_NC_string(NC_string *ncstrp, const char *str)
-#endif
  {
 	size_t slen;