Merge pull request #2 from NetCDF-World-Domination-Council/ejh_wkliao

wkliao changes

Author: edhartnett

CMakeLists.txt

@@ -1303,6 +1303,11 @@ IF(SIZEOF_UINT)
   SET(HAVE_UINT TRUE)
 ENDIF(SIZEOF_UINT)
 
+CHECK_TYPE_SIZE("schar"      SIZEOF_SCHAR)
+IF(SIZEOF_SCHAR)
+  SET(HAVE_SCHAR TRUE)
+ENDIF(SIZEOF_SCHAR)
+
 CHECK_TYPE_SIZE("long"      SIZEOF_LONG)
 CHECK_TYPE_SIZE("long long" SIZEOF_LONG_LONG)
 IF(SIZEOF_LONG_LONG)

configure.ac

@@ -882,8 +882,8 @@ $SLEEPCMD
 AC_CHECK_SIZEOF(size_t)
 $SLEEPCMD
 AC_CHECK_SIZEOF(unsigned long long)
-$SLEEPCMD
-AC_CHECK_SIZEOF(unsigned long long)
+
+AM_CONDITIONAL(ENABLE_CDF5, [test "$ac_cv_sizeof_size_t" -ge "8"])
 
 $SLEEPCMD
 if test "$ac_cv_type_uchar" = yes ; then

include/nc3dispatch.h

@@ -158,14 +158,17 @@ NC3_def_var(int ncid, const char *name,
 
 extern int
 NC3_inq_var(int ncid, int varid, char *name,
-	 nc_type *xtypep, int *ndimsp, int *dimidsp, int *nattsp);
+	 nc_type *xtypep, int *ndimsp, int *dimidsp, int *nattsp,
+	 int *no_fill, void *fill_valuep);
 
 extern int
 NC3_inq_varid(int ncid, const char *name, int *varidp);
 
 extern int
 NC3_rename_var(int ncid, int varid, const char *name);
 
+extern int
+NC3_def_var_fill(int,int,int,const void*);
 
 extern int
 NC3_put_vara(int ncid, int varid,

include/nc3internal.h

@@ -186,6 +186,7 @@ typedef struct NC_var {
 	nc_type type;		/* the discriminant */
 	size_t len;		/* the total length originally allocated */
 	off_t begin;
+	int no_fill;		/* whether fill mode is ON or OFF */
 } NC_var;
 
 typedef struct NC_vararray {
@@ -427,6 +428,9 @@ nc_put_rec(int ncid, size_t recnum, void *const *datap);
 extern int
 NC_check_vlens(NC3_INFO *ncp);
 
+extern int
+NC_check_voffs(NC3_INFO *ncp);
+
 /* Define accessors for the dispatchdata */
 #define NC3_DATA(nc) ((NC3_INFO*)(nc)->dispatchdata)
 #define NC3_DATA_SET(nc,data) ((nc)->dispatchdata = (void*)(data))

include/ncdispatch.h

@@ -9,7 +9,9 @@
 #ifndef _DISPATCH_H
 #define _DISPATCH_H
 
+#if HAVE_CONFIG_H
 #include "config.h"
+#endif
 #include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
@@ -250,6 +252,7 @@ int (*inq_var_all)(int ncid, int varid, char *name, nc_type *xtypep,
               );
 
 int (*var_par_access)(int, int, int);
+int (*def_var_fill)(int, int, int, const void*);
 
 /* Note the following may still be invoked by netcdf client code
    even when the file is a classic file; they will just return an error or
@@ -289,7 +292,6 @@ int (*def_opaque)(int, size_t, const char*, nc_type*);
 int (*def_var_deflate)(int, int, int, int, int);
 int (*def_var_fletcher32)(int, int, int);
 int (*def_var_chunking)(int, int, int, const size_t*);
-int (*def_var_fill)(int, int, int, const void*);
 int (*def_var_endian)(int, int, int);
 int (*def_var_filter)(int, int, unsigned int, size_t, const unsigned int*);
 int (*set_var_chunk_cache)(int, int, size_t, size_t, float);

libdap2/ncd2dispatch.c

@@ -137,6 +137,7 @@ NCDEFAULT_put_varm,
 NCD2_inq_var_all,
 
 NCD2_var_par_access,
+NCD2_def_var_fill,
 
 #ifdef USE_NETCDF4
 NCD2_show_metadata,
@@ -172,7 +173,6 @@ NCD2_def_opaque,
 NCD2_def_var_deflate,
 NCD2_def_var_fletcher32,
 NCD2_def_var_chunking,
-NCD2_def_var_fill,
 NCD2_def_var_endian,
 NCD2_def_var_filter,
 NCD2_set_var_chunk_cache,
@@ -2434,6 +2434,15 @@ NCD2_var_par_access(int ncid, int p2, int p3)
     return THROW(NC_ENOPAR);
 }
 
+int
+NCD2_def_var_fill(int ncid, int p2, int p3, const void* p4)
+{
+    NC* drno;
+    int ret;
+    if((ret = NC_check_id(ncid, (NC**)&drno)) != NC_NOERR) return THROW(ret);
+    ret = nc_def_var_fill(getnc3id(drno), p2, p3, p4);
+    return THROW(ret);
+}
 
 #ifdef USE_NETCDF4
 
@@ -2763,16 +2772,6 @@ NCD2_def_var_chunking(int ncid, int p2, int p3, const size_t* p4)
     return THROW(ret);
 }
 
-int
-NCD2_def_var_fill(int ncid, int p2, int p3, const void* p4)
-{
-    NC* drno;
-    int ret;
-    if((ret = NC_check_id(ncid, (NC**)&drno)) != NC_NOERR) return THROW(ret);
-    ret = nc_def_var_fill(getnc3id(drno), p2, p3, p4);
-    return THROW(ret);
-}
-
 int
 NCD2_def_var_endian(int ncid, int p2, int p3)
 {

libdap2/ncd2dispatch.h

@@ -158,6 +158,9 @@ NCD2_rename_var(int ncid, int varid, const char *name);
 extern int
 NCD2_var_par_access(int, int, int);
 
+extern int
+NCD2_def_var_fill(int, int, int, const void *);
+
   /* netCDF4 API only */
 #ifdef USE_NETCDF4
   extern int
@@ -241,9 +244,6 @@ NCD2_var_par_access(int, int, int);
   extern int
   NCD2_def_var_chunking(int, int, int, const size_t *);
 
-  extern int
-  NCD2_def_var_fill(int, int, int, const void *);
-
   extern int
   NCD2_def_var_endian(int, int, int);
 

libdap4/ncd4dispatch.c

@@ -853,6 +853,7 @@ NCDEFAULT_put_varm,
 NCD4_inq_var_all,
 
 NCD4_var_par_access,
+NCD4_def_var_fill,
 
 #ifdef USE_NETCDF4
 NCD4_show_metadata,
@@ -888,7 +889,6 @@ NCD4_def_opaque,
 NCD4_def_var_deflate,
 NCD4_def_var_fletcher32,
 NCD4_def_var_chunking,
-NCD4_def_var_fill,
 NCD4_def_var_endian,
 NCD4_def_var_filter,
 NCD4_set_var_chunk_cache,

libdispatch/dfile.c

@@ -21,6 +21,8 @@
 #ifdef HAVE_SYS_STAT_H
 #include <sys/stat.h>
 #endif
+#include <unistd.h> /* lseek() */
+
 #include "ncdispatch.h"
 #include "netcdf_mem.h"
 #include "ncwinpath.h"
@@ -2175,7 +2177,6 @@ openmagic(struct MagicFile* file)
     }
 #ifdef USE_PARALLEL
     if (file->use_parallel) {
-	MPI_Status mstatus;
 	int retval;
 	MPI_Offset size;
 	MPI_Comm comm = MPI_COMM_WORLD;
@@ -2206,17 +2207,17 @@ openmagic(struct MagicFile* file)
 	    {status = errno; goto done;}
 	/* Get its length */
 	{
-#ifdef _MSC_VER
 	int fd = fileno(file->fp);
+#ifdef _MSC_VER
 	__int64 len64 = _filelengthi64(fd);
 	if(len64 < 0)
             {status = errno; goto done;}
 	file->filelen = (long long)len64;
 #else
-	long size;
-	if((status = fseek(file->fp, 0L, SEEK_END)) < 0)
+	off_t size;
+	size = lseek(fd, 0, SEEK_END);
+	if(size == -1)
 	    {status = errno; goto done;}
-	size = ftell(file->fp);
 	file->filelen = (long long)size;
 #endif
 	rewind(file->fp);
@@ -2249,12 +2250,8 @@ readmagic(struct MagicFile* file, long pos, char* magic)
     if (file->use_parallel) {
 	MPI_Status mstatus;
 	int retval;
-	MPI_Offset offset;
-	offset = pos;
-	if((retval = MPI_File_seek(file->fh, offset, MPI_SEEK_SET)) != MPI_SUCCESS)
-	    {status = NC_EPARINIT; goto done;}	
-	if((retval = MPI_File_read(file->fh, magic, MAGIC_NUMBER_LEN, MPI_CHAR,
-				 &mstatus)) != MPI_SUCCESS)
+	if((retval = MPI_File_read_at_all(file->fh, pos, magic,
+                     MAGIC_NUMBER_LEN, MPI_CHAR, &mstatus)) != MPI_SUCCESS)
 	    {status = NC_EPARINIT; goto done;}
 	goto done;
     }
@@ -2293,7 +2290,6 @@ closemagic(struct MagicFile* file)
     if(file->inmemory) goto done; /* noop*/
 #ifdef USE_PARALLEL
     if (file->use_parallel) {
-	MPI_Status mstatus;
 	int retval;
 	if((retval = MPI_File_close(&file->fh)) != MPI_SUCCESS)
 		{status = NC_EPARINIT; goto done;}