merge trunk into this branch

CMakeLists.txt

@@ -532,7 +532,7 @@ ENDIF()
 
 # Options to enable parallel IO, tests.
 SET(STATUS_PNETCDF "OFF")
-OPTION(ENABLE_PNETCDF "Build netCDF-4 with parallel I/O for classic and 64-bit offset files using parallel-netcdf." OFF)
+OPTION(ENABLE_PNETCDF "Build with parallel I/O for classic and 64-bit offset files using parallel-netcdf." OFF)
 IF(ENABLE_PNETCDF)
 	# Check for ncmpi_create in libpnetcdf, define USE_PNETCDF
 	# Does the user want to turn on PNETCDF read ability?
@@ -546,6 +546,8 @@ IF(ENABLE_PNETCDF)
 	SET(STATUS_PNETCDF "ON")	
 	INCLUDE_DIRECTORIES(${PNETCDF_INCLUDE_DIR})
 	SET(HAVE_LIBPNETCDF ON)
+        # pnetcdf => parallel
+        SET(STATUS_PARALLEL "ON")
 ENDIF()
 
 
@@ -704,6 +706,10 @@ add_subdirectory("include")
 add_subdirectory(libdispatch)
 add_subdirectory(libsrc)
 
+IF (USE_PNETCDF)
+add_subdirectory(libsrc5)
+ENDIF (USE_HDF5)
+
 IF (USE_HDF5)
 add_subdirectory(libsrc4)
 ENDIF (USE_HDF5)

Makefile.am

@@ -64,9 +64,9 @@ if BUILD_CDMREMOTE
 LIBCDMR = libcdmr
 endif
 
-# Build librpc
+# Build pnetcdf
-if BUILD_RPC
+if USE_PNETCDF
-LIBRPC = librpc
+LIBSRC5 = libsrc5
 endif
 
 # Build UDUNITS?
@@ -88,7 +88,7 @@ endif
 # and run. ncgen must come before ncdump, because their tests
 # depend on it. 
 SUBDIRS = include $(OCLIB) $(H5_TEST_DIR) libdispatch libsrc		\
-$(LIBSRC4_DIR) $(DAP2) $(LIBCDMR) $(LIBRPC) liblib  \
+$(LIBSRC4_DIR) $(DAP2) $(LIBCDMR) $(LIBSRC5) liblib  \
 $(NCGEN3) $(NCGEN) $(NCDUMP) \
 $(TESTDIRS) \
 man4 $(EXAMPLES) \

cf

@@ -8,7 +8,7 @@ fi
 
 HDF5=1
 DAP=1
-PNETCDF=1
+#PNETCDF=1
 #RPC=1
 #PGI=1
 #M32=1

configure.ac

@@ -133,7 +133,7 @@ AC_MSG_RESULT($enable_hdf4_file_tests)
 # Does the user want to turn on PNETCDF read ability?
 AC_MSG_CHECKING([whether parallel I/O for classic and 64-bit offset files using parallel-netcdf is to be enabled])
 AC_ARG_ENABLE([pnetcdf], [AS_HELP_STRING([--enable-pnetcdf],
-              [build netcdf-4 with parallel I/O for classic and 64-bit offset files using parallel-netcdf])])
+              [build with parallel I/O for classic and 64-bit offset files using parallel-netcdf])])
 test "x$enable_pnetcdf" = xyes || enable_pnetcdf=no
 AC_MSG_RESULT($enable_pnetcdf)
 
@@ -687,18 +687,6 @@ if test "x$enable_netcdf_4" = xyes; then
    if test "x$ac_cv_func_H5Pget_fapl_mpio" = xyes -o "x$ac_cv_func_H5Pget_fapl_mpiposix" = xyes; then
       enable_parallel=yes
       AC_DEFINE([USE_PARALLEL], [1], [if true, parallel netCDF-4 is in use])
-
-      # Using pnetcdf for classic parallel I/O?
-      if test "x$enable_pnetcdf" = xyes; then
-         AC_CHECK_LIB([pnetcdf], [ncmpi_create], [], 
-	 [AC_MSG_ERROR([Cannot link to pnetcdf library, yet --enable-pnetcdf was used.])])
-
-dnl          AC_CHECK_HEADERS([pnetcdf.h], [], [nc4_pnetcdf_h_missing=yes)	   
-dnl 	 if test ! "x$HAVE_PNETCDF" = x1; then
-dnl             AC_MSG_ERROR([Cannot find pnetcdf header, yet --enable-pnetcdf was used.])
-dnl 	 fi
-         AC_DEFINE([USE_PNETCDF], [1], [if true, parallel netCDF is used])      	 
-      fi
    fi
    
    AC_MSG_CHECKING([whether parallel I/O features are to be included])
@@ -739,6 +727,19 @@ if test "x$enable_logging" = xyes; then
    AC_DEFINE([LOGGING], 1, [If true, turn on logging.])
 fi
 
+# Using pnetcdf for classic parallel I/O?
+if test "x$enable_pnetcdf" = xyes; then
+  AC_CHECK_LIB([pnetcdf], [ncmpi_create], [], 
+  [AC_MSG_ERROR([Cannot link to pnetcdf library, yet --enable-pnetcdf was used.])])
+  AC_DEFINE([USE_PNETCDF], [1], [if true, parallel netCDF is used])
+
+  # pnetcdf => parallel
+  # If parallel is in use, enable it in the C code. Also add some stuff to netcdf.h.
+  enable_parallel=yes
+  AC_DEFINE([USE_PARALLEL], [1], [if true, pnetcdf or parallel netcdf-4 is in use])
+fi
+
+
 # Like other libraries, udunits and libcf
 # are no long part of the netcdf distribution.
 
@@ -886,6 +887,7 @@ AC_CONFIG_FILES([Makefile
                  man4/images/Makefile
                  libsrc/Makefile
                  libsrc4/Makefile
+                 libsrc5/Makefile
                  nctest/Makefile
                  nc_test4/Makefile
                  nc_test/Makefile
@@ -898,7 +900,6 @@ AC_CONFIG_FILES([Makefile
                  oc2/Makefile
                  libdap2/Makefile
                  libcdmr/Makefile
-                 librpc/Makefile
                  libdispatch/Makefile
                  liblib/Makefile
                  ncdump/cdl4/Makefile

include/nc4internal.h

@@ -273,21 +273,6 @@ typedef struct  NC_HDF5_FILE_INFO
    int ignore_creationorder;
    int hdf4;
    int sdid;
-
-#ifdef USE_PNETCDF
-   /* pnetcdf_file will be true if the file is created/opened with the
-    * parallel-netcdf library. pnetcdf_access_mode keeps track of
-    * whether independpent or collective mode is
-    * desired. pnetcdf_ndims keeps track of how many dims each var
-    * has, which I need to know to convert start, count, and stride
-    * arrays from size_t to MPI_Offset. (I can't use an inq function
-    * to find out the number of dims, because these are collective in
-    * pnetcdf.) */
-   int pnetcdf_file;
-   int pnetcdf_access_mode;
-   int pnetcdf_ndims[NC_MAX_VARS];
-#endif /* USE_PNETCDF */
-
 } NC_HDF5_FILE_INFO_T;
 
 /* These functions only use the netcdf API calls, so they will work on

include/ncdispatch.h

@@ -85,6 +85,8 @@ extern int nc_put_vara_ulonglong(int ncid, int varid,
 #define NC_DISPATCH_NC4    2
 #define NC_DISPATCH_NCD    4
 #define NC_DISPATCH_NCR    8
+#define NC_DISPATCH_NC5    16
+
 
 /* Define a type for use when doing e.g. nc_get_vara_long, etc. */
 /* Should matche values in libsrc4/netcdf.h */
@@ -107,15 +109,27 @@ extern int nc_put_vara_ulonglong(int ncid, int varid,
 /* Define an alias for int to indicate an error return */
 typedef int NCerror;
 
+/* WARNING: this must match libsrc4/netcdf.h */
+#ifndef MPI_Comm
+#define MPI_Comm int
+#endif
+#ifndef MPI_Info
+#define MPI_Info int
+#endif
+#ifndef MPI_COMM_WORLD
+#define MPI_COMM_WORLD 0
+#endif
+#ifndef MPI_INFO_NULL
+#define MPI_INFO_NULL 0
+#endif
+
 /* Define a struct to hold the MPI info so it can be passed down the
  * call stack. This is used internally by the netCDF library. It
  * should not be used by netcdf users. */
-#ifdef USE_PARALLEL
 typedef struct NC_MPI_INFO {
     MPI_Comm comm;
     MPI_Info info;
 } NC_MPI_INFO;
-#endif
 
 /* Define known dispatch tables and initializers */
 
@@ -133,6 +147,11 @@ extern NC_Dispatch* NCD3_dispatch_table;
 extern int NCD3_initialize(void);
 #endif
 
+#ifdef USE_PNETCDF
+extern NC_Dispatch* NC5_dispatch_table;
+extern int NC5_initialize(void);
+#endif
+
 #ifdef USE_NETCDF4
 
 extern NC_Dispatch* NC4_dispatch_table;
@@ -172,17 +191,6 @@ struct nc_vlen_t;
 
 struct NC;
 
-/* WARNING: this must match libsrc4/netcdf.h */
-#ifndef USE_PARALLEL
-#ifndef MPI_Comm
-#define MPI_Comm int
-#define MPI_Info int
-#define MPI_COMM_WORLD 0
-#ifndef MPI_INFO_NULL
-#define MPI_INFO_NULL 0
-#endif
-#endif
-#endif
 
 int NC_create(const char *path, int cmode,
 	      size_t initialsz, int basepe, size_t *chunksizehintp, 
@@ -271,13 +279,14 @@ int (*inq_var_all)(int ncid, int varid, char *name, nc_type *xtypep,
                int *no_fill, void *fill_valuep, int *endiannessp, 
 	       int *options_maskp, int *pixels_per_blockp);
 
+int (*var_par_access)(int, int, int);
+
 /* Note the following may still be invoked by netcdf client code
    even when the file is a classic file
 */
 #ifdef USE_NETCDF4
 int (*show_metadata)(int);
 int (*inq_unlimdims)(int, int*, int*);
-int (*var_par_access)(int, int, int);
 int (*inq_ncid)(int, const char*, int*);
 int (*inq_grps)(int, int*, int*);
 int (*inq_grpname)(int, char*);
@@ -313,7 +322,6 @@ int (*def_var_endian)(int, int, int);
 int (*set_var_chunk_cache)(int, int, size_t, size_t, float);
 int (*get_var_chunk_cache)(int ncid, int varid, size_t *sizep, size_t *nelemsp, float *preemptionp);
 #endif /*USE_NETCDF4*/
-
 };
 
 /* Following functions must be handled as non-dispatch */

libdap2/Make0

@@ -2,12 +2,12 @@ NCLIB=../liblib/.libs/libnetcdf.a
 NCINCL=-I ../liblib
 
 #CYGWIN
-LFLAG=-L/usr/local/lib
+#LFLAG=-L/usr/local/lib
 #HDF5LIB=/usr/local/lib/libhdf5_hl.a /usr/local/lib/libhdf5.a
 
 #!CYGWIN
-#LFLAG=-L/upc/share/ed/local/${HOST}/lib
+LFLAG=-L/upc/share/ed/local/${HOST}/lib
-#HDF5LIB=/share/ed/local/${HOST}/lib/libhdf5_hl.a /share/ed/local/${HOST}/lib/libhdf5.a
+HDF5LIB=/share/ed/local/${HOST}/lib/libhdf5_hl.a /share/ed/local/${HOST}/lib/libhdf5.a
 
 CURLLIB=-lcurl
 ZLIB=-lz
@@ -258,7 +258,7 @@ fix::
 	done
 
 ##################################################
-T=civ
+T=civ2
 
 v::
 	cc -g -c ${T}.c ${INCL}

libdap2/dapattr3.c

@@ -25,7 +25,7 @@ dapmerge3(NCDAPCOMMON* nccomm, CDFnode* ddsroot, OCddsnode dasroot)
     NClist* allnodes;
     OClink conn;
     char* ocname = NULL;
-
+    char** values = NULL;
     conn = nccomm->oc.conn;
 
     if(ddsroot == NULL || dasroot == NULL) return NC_NOERR;
@@ -44,7 +44,7 @@ dapmerge3(NCDAPCOMMON* nccomm, CDFnode* ddsroot, OCddsnode dasroot)
 	OCCHECK(oc_dds_attr_count(conn,ocnode,&attrcount));
 	for(j=0;j<attrcount;j++) {
 	    size_t nvalues;
-	    char** values = NULL;
+	    
 	    NCattribute* att = NULL;
 
 	    if(ocname != NULL) {
@@ -103,11 +103,13 @@ fprintf(stderr,"%s.Unlimited_Dimension=%s\n",node->ocname,nccomm->cdf.recorddimn
 	    if(values) {
 		oc_reclaim_strings(nvalues,values);
 		free(values);
+		values = NULL;
 	    }
 	}
     }
 
 done:
+    if(values != NULL) free(values);
     if(ocname != NULL) free(ocname);
     if(ocstat != OC_NOERR) ncstat = ocerrtoncerr(ocstat);
     return THROW(ncstat);
@@ -120,7 +122,7 @@ buildattribute(char* name, nc_type ptype,
 {
     int i;
     NCerror ncstat = NC_NOERR;
-    NCattribute* att;
+    NCattribute* att = NULL;
 
     att = (NCattribute*)calloc(1,sizeof(NCattribute));
     MEMCHECK(att,NC_ENOMEM);
@@ -132,6 +134,8 @@ buildattribute(char* name, nc_type ptype,
 	nclistpush(att->values,(void*)nulldup(values[i]));
 
     if(attp) *attp = att;
+    else
+      free(att);
 
     return THROW(ncstat);
 }

libdap2/env

@@ -1,8 +1,9 @@
 PARMS=""; ARGS=""; CON="" ; CE="";  OCON="" ; VAR=""
 alias q0=;alias qq=;alias qv=;alias q=;alias  qh=;alias qqh=;alias qall=;alias qv=;alias qo=;
 
-#TOP="/home/dmh/mach/trunk"
+TOP="/home/dmh/mach/trunk"
-TOP="/cygdrive/f/svn/trunk"
+TOP="/home/dmh/mach/pnetcdf"
+#TOP="/cygdrive/f/svn/trunk"
 #TOP="/cygdrive/c/Users/dmh/svn/trunk"
 
 #PROG=./ncd
@@ -10,8 +11,7 @@ PROG="$TOP/ncdump/ncdump"
 
 P=`pwd`
 
-F="http://motherlode.ucar.edu:8081/dts/ingrid"
+F="file://${TOP}/ncdap_test/testdata3/synth9"
-CON="v3H[0:0][0:43]"
 
 PARMS="[log]"
 #PARMS="${PARMS}[netcdf3]"
@@ -107,4 +107,6 @@ CON="U50M_EOSGRID_Data_Fields[0:23][282:282][441:441]"
 #CON="OneD.amp,TwoD.amp,ThreeD.amp"
 F="http://goldsmr2.sci.gsfc.nasa.gov/opendap/hyrax/MERRA/MAT1NXSLV.5.2.0/1990/01/MERRA100.prod.assim.tavg1_2d_slv_Nx.19900101.hdf"
 CON="U50M_EOSGRID_Data_Fields[0:23][282:282][441:441],XDim_EOSGRID"
+F="http://motherlode.ucar.edu:8081/dts/ingrid"
+CON="v3H[0:0][0:43]"
 fi

libdap2/ncd3dispatch.c

@@ -88,10 +88,11 @@ NCDEFAULT_put_varm,
 
 NULL, /*inq_var_all*/
 
+NULL, /*var_par_access*/
+
 #ifdef USE_NETCDF4
 NULL, /*show_metadata*/
 NULL, /*inq_unlimdims*/
-NULL, /*var_par_access*/
 NULL, /*inq_ncid*/
 NULL, /*inq_grps*/
 NULL, /*inq_grpname*/

libdap2/ncdap3.c

@@ -79,9 +79,6 @@ NCD3_open(const char * path, int mode,
     NCDAPCOMMON* dapcomm = NULL;
     const char* value;
 
-    /* We will use a fake file descriptor as our internal in-memory filename */
-    char tmpname[32];
-
     if(!nc3dinitialized) nc3dinitialize();
 
     if(path == NULL)
@@ -137,11 +134,18 @@ NCD3_open(const char * path, int mode,
     }
 
     /* Use libsrc code for storing metadata */
+    {
+	char tmpname[32];
 
-    snprintf(tmpname,sizeof(tmpname),"%d",drno->int_ncid);
+        /* Create fake file name: exact name must be unique,
-    /* Now, use the file to create the netcdf file; always 64 bit */
+           but is otherwise irrelevant because we are using NC_DISKLESS
-    ncstat = nc_create(tmpname,NC_DISKLESS|NC_64BIT_OFFSET,&drno->substrate);
+        */
-    if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}
+        snprintf(tmpname,sizeof(tmpname),"%d",drno->int_ncid);
+
+        /* Now, use the file to create the netcdf file; force classic.  */
+        ncstat = nc_create(tmpname,NC_DISKLESS|NC_CLASSIC_MODEL,&drno->substrate);
+        if(ncstat != NC_NOERR) {THROWCHK(ncstat); goto done;}
+    }
 
     /* Avoid fill */
     nc_set_fill(drno->substrate,NC_NOFILL,NULL);

libdispatch/dfile.c

@@ -24,6 +24,17 @@ Research/Unidata. See COPYRIGHT file for more info.
 #endif
 #include "ncdispatch.h"
 
+/* Define an enum over the possible set of
+   File Types
+*/
+enum FileType {
+FT_UNKNOWN,
+FT_HDF,
+FT_NC,
+FT_PNETCDF
+};
+
+
 static int nc_initialized = 0;
 
 /** \defgroup datasets NetCDF Files
@@ -82,16 +93,15 @@ nc_local_initialize(void)
 
 static int
 NC_check_file_type(const char *path, int use_parallel, void *mpi_info,
-		   int *cdf, int *hdf)
+		   enum FileType* filetype, int* version)
 {
    char magic[MAGIC_NUMBER_LEN];
     
-   *hdf = 0; *cdf = 0;
+   *filetype = FT_UNKNOWN;
 
    /* Get the 4-byte magic from the beginning of the file. Don't use posix
     * for parallel, use the MPI functions instead. */
 #ifdef USE_PARALLEL_MPIO
-/* Note that this assumes netcdf-4 support is enabled */
    if (use_parallel) 
    {
       MPI_File fh;
@@ -112,8 +122,6 @@ NC_check_file_type(const char *path, int use_parallel, void *mpi_info,
 	 return NC_EPARINIT;
       if((retval = MPI_File_close(&fh)) != MPI_SUCCESS)
 	 return NC_EPARINIT;
-      /* Pretend this is an HDF5 file */
-      *hdf = 5;
    } else
 #endif /* USE_PARALLEL */
    {
@@ -127,28 +135,34 @@ NC_check_file_type(const char *path, int use_parallel, void *mpi_info,
 	 return errno;
       i = fread(magic, MAGIC_NUMBER_LEN, 1, fp);
       fclose(fp);
-	  if(i == 0 && errno == 22) //if file size < 4, Windows fread returns 0, errno 22.
+      if(i == 0 && errno == 22) //if file size < 4, Windows fread returns 0, errno 22.
-		return NC_ENOTNC;
+	return NC_ENOTNC;
       if(i != 1) 
-		 return errno;
+	return errno;
+    }
     
-      /* Ignore the first byte for HDF */
+    /* Look at the magic number */
-      if(magic[1] == 'H' && magic[2] == 'D' && magic[3] == 'F')
+    /* Ignore the first byte for HDF */
-         *hdf = 5;
+    if(magic[1] == 'H' && magic[2] == 'D' && magic[3] == 'F') {
-      else if(magic[0] == '\016' && magic[1] == '\003'
+	*filetype = FT_HDF;
-              && magic[2] == '\023' && magic[3] == '\001')
+	*version = 5;
-         *hdf = 4;
+    } else if(magic[0] == '\016' && magic[1] == '\003'
-      else if(magic[0] == 'C' && magic[1] == 'D' && magic[2] == 'F') 
+              && magic[2] == '\023' && magic[3] == '\001') {
-      {
+	*filetype = FT_HDF;
-         if(magic[3] == '\001') 
+	*version = 4;
-            *cdf = 1; /* netcdf classic version 1 */
+    } else if(magic[0] == 'C' && magic[1] == 'D' && magic[2] == 'F') {
+	*filetype = FT_NC;
+        if(magic[3] == '\001') 
+            *version = 1; /* netcdf classic version 1 */
          else if(magic[3] == '\002') 
-            *cdf = 2; /* netcdf classic version 2 */
+            *version = 2; /* netcdf classic version 2 */
-         else
+         else if(magic[3] == '\005') {
+	    *filetype = FT_PNETCDF;
+            *version = 5; /* pnetcdf file */
+         } else
             return NC_ENOTNC;
-      } else
+     } else
             return NC_ENOTNC;
-    }       
    return NC_NOERR;
 }
 
@@ -1444,8 +1458,12 @@ NC_create(const char *path, int cmode, size_t initialsz,
 
    /* Look to the incoming cmode for hints */
    if(model == 0) {
-      if(cmode & NC_NETCDF4 || cmode & NC_PNETCDF)
+      if(cmode & NC_NETCDF4)
 	model = NC_DISPATCH_NC4;
+      else if(cmode & NC_PNETCDF)
+	model = NC_DISPATCH_NC5;
+      else if(cmode & NC_CLASSIC_MODEL)
+	model = NC_DISPATCH_NC3;
    }
 
    if(model == 0) {
@@ -1498,6 +1516,11 @@ NC_create(const char *path, int cmode, size_t initialsz,
       if(model == (NC_DISPATCH_NC3 | NC_DISPATCH_NCD))
 	dispatcher = NCD3_dispatch_table;
       else
+#endif
+#ifdef USE_PNETCDF
+      if(model == (NC_DISPATCH_NC5))
+	dispatcher = NC5_dispatch_table;
+      else
 #endif
       if(model == (NC_DISPATCH_NC3))
  	dispatcher = NC3_dispatch_table;
@@ -1550,8 +1573,8 @@ NC_open(const char *path, int cmode,
    /* Need two pieces of information for now */
    int model = 0;
    int isurl = 0; 
-   int cdfversion = 0;
+   int version;
-   int hdfversion = 0;
+   enum FileType filetype;
 
    if(!nc_initialized) {
       stat = NC_initialize();
@@ -1564,23 +1587,36 @@ NC_open(const char *path, int cmode,
    isurl = NC_testurl(path);
    if(isurl)
       model = NC_urlmodel(path);
-
+   else {
-   if(!isurl) {
+      filetype = FT_UNKNOWN;
+      version = 0;
+      model = 0;
       /* Look at the file if it exists */
-      stat = NC_check_file_type(path,useparallel,mpi_info,&cdfversion,&hdfversion);
+      stat = NC_check_file_type(path,useparallel,mpi_info,
+				&filetype,&version);
       if(stat == NC_NOERR) {
-	 if(hdfversion != 0) {
+	switch (filetype) {
+	case FT_NC:
+	    if(version == 1 || version == 2)
+		model = NC_DISPATCH_NC3;
+	    break;
+	case FT_HDF:
 	    model = NC_DISPATCH_NC4;
-	 } else if(cdfversion != 0) {
+	    break;
-	    model = NC_DISPATCH_NC3;
+	case FT_PNETCDF:
-	 }
+	    model = NC_DISPATCH_NC5;
+	    break;
+	default:
+	    return NC_ENOTNC;
+	}
       } else /* presumably not a netcdf file */
 	return stat;
    }
 
    /* Look to the incoming cmode for hints */
    if(model == 0) {
-      if(cmode & NC_NETCDF4 || cmode & NC_PNETCDF) model |= NC_DISPATCH_NC4;
+      if(cmode & NC_PNETCDF) model |= NC_DISPATCH_NC5;
+      else if(cmode & NC_NETCDF4) model |= NC_DISPATCH_NC4;
    }
 
    if(model == 0) model = NC_DISPATCH_NC3; /* final default */
@@ -1590,7 +1626,10 @@ NC_open(const char *path, int cmode,
       cmode |= NC_NETCDF4;
    else if(model & NC_DISPATCH_NC3) {
       cmode &= ~NC_NETCDF4; /* must be netcdf-3 */
-      if(cdfversion == 2) cmode |= NC_64BIT_OFFSET;
+      if(version == 2) cmode |= NC_64BIT_OFFSET;
+   } else if(model & NC_DISPATCH_NC5) {
+      cmode &= ~(NC_NETCDF4 | NC_64BIT_OFFSET); /* must be pnetcdf */ 
+      cmode |= NC_PNETCDF;
    }
 
    if((cmode & NC_MPIIO && cmode & NC_MPIPOSIX))
@@ -1611,6 +1650,11 @@ NC_open(const char *path, int cmode,
 	dispatcher = NCD3_dispatch_table;
    else
 #endif
+#if  defined(USE_PNETCDF)
+   if(model == (NC_DISPATCH_NC5))
+	dispatcher = NC5_dispatch_table;
+   else
+#endif
 #if defined(USE_NETCDF4)
    if(model == (NC_DISPATCH_NC4))
 	dispatcher = NC4_dispatch_table;

libdispatch/dsubstrate.c

@@ -1,8 +1,18 @@
 /** \substrate
 Define the substrate dispatch table and functions
 
-These functions end up calling functions in one of the dispatch layers
+The idea of a substrate is that for some dispatch
-(netCDF-4, dap server, etc) using the substrate field of struct NC.
+tables, it is convenient to delegate many of its functions
+of some other dispatch table, called the substrate.
+For example, the libdap2 code needs to create
+metadata. Rather than duplicate the code in libsrc,
+it is convenient to create a temporary
+netcdf-3 "file" (using in-memory data storage)
+and delegate the creation and inquiries about
+the metadata to that substrate netcdf-3 object.
+
+So, these functions end up calling functions in another
+dispatch table using the substrate field of struct NC.
 
 Copyright 2010 University Corporation for Atmospheric
 Research/Unidata. See COPYRIGHT file for more info.  
@@ -854,12 +864,12 @@ NCSUB_put_varm,
 
 NCSUB_inq_var_all,
 
+NCSUB_var_par_access,
+
 #ifdef USE_NETCDF4
 NCSUB_show_metadata,
 NCSUB_inq_unlimdims,
 
-NCSUB_var_par_access,
-
 NCSUB_inq_ncid,
 NCSUB_inq_grps,
 NCSUB_inq_grpname,

liblib/CMakeLists.txt

@@ -12,6 +12,10 @@ IF(USE_HDF5 OR USE_NETCDF4)
 	SET(liblib_LIBS ${liblib_LIBS} netcdf4)
 ENDIF()
 
+IF(USE_PNETCDF)
+	SET(liblib_LIBS ${liblib_LIBS} netcdf5)
+ENDIF()
+
 IF(USE_DAP)
 	SET(liblib_LIBS ${liblib_LIBS} oc2 dap2)
 ENDIF()

liblib/Makefile.am

@@ -33,9 +33,15 @@ endif # BUILD_V2
 # The output library will always include netcdf3 and dispatch
 # libraries
 libnetcdf_la_LIBADD += ${top_builddir}/libdispatch/libdispatch.la	\
-${top_builddir}/libsrc/libnetcdf3.la
+			${top_builddir}/libsrc/libnetcdf3.la
 
-# netcdf3 + dap
+# + pnetcdf
+if USE_PNETCDF
+AM_CPPFLAGS += -I${top_srcdir}/libsrc5
+libnetcdf_la_LIBADD += ${top_builddir}/libsrc5/libnetcdf5.la
+endif # USE_PNETCDF
+
+# + dap
 if USE_DAP
 AM_CPPFLAGS += -I${top_srcdir}/libdap2 -I${top_srcdir}/oc
 libnetcdf_la_LIBADD += ${top_builddir}/libdap2/libdap2.la

liblib/stub.c

@@ -8,6 +8,8 @@
 
 extern int NC3_initialize(void);
 
+extern int NCSUBSTRATE_initialize(void);
+
 #ifdef USE_NETCDF4
 extern int NC4_initialize(void);
 #endif
@@ -23,10 +25,18 @@ extern int NCD4_initialize(void);
 extern int NCCR_initialize(void);
 #endif
 
-#ifdef BUILD_RPC
+#ifdef USE_PNETCDF
-extern int NCRPC_initialize(void);
+extern int NC5_initialize(void);
 #endif
 
+/**
+This procedure invokes all defined
+initializers, and there is an initializer
+for every known dispatch table.
+So if you modify the format of NC_Dispatch,
+then you need to fix it everywhere.
+*/
+
 int
 NC_initialize(void)
 {
@@ -43,6 +53,10 @@ NC_initialize(void)
     if((stat = NCD3_initialize())) return stat;
 #endif
 
+#ifdef USE_PNETCDF
+    if((stat = NC5_initialize())) return stat;
+#endif
+
 #ifdef USE_NETCDF4
     if((stat = NC4_initialize())) return stat;
 
@@ -58,12 +72,10 @@ NC_initialize(void)
     if((stat = NCCR_initialize())) return stat;
 #endif
 
-#ifdef USE_RPC
-    if((stat = NCRPC_initialize())) return stat;
-#endif
-
 #endif /* USE_NETCDF4 */
 
+    /* Finally, initialize the SUBSTRATE table (dsubstrate.c) */
+    if((stat = NCSUBSTRATE_initialize())) return stat;
 
     return NC_NOERR;
 }

libsrc/nc3dispatch.c

@@ -37,10 +37,11 @@ static int NC3_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep,
                int *no_fill, void *fill_valuep, int *endiannessp, 
 	       int *options_maskp, int *pixels_per_blockp);
 
+static int NC3_var_par_access(int,int,int);
+
 #ifdef USE_NETCDF4
 static int NC3_show_metadata(int);
 static int NC3_inq_unlimdims(int,int*,int*);
-static int NC3_var_par_access(int,int,int);
 static int NC3_inq_ncid(int,const char*,int*);
 static int NC3_inq_grps(int,int*,int*);
 static int NC3_inq_grpname(int,char*);
@@ -122,10 +123,11 @@ NCDEFAULT_put_varm,
 
 NC3_inq_var_all,
 
+NC3_var_par_access,
+
 #ifdef USE_NETCDF4
 NC3_show_metadata,
 NC3_inq_unlimdims,
-NC3_var_par_access,
 NC3_inq_ncid,
 NC3_inq_grps,
 NC3_inq_grpname,
@@ -194,6 +196,12 @@ NC3_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep,
     return NC_NOERR;
 }
 
+static int
+NC3_var_par_access(int ncid, int varid, int par_access)
+{
+    return NC_NOERR; /* no-op for netcdf classic */
+}
+    
 #ifdef USE_NETCDF4
 
 static int
@@ -488,11 +496,5 @@ NC3_def_var_endian(int ncid, int varid, int endianness)
     return NC_ENOTNC4;
 }
 
-static int
-NC3_var_par_access(int ncid, int varid, int par_access)
-{
-    return NC_ENOTNC4;
-}
-    
 #endif /*USE_NETCDF4*/
     

libsrc4/nc4attr.c

@@ -17,7 +17,7 @@ conditions.
 #include "nc4dispatch.h"
 #include "ncdispatch.h"
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
 #include <pnetcdf.h>
 #endif
 
@@ -478,7 +478,7 @@ NC4_inq_att(int ncid, int varid, const char *name, nc_type *xtypep, size_t *lenp
    h5 = NC4_DATA(nc);
    assert(h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
    {
@@ -512,7 +512,7 @@ NC4_inq_attid(int ncid, int varid, const char *name, int *attnump)
    h5 = NC4_DATA(nc);
    assert(h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_inq_attid(nc->int_ncid, varid, name, attnump);
@@ -544,7 +544,7 @@ NC4_inq_attname(int ncid, int varid, int attnum, char *name)
    h5 = NC4_DATA(nc);
    assert(h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_inq_attname(nc->int_ncid, varid, attnum, name);
@@ -596,7 +596,7 @@ NC4_rename_att(int ncid, int varid, const char *name,
    if (h5->no_write)
      return NC_EPERM;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_rename_att(nc->int_ncid, varid, name, newname);
@@ -702,7 +702,7 @@ NC4_del_att(int ncid, int varid, const char *name)
    if (h5->no_write)
       return NC_EPERM;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_del_att(nc->int_ncid, varid, name);   
@@ -797,12 +797,13 @@ nc4_put_att_tc(int ncid, int varid, const char *name, nc_type file_type,
    h5 = NC4_DATA(nc);
    assert(h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
    {
       if (mem_type == NC_UBYTE)
 	 mem_type = NC_BYTE;
+
       switch(mem_type)
       {
 	 case NC_BYTE:
@@ -859,12 +860,13 @@ nc4_get_att_tc(int ncid, int varid, const char *name, nc_type mem_type,
    h5 = NC4_DATA(nc);
    assert(h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
    {
       if (mem_type == NC_UBYTE)
 	 mem_type = NC_BYTE;
+
       switch(mem_type)
       {
 	 case NC_BYTE:

libsrc4/nc4dim.c

@@ -14,7 +14,7 @@ $Id: nc4dim.c,v 1.41 2010/05/25 17:54:23 dmh Exp $
 #include "nc4internal.h"
 #include "nc4dispatch.h"
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
 #include <pnetcdf.h>
 #endif
 
@@ -37,7 +37,7 @@ NC4_inq_unlimdim(int ncid, int *unlimdimidp)
       return retval;
    assert(h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_inq_unlimdim(nc->int_ncid, unlimdimidp);
@@ -87,7 +87,7 @@ NC4_def_dim(int ncid, const char *name, size_t len, int *idp)
    if (h5->no_write)
      return NC_EPERM;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_def_dim(nc->int_ncid, name, len, idp);
@@ -169,7 +169,7 @@ NC4_inq_dimid(int ncid, const char *name, int *idp)
    assert(h5);
    assert(nc && grp);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_inq_dimid(nc->int_ncid, name, idp);
@@ -213,7 +213,7 @@ NC4_inq_dim(int ncid, int dimid, char *name, size_t *lenp)
    assert(h5);
    assert(nc && grp);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
    {
@@ -291,7 +291,7 @@ NC4_rename_dim(int ncid, int dimid, const char *name)
    if (h5->no_write)
       return NC_EPERM;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_rename_dim(nc->int_ncid, dimid, name);

libsrc4/nc4dispatch.c

@@ -56,11 +56,11 @@ NCDEFAULT_put_varm,
 
 NC4_inq_var_all,
 
+NC4_var_par_access,
+
 NC4_show_metadata,
 NC4_inq_unlimdims,
 
-NC4_var_par_access,
-
 NC4_inq_ncid,
 NC4_inq_grps,
 NC4_inq_grpname,

libsrc4/nc4file.c

@@ -19,7 +19,7 @@ COPYRIGHT file for copying and redistribution conditions.
 #include <mfhdf.h>
 #endif
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
 #include <pnetcdf.h>
 #endif
 
@@ -252,7 +252,7 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
    nc4_info = NC4_DATA(nc);
    assert(nc4_info && nc4_info->root_grp);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
     if (cmode & NC_PNETCDF)
 	return NC_NOERR;
 #endif
@@ -429,7 +429,7 @@ NC4_create(const char* path, int cmode, size_t initialsz, int basepe,
    nc_file->int_ncid = nc_file->ext_ncid;
    res = nc4_create_file(path, cmode, comm, info, nc_file);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    if (cmode & NC_PNETCDF)
    {
       NC_HDF5_FILE_INFO_T* nc4_info;
@@ -2752,7 +2752,7 @@ NC4_open(const char *path, int mode, int basepe, size_t *chunksizehintp,
 
    /* Depending on the type of file, open it. */
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    if(mode & NC_PNETCDF) {
 	/* this is not really an hdf file */
       int pnetcdf_nvars, i;
@@ -2837,7 +2837,7 @@ NC4_set_fill(int ncid, int fillmode, int *old_modep)
 
    nc4_info->fill_mode = fillmode;	
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (nc4_info->pnetcdf_file)
      return ncmpi_set_fill(nc->int_ncid, fillmode, old_modep);
@@ -2862,7 +2862,7 @@ NC4_redef(int ncid)
       return NC_EBADID;
    assert(nc4_info);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (nc4_info->pnetcdf_file)
       return ncmpi_redef(nc->int_ncid);
@@ -2911,7 +2911,7 @@ static int NC4_enddef(int ncid)
       return NC_EBADID;
    assert(nc4_info);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    if (nc4_info->pnetcdf_file)
    {
       int res;
@@ -2991,7 +2991,7 @@ NC4_sync(int ncid)
       return NC_EBADID;
    assert(nc4_info);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (nc4_info->pnetcdf_file)
       return ncmpi_sync(nc->int_ncid);
@@ -3100,7 +3100,7 @@ NC4_abort(int ncid)
 
    assert(nc4_info);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (nc4_info->pnetcdf_file)
       return ncmpi_abort(nc->int_ncid);
@@ -3146,7 +3146,7 @@ NC4_close(int ncid)
    if (grp->parent)
       return NC_EBADGRPID;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_close(nc->int_ncid);
@@ -3180,7 +3180,7 @@ NC4_inq(int ncid, int *ndimsp, int *nvarsp, int *nattsp, int *unlimdimidp)
 
    assert(h5 && grp && nc);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_inq(nc->int_ncid, ndimsp, nvarsp, nattsp, unlimdimidp);

libsrc4/nc4hdf.c

@@ -19,7 +19,7 @@
 #include <H5DSpublic.h>
 #include <math.h>
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
 #include <pnetcdf.h>
 #endif
 

libsrc4/nc4internal.c

@@ -18,7 +18,7 @@ conditions.
 #include "ncdispatch.h" /* from libdispatch */
 #include <utf8proc.h>
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
 #include <pnetcdf.h>
 #endif
 
@@ -267,7 +267,7 @@ nc4_find_nc_grp_h5(int ncid, NC **nc, NC_GRP_INFO_T **grpp,
     *nc = f;
 
 #if 0 /* I do not understand this code at all */
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
     if (h5->pnetcdf_file) {
       *h5p = NULL;
       *grpp = NULL;

libsrc4/nc4type.c

@@ -115,9 +115,10 @@ NC4_inq_typeid(int ncid, const char *name, nc_type *typeidp)
    /* Normalize name. */
    if (!(norm_name = (char*)malloc(strlen(name) + 1)))
       return NC_ENOMEM;
-   if ((retval = nc4_normalize_name(name, norm_name)))
+   if ((retval = nc4_normalize_name(name, norm_name))) {
-      return retval;
+     free(norm_name);
-
+     return retval;
+   }
    /* Is the type in this group? If not, search parents. */
    for (grp2 = grp; grp2; grp2 = grp2->parent)
       for (type = grp2->type; type; type = type->next)

libsrc4/nc4var.c

@@ -13,7 +13,7 @@ conditions.
 #include "nc4dispatch.h"
 #include <math.h>
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
 #include <pnetcdf.h>
 #endif
 
@@ -576,7 +576,7 @@ NC4_def_var(int ncid, const char *name, nc_type xtype, int ndims,
    if (!(nc = nc4_find_nc_file(ncid,&h5)))
       return NC_EBADID;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
    {
@@ -623,7 +623,7 @@ NC4_inq_var_all(int ncid, int varid, char *name, nc_type *xtypep,
    assert(nc);
    assert(grp && h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_inq_var(nc->int_ncid, varid, name, xtypep, ndimsp, 
@@ -1079,7 +1079,7 @@ NC4_inq_varid(int ncid, const char *name, int *varidp)
    NC_VAR_INFO_T *var;
    char norm_name[NC_MAX_NAME + 1];
    int retval;
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    NC_HDF5_FILE_INFO_T *h5;
 #endif
    
@@ -1094,7 +1094,7 @@ NC4_inq_varid(int ncid, const char *name, int *varidp)
    if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, NULL)))
       return retval;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    h5 = NC4_DATA(nc);
    assert(h5);
    /* Take care of files created/opened with parallel-netcdf library. */
@@ -1141,7 +1141,7 @@ NC4_rename_var(int ncid, int varid, const char *name)
    
    assert(h5);
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
       return ncmpi_rename_var(nc->int_ncid, varid, name);
@@ -1219,7 +1219,7 @@ NC4_var_par_access(int ncid, int varid, int par_access)
    if ((retval = nc4_find_nc_grp_h5(ncid, &nc, &grp, &h5)))
       return retval;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Handle files opened/created with parallel-netcdf library. */
    if (h5->pnetcdf_file)
    {
@@ -1259,7 +1259,7 @@ nc4_put_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long,
 {
    NC *nc;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    NC_HDF5_FILE_INFO_T *h5;
 #endif
    
@@ -1269,7 +1269,7 @@ nc4_put_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long,
    if (!(nc = nc4_find_nc_file(ncid,NULL)))
       return NC_EBADID;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    h5 = NC4_DATA(nc);
    assert(h5);
 
@@ -1399,7 +1399,7 @@ nc4_get_vara_tc(int ncid, int varid, nc_type mem_type, int mem_type_is_long,
    if (!(nc = nc4_find_nc_file(ncid,&h5)))
       return NC_EBADID;
    
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Handle files opened/created with the parallel-netcdf library. */
    if (h5->pnetcdf_file)
    {

libsrc4/ncfunc.c

@@ -91,7 +91,7 @@ NC4_inq_format(int ncid, int *formatp)
    if (!(nc = nc4_find_nc_file(ncid,&h5)))
       return NC_EBADID;
 
-#ifdef USE_PNETCDF
+#if 0 /*def USE_PNETCDF*/
    /* Take care of files created/opened with parallel-netcdf library. */
    if (h5->pnetcdf_file)
      return ncmpi_inq_format(nc->int_ncid, formatp);

libsrc5/CMakeLists.txt

@@ -0,0 +1,10 @@
+SET(CMAKE_INCLUDE_CURRENT_DIR ON)
+
+INCLUDE_DIRECTORIES(".")
+
+
+SET(libsrc5_SOURCES nc5dispatch.c)
+
+add_library(netcdf5 OBJECT ${libsrc_SOURCES}) 
+
+

libsrc5/Makefile.am

@@ -0,0 +1,24 @@
+## This is an automake file, part of Unidata's netCDF package.
+# Copyright 2005, see the COPYRIGHT file for more information.
+
+# This automake file is in charge of building the libsrc directory,
+# which contains the classic library code.
+
+include $(top_srcdir)/lib_flags.am
+
+libnetcdf5_la_CPPFLAGS = ${AM_CPPFLAGS}
+
+# This is the code for a dispatch table for pnetcdf
+# (which has CDF5 as its magic number)
+
+# Turn on a pre-processor flag when building a DLL for windows.
+if BUILD_DLL
+libnetcdf5_la_CPPFLAGS += -DDLL_EXPORT
+endif # BUILD_DLL
+
+# These files comprise the pnetcdf dispatch library code.
+libnetcdf5_la_SOURCES = nc5dispatch.c
+
+noinst_LTLIBRARIES = libnetcdf5.la
+
+EXTRA_DIST = CMakeLists.txt 

nc_test/Makefile.am

@@ -22,6 +22,10 @@ if USE_NETCDF4
 TESTPROGRAMS += tst_atts
 endif
 
+if USE_PNETCDF
+TESTPROGRAMS += tst_parallel2 tst_pnetcdf
+endif
+
 # if EXTRA_TESTS
 # TESTPROGRAMS += 
 # endif # EXTRA_TESTS
@@ -70,6 +74,10 @@ TESTS += run_diskless2.sh
 endif
 endif
 
+if USE_PNETCDF
+TESTS += run_pnetcdf_test.sh
+endif
+
 # This will run a bunch of the test programs with valgrind, the memory
 # checking tool. (Valgrind must be present for this to work.)
 if USE_VALGRIND_TESTS
@@ -84,7 +92,7 @@ endif # USE_VALGRIND_TESTS
 # Distribute the .c files so that m4 isn't required on the users
 # machine.
 EXTRA_DIST = test_get.m4 test_put.m4 run_valgrind_tests.sh \
-run_diskless.sh run_diskless2.sh run_mmap.sh
+run_diskless.sh run_diskless2.sh run_mmap.sh run_pnetcdf_test.sh
 
 # ref_tst_diskless2.cdl is for diff comparison and to produce tst_diskless2.c
 EXTRA_DIST += ref_tst_diskless2.cdl CMakeLists.txt

nc_test/tst_atts3.c

@@ -120,21 +120,23 @@ tst_att_ordering(int cmode)
 int
 main(int argc, char **argv)
 {
-    (void) signal(SIGFPE, SIG_IGN);
-
     signed char schar_in[ATT_LEN], schar_out[ATT_LEN] = {NC_MIN_BYTE, 1, NC_MAX_BYTE};
     unsigned char uchar_in[ATT_LEN];
     short short_in[ATT_LEN], short_out[ATT_LEN] = {NC_MIN_SHORT, -128, NC_MAX_SHORT};
-    unsigned short ushort_in[ATT_LEN], ushort_out[ATT_LEN] = {0, 128, NC_MAX_USHORT};
     int int_in[ATT_LEN], int_out[ATT_LEN] = {-100000, 128, 100000};
-    long long_in[ATT_LEN];
-    unsigned int uint_in[ATT_LEN], uint_out[ATT_LEN] = {0, 128, NC_MAX_UINT};
     float float_in[ATT_LEN], float_out[ATT_LEN] = {-0.5, 0.25, 0.125};
     double double_in[ATT_LEN], double_out[ATT_LEN] = {-0.25, .5, 0.125};
     long long longlong_in[ATT_LEN] = {-1LL, -1LL, -1LL};
+#ifdef USE_NETCDF4
+    long long_in[ATT_LEN];
+    unsigned short ushort_in[ATT_LEN], ushort_out[ATT_LEN] = {0, 128, NC_MAX_USHORT};
+    unsigned int uint_in[ATT_LEN], uint_out[ATT_LEN] = {0, 128, NC_MAX_UINT};
     long long longlong_out[ATT_LEN] = {-3123456789LL, 128LL, 3123456789LL};
     unsigned long long ulonglong_in[ATT_LEN] = {NC_MAX_UINT64, NC_MAX_UINT64, NC_MAX_UINT64};
     unsigned long long ulonglong_out[ATT_LEN] = {0LL, 128LL, 3123456789LL};
+#endif
+
+    (void) signal(SIGFPE, SIG_IGN);
 
    printf("\n*** Testing netcdf-3 attribute functions.\n");
    printf("*** testing really simple global atts...");

nc_test/tst_pnetcdf.c

@@ -14,6 +14,7 @@
 #include <string.h>
 #include <mpi.h>
 #include <netcdf.h>
+#include <netcdf_par.h>
 #include <assert.h>
 
 #define NVARS 6

nc_test4/Makefile.am

@@ -107,17 +107,12 @@ if TEST_PARALLEL
 check_PROGRAMS += tst_mpi_parallel tst_parallel tst_parallel3	\
 tst_parallel4 tst_nc4perf
 TESTS += run_par_test.sh
-# More tests run with --enable-pnetcdf
-if USE_PNETCDF
-check_PROGRAMS += tst_parallel2 tst_pnetcdf
-TESTS += run_pnetcdf_test.sh
-endif
 endif
 
 EXTRA_DIST = run_par_test.sh run_bm.sh run_bm_test1.sh run_bm_test2.sh	\
 run_bm_radar_2D.sh run_bm_radar_2D_compression1.sh run_par_bm_test.sh	\
 run_bm_elena.sh run_par_bm_radar_2D.sh run_bm_radar_2D_endianness1.sh	\
-run_tst_chunks.sh ref_chunks1.cdl ref_chunks2.cdl run_pnetcdf_test.sh	\
+run_tst_chunks.sh ref_chunks1.cdl ref_chunks2.cdl 			\
 run_get_hdf4_files.sh run_valgrind_tests.sh run_valgrind_tests2.sh	\
 run_bm_ar4.sh ref_tst_compounds.nc run_hdf4_valgrind_tests.sh		\
 ref_tst_xplatform2_1.nc ref_tst_xplatform2_2.nc ref_tst_dims.nc		\

ncdap_test/testdata3/synth9.das

@@ -4,4 +4,4 @@ Attributes {
           Int32 a1 32;
 	}
       }
-    }
+}

ncdap_test/testdata3/synth9.dods

@@ -0,0 +1,11 @@
+Dataset {
+      Grid {
+        Array:
+          Float32 temp[lat=2][long=2];
+        Maps:
+          Int32 lat[lat=2];
+          Int32 long[long=2];
+      } G1;
+      Int32 lat[lat=2];
+      Int32 long[long=2];
+    } TEST3;

ncgen/bindata.c

@@ -32,12 +32,13 @@ bin_constant(Generator* generator, Constant* con, Bytebuffer* buf,...)
     }
     switch (con->nctype) {
     case NC_OPAQUE: {
-        unsigned char* bytes;
+        unsigned char* bytes = NULL;
         size_t len;
 	/* Assume the opaque string has been normalized */
         bytes=makebytestring(con->value.opaquev.stringv,&len);
         bbAppendn(buf,(void*)bytes,len);
-        } break;
+	free(bytes);
+    } break;
     case NC_CHAR:
         bbAppendn(buf,&con->value.charv,sizeof(con->value.charv));
         break;

ncgen/cvt.c

@@ -606,6 +606,7 @@ convertstringtochars(Constant* str)
 	con.nctype = NC_CHAR;
         con.lineno = str->lineno;
         con.value.charv = s[i];
+	con.filled = 0;
 	dlappend(dl,&con);
     }
     return dl;

oc2/Makefile.am

@@ -8,7 +8,7 @@
 # $Id: Makefile.am,v 1.1 2010/05/23 21:05:33 dmh Exp $
 
 # Cause C preprocessor to search current and parent directory.
-AM_CPPFLAGS =  -I$(top_srcdir) -I$(top_srcdir)/include
+AM_CPPFLAGS =  -I.. -I$(top_srcdir) -I$(top_srcdir)/include
 
 # OC Sources; include the daptab.[ch] to avoid the need for bison by user
 SRC=oc.c \

oc2/daplex.c

@@ -309,6 +309,8 @@ daplexinit(char* input, DAPlexstate** lexstatep)
     lexstate->yytext = ocbytesnew();
     lexstate->reclaim = oclistnew();
     dapsetwordchars(lexstate,0); /* Assume DDS */
+    if(!lexstatep)
+      free(lexstate);
 }
 
 void