From 665c2c33b2e907d8116e799bcc243c9a8e84963d Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Fri, 15 Mar 2013 21:44:59 +0000
Subject: [PATCH 01/14] synchronize oc2 with oc2.0

---
 oc2/daplex.c     |   8 +--
 oc2/oc.c         | 146 +++++++++++++++++++++++++++++++++++++++++++++--
 oc2/oc.h         |  19 ++++++
 oc2/occompile.c  |  42 ++++++++++++--
 oc2/ocinternal.h |   1 -
 oc2/oclog.c      |   4 +-
 oc2/ocnode.h     |   1 +
 7 files changed, 204 insertions(+), 17 deletions(-)

diff --git a/oc2/daplex.c b/oc2/daplex.c
index b7858fa1f..c92e54b57 100644
--- a/oc2/daplex.c
+++ b/oc2/daplex.c
@@ -300,8 +300,10 @@ dapsetwordchars(DAPlexstate* lexstate, int kind)
 void
 daplexinit(char* input, DAPlexstate** lexstatep)
 {
-    DAPlexstate* lexstate = (DAPlexstate*)malloc(sizeof(DAPlexstate));
-    if(lexstatep) *lexstatep = lexstate;
+    DAPlexstate* lexstate;
+    if(lexstatep == NULL) return; /* no point in building it */
+    lexstate = (DAPlexstate*)malloc(sizeof(DAPlexstate));
+    *lexstatep = lexstate;
     if(lexstate == NULL) return;
     memset((void*)lexstate,0,sizeof(DAPlexstate));
     lexstate->input = strdup(input);
@@ -309,8 +311,6 @@ daplexinit(char* input, DAPlexstate** lexstatep)
     lexstate->yytext = ocbytesnew();
     lexstate->reclaim = oclistnew();
     dapsetwordchars(lexstate,0); /* Assume DDS */
-    if(!lexstatep)
-      free(lexstate);
 }
 
 void
diff --git a/oc2/oc.c b/oc2/oc.c
index 67cf8f256..55b560fd1 100644
--- a/oc2/oc.c
+++ b/oc2/oc.c
@@ -539,7 +539,7 @@ Obtain a dds node by name from a dds structure or dataset node.
 \param[in] link The link through which the server is accessed.
 \param[in] ddsnode The container node of interest.
 \param[in] name The name of the field to return.
-\param[out] fieldnodep  A pointer into which the name'th field node is stored.
+\param[out] fieldp  A pointer into which the name'th field node is stored.
 
 \retval OC_NOERR The procedure executed normally.
 \retval OC_EINDEX No field with the given name was found.
@@ -836,7 +836,7 @@ oc_das_attr(OCobject link, OCobject dasnode, size_t index, OCtype* atomtypep, ch
 /**@}*/
 
 /**************************************************/
-/*! Node Interconnection Management */
+/*!\defgroup Interconnection Node Interconnection Management */
 
 /**@{*/
 
@@ -875,7 +875,7 @@ oc_merge_das(OCobject link, OCobject dasroot, OCobject ddsroot)
 
 /**************************************************/
 
-/*! Data Management */
+/*!\defgroup Data Data Management */
 /**@{*/
 
 /*!
@@ -963,8 +963,14 @@ OCerror
 oc_data_fieldbyname(OCobject link, OCobject datanode, const char* name, OCobject* fieldp)
 {
     OCerror err = OC_NOERR;
+    OCstate* state;
+    OCdata* data;
     size_t count,i;
     OCobject ddsnode;
+    OCVERIFY(OC_State,link);
+    OCDEREF(OCstate*,state,link);
+    OCVERIFY(OC_Data,datanode);
+    OCDEREF(OCdata*,data,datanode);
 
     /* Get the dds node for this datanode */
     err = oc_data_ddsnode(link,datanode,&ddsnode);
@@ -1492,11 +1498,140 @@ oc_data_readn(OCobject link, OCobject datanode,
 }
 
 
+
+/*!
+This procedure has the same semantics as oc_data_read.
+However, it takes an OCddsnode as argument.
+The limitation is that the DDS node must be a top-level,
+atomic variable.
+Top-level means that it is not nested in a Sequence or a
+dimensioned Structure; being in a Grid is ok as is being in
+a scalar structure.
+
+\param[in] link The link through which the server is accessed.
+\param[in] ddsnode The dds node instance of interest.
+\param[in] start A vector of indices specifying the starting element
+to return.
+\param[in] edges A vector of indices specifying the count in each dimension
+of the number of elements to return.
+\param[in] memsize The size (in bytes) of the memory argument.
+\param[out] memory User allocated memory into which the extracted
+data is to be stored. The caller is responsible for allocating and free'ing
+this argument.
+
+\retval OC_NOERR The procedure executed normally.
+\retval OC_EINVAL The memsize argument is too small to hold
+the specified data.
+\retval OC_EINVALCOORDS The start and/or edges argument is outside
+the range of legal indices.
+\retval OC_EDATADDS The data retrieved from the server was malformed
+and the read request cannot be completed.
+
+*/
+
+OCerror
+oc_dds_read(OCobject link, OCobject ddsnode,
+                 size_t* start, size_t* edges,
+	         size_t memsize, void* memory)
+{
+    OCdata* data;
+    OCnode* dds;
+
+    OCVERIFY(OC_Node,ddsnode);
+    OCDEREF(OCnode*,dds,ddsnode);
+
+    /* Get the data associated with this top-level node */
+    data = dds->data;
+    if(data == NULL) return OC_EINVAL;
+    return oc_data_read(link,data,start,edges,memsize,memory);
+}
+
+
+/*!
+This procedure is a variant of oc_data_read for reading a single scalar.
+This procedure has the same semantics as oc_data_readscalar.
+However, it takes an OCddsnode as argument.
+The limitation is that the DDS node must be a top-level, atomic variable.
+Top-level means that it is not nested in a Sequence or a
+dimensioned Structure; being in a Grid is ok as is being in
+a scalar structure.
+
+\param[in] link The link through which the server is accessed.
+\param[in] ddsnode The dds node instance of interest.
+\param[in] memsize The size (in bytes) of the memory argument.
+\param[out] memory User allocated memory into which the extracted
+data is to be stored. The caller is responsible for allocating and free'ing
+this argument.
+
+\retval OC_NOERR The procedure executed normally.
+\retval OC_EINVAL The memsize argument is too small to hold
+the specified data.
+\retval OC_ESCALAR The data instance is not a scalar.
+\retval OC_EDATADDS The data retrieved from the server was malformed
+and the read request cannot be completed.
+\retval OC_EINVAL  One of the arguments (link, etc.) was invalid.
+*/
+
+OCerror
+oc_dds_readscalar(OCobject link, OCobject ddsnode,
+	         size_t memsize, void* memory)
+{
+    return oc_dds_readn(link,ddsnode,NULL,0,memsize,memory);
+}
+
+/*!
+This procedure is a variant of oc_dds_read for reading
+nelements of values starting at a given index position.
+If the variable is a scalar, then the
+index vector and count will be ignored.
+This procedure has the same semantics as oc_data_readn.
+However, it takes an OCddsnode as argument.
+The limitation is that the DDS node must be a top-level, atomic variable.
+Top-level means that it is not nested in a Sequence or a
+dimensioned Structure; being in a Grid is ok as is being in
+a scalar structure.
+
+\param[in] link The link through which the server is accessed.
+\param[in] ddsnode The dds node instance of interest.
+\param[in] start A vector of indices specifying the starting element
+to return.
+\param[in] N The number of elements to read. Reading is assumed
+to use row-major order.
+\param[in] memsize The size (in bytes) of the memory argument.
+\param[out] memory User allocated memory into which the extracted
+data is to be stored. The caller is responsible for allocating and free'ing
+this argument.
+
+\retval OC_NOERR The procedure executed normally.
+\retval OC_EINVAL The memsize argument is too small to hold
+the specified data.
+\retval OC_EINVALCOORDS The start and/or count argument is outside
+the range of legal indices.
+\retval OC_EDATADDS The data retrieved from the server was malformed
+and the read request cannot be completed.
+\retval OC_EINVAL  One of the arguments (link, etc.) was invalid.
+*/
+
+OCerror
+oc_dds_readn(OCobject link, OCobject ddsnode,
+                 size_t* start, size_t N,
+	         size_t memsize, void* memory)
+{
+    OCdata* data;
+    OCnode* dds;
+
+    OCVERIFY(OC_Node,ddsnode);
+    OCDEREF(OCnode*,dds,ddsnode);
+
+    /* Get the data associated with this top-level node */
+    data = dds->data;
+    if(data == NULL) return OC_EINVAL;
+    return oc_data_readn(link,data,start,N,memsize,memory);
+}
+
 /**@}*/
 
 /**************************************************/
-/* OCtype Management */
-
 /*!\defgroup OCtype OCtype Management
 @{*/
 
@@ -1775,6 +1910,7 @@ oc_ping(const char* url)
 /*!
 Set the user agent field.
 
+\param[in] link The link through which the server is accessed.
 \param[in] agent The user agent string
 
 \retval OC_NOERR if the request succeeded.
diff --git a/oc2/oc.h b/oc2/oc.h
index fa84a1d1f..496c88587 100644
--- a/oc2/oc.h
+++ b/oc2/oc.h
@@ -400,12 +400,14 @@ extern OCerror oc_data_recordcount(OClink, OCdatanode, size_t*);
    If scalar, then index and count are ignored.
    Caller is responsible for allocating memory(of proper size)
    and free'ing it.
+   See also oc_dds_read().
 */
 extern OCerror oc_data_read(OClink, OCdatanode, size_t*, size_t*, size_t, void*);
 
 /* Like oc_data_read, but for reading a scalar.
    Caller is responsible for allocating memory(of proper size)
    and free'ing it.
+   See also oc_dds_readscalar().
 */
 extern OCerror oc_data_readscalar(OClink, OCdatanode, size_t, void*);
 
@@ -413,6 +415,7 @@ extern OCerror oc_data_readscalar(OClink, OCdatanode, size_t, void*);
    and count of the number of elements to read.
    Caller is responsible for allocating memory(of proper size)
    and free'ing it.
+   See also oc_dds_readn().
 */
 extern OCerror oc_data_readn(OClink, OCdatanode, size_t*, size_t, size_t, void*);
 
@@ -446,6 +449,22 @@ extern int oc_data_indexed(OClink, OCdatanode);
 */
 extern int oc_data_indexable(OClink, OCdatanode);
 
+/**************************************************/
+/* 
+For top-level, atomic variables, it is possible to directly
+read the associated data without having to use the oc_data_XXX
+procedures. Provide special procedures to support this.
+*/
+
+/* See oc_data_read for semantics */
+extern OCerror oc_dds_read(OClink, OCddsnode, size_t*, size_t*, size_t, void*);
+
+/* See oc_data_readscalar for semantics */
+extern OCerror oc_dds_readscalar(OClink, OCddsnode, size_t, void*);
+
+/* See oc_data_readn for semantics */
+extern OCerror oc_dds_readn(OClink, OCddsnode, size_t*, size_t, size_t, void*);
+
 /**************************************************/
 /* Misc. OCtype-related functions */
 
diff --git a/oc2/occompile.c b/oc2/occompile.c
index 40c74481f..866d9f59e 100644
--- a/oc2/occompile.c
+++ b/oc2/occompile.c
@@ -12,14 +12,18 @@
 #include "ocdebug.h"
 #include "ocdump.h"
 
+/* Mnemonic */
+#define TOPLEVEL 1
+
 /* Forward */
 static OCdata* newocdata(OCnode* template);
 static size_t ocxdrsize(OCtype etype,int isscalar);
 static OCerror occompile1(OCstate*, OCnode*, XXDR*, OCdata**);
 static OCerror occompilerecord(OCstate*, OCnode*, XXDR*, OCdata**);
-static OCerror occompilefields(OCstate*, OCdata*, XXDR*);
+static OCerror occompilefields(OCstate*, OCdata*, XXDR*, int istoplevel);
 static OCerror occompileatomic(OCstate*, OCdata*, XXDR*);
 static int ocerrorstring(XXDR* xdrs);
+static int istoplevel(OCnode* node);
 
 /* Sequence tag constant */
 const char StartOfSequence = '\x5A';
@@ -86,13 +90,13 @@ occompile1(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** datap)
 
     case OC_Dataset:
     case OC_Grid: /* Always scalars */
-	ocstat = occompilefields(state,data,xxdrs);
+	ocstat = occompilefields(state,data,xxdrs,istoplevel(xnode));
 	if(ocstat != OC_NOERR) goto fail;
 	break;
 
     case OC_Structure:
 	if(xnode->array.rank == 0) {/* scalar */
-	    ocstat = occompilefields(state,data,xxdrs);
+	    ocstat = occompilefields(state,data,xxdrs,istoplevel(xnode));
 	    if(ocstat != OC_NOERR) goto fail;
 	} else { /* dimensioned structure */
 	    unsigned int xdrcount;
@@ -124,7 +128,7 @@ occompile1(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** datap)
   	        /* capture the current instance position */
 		instance->xdroffset = xxdr_getpos(xxdrs);
 	        /* Now compile the fields of this instance */
-		ocstat = occompilefields(state,instance,xxdrs);
+		ocstat = occompilefields(state,instance,xxdrs,!TOPLEVEL);
 		if(ocstat != OC_NOERR) {goto fail;}
 	    }
 	}
@@ -210,7 +214,7 @@ occompilerecord(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** recordp)
     /* capture the current record position */
     record->xdroffset = xxdr_getpos(xxdrs);
     /* Compile the fields of this record */
-    ocstat = OCTHROW(occompilefields(state,record,xxdrs));
+    ocstat = OCTHROW(occompilefields(state,record,xxdrs,!TOPLEVEL));
     if(ocstat == OC_NOERR) {
         if(recordp) *recordp = record;
     }
@@ -218,7 +222,7 @@ occompilerecord(OCstate* state, OCnode* xnode, XXDR* xxdrs, OCdata** recordp)
 }
 
 static OCerror
-occompilefields(OCstate* state, OCdata* data, XXDR* xxdrs)
+occompilefields(OCstate* state, OCdata* data, XXDR* xxdrs, int istoplevel)
 {
     int i;
     OCerror ocstat = OC_NOERR;
@@ -246,6 +250,15 @@ occompilefields(OCstate* state, OCdata* data, XXDR* xxdrs)
         fieldinstance->index = i;
     }
 
+    /* If top-level, then link the OCnode to the OCdata directly */
+    if(istoplevel) {
+	for(i=0;i<nelements;i++) {
+            OCnode* fieldnode = (OCnode*)oclistget(xnode->subnodes,i);
+            OCdata* fieldinstance = data->instances[i];
+	    fieldnode->data = fieldinstance;
+	}
+    }
+
 done:
     return OCTHROW(ocstat);
 
@@ -373,6 +386,23 @@ newocdata(OCnode* template)
     return data;
 }
 
+static int
+istoplevel(OCnode* node)
+{
+    if(node == NULL)
+	return 1; /* base case */
+    if(!istoplevel(node->container))
+	return 0;
+    switch (node->octype) {
+    case OC_Dataset: case OC_Grid: case OC_Atomic: return 1;
+    case OC_Structure:
+	return (node->array.rank == 0 ? 1 : 0); /* Toplevel if scalar */ 
+    case OC_Sequence: default: return 0;
+    }
+    return 1;
+}
+
+
 /* XDR representation size depends on if this is scalar or not */
 static size_t
 ocxdrsize(OCtype etype, int isscalar)
diff --git a/oc2/ocinternal.h b/oc2/ocinternal.h
index 2ef74069d..42ec1e6ab 100644
--- a/oc2/ocinternal.h
+++ b/oc2/ocinternal.h
@@ -205,5 +205,4 @@ extern int ocinternalinitialize(void);
 
 extern OCerror ocsetuseragent(OCstate* state, const char* agent);
 
-
 #endif /*COMMON_H*/
diff --git a/oc2/oclog.c b/oc2/oclog.c
index 5cd4e3f84..7c17ad2e3 100644
--- a/oc2/oclog.c
+++ b/oc2/oclog.c
@@ -152,7 +152,7 @@ number of arguments and operates like the stdio
 printf function.
 
 \param[in] tag Indicate the kind of this log message.
-\param[in] format Format specification as with printf.
+\param[in] fmt Format specification as with printf.
 */
 
 void
@@ -186,8 +186,10 @@ oclogtext(int tag, const char* text)
 /*!
 Send arbitrarily long text as a logging message.
 Each line will be sent using oclog with the specified tag.
+
 \param[in] tag Indicate the kind of this log message.
 \param[in] text Arbitrary text to send as a logging message.
+\param[in] count Maximum ength of the text to write.
 */
 
 void
diff --git a/oc2/ocnode.h b/oc2/ocnode.h
index baf45e300..3e22390e0 100644
--- a/oc2/ocnode.h
+++ b/oc2/ocnode.h
@@ -57,6 +57,7 @@ struct OCnode {
     OClist* subnodes; /*oclist<OCnode*>*/
     /*int     attributed;*/ /* 1 if merge was done*/
     OClist* attributes; /* oclist<OCattribute*>*/
+    OCdata* data; /* Defined only if this node is a top-level atomic variable*/
 };
 
 #if SIZEOF_SIZE_T == 4

From 11c2083b1c38149c6e3df224362530ff350085e9 Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Sun, 17 Mar 2013 21:23:28 +0000
Subject: [PATCH 02/14] Add note about nc_put/get_varm to discourage their use

---
 libdispatch/dvarget.c | 4 ++++
 libdispatch/dvarput.c | 4 ++++
 2 files changed, 8 insertions(+)

diff --git a/libdispatch/dvarget.c b/libdispatch/dvarget.c
index 0a33b916f..8919dab97 100644
--- a/libdispatch/dvarget.c
+++ b/libdispatch/dvarget.c
@@ -1383,6 +1383,10 @@ atomic type; it will not read user defined types. For this
 function, the type of the data in memory must match the type
 of the variable - no data conversion is done.
 
+Use of this family of functions is discouraged, although not
+formally deprecated. The reason is the complexity of the
+algorithm makes its use difficult for users to properly use.
+
 \param ncid NetCDF or group ID, from a previous call to nc_open(),
 nc_create(), nc_def_grp(), or associated inquiry functions such as 
 nc_inq_ncid().
diff --git a/libdispatch/dvarput.c b/libdispatch/dvarput.c
index 90f0b9395..28b4b66ca 100644
--- a/libdispatch/dvarput.c
+++ b/libdispatch/dvarput.c
@@ -1305,6 +1305,10 @@ atomic type; it will not write user defined types. For this
 function, the type of the data in memory must match the type
 of the variable - no data conversion is done.
 
+Use of this family of functions is discouraged, although not
+formally deprecated. The reason is the complexity of the
+algorithm makes its use difficult for users to properly use.
+
 \param ncid NetCDF or group ID, from a previous call to nc_open(),
 nc_create(), nc_def_grp(), or associated inquiry functions such as 
 nc_inq_ncid().

From f26a4a559a7a0cabe6916df64b57b70a4e282975 Mon Sep 17 00:00:00 2001
From: Ward Fisher <wfisher@unidata.ucar.edu>
Date: Tue, 19 Mar 2013 22:40:15 +0000
Subject: [PATCH 03/14] Merged latest from netcdf-cmake branch.

Addressed several cmake-related issues, in terms of
building on Windows.  Also added XGetopt.c to
EXTRA_dist in Makefile.am files.
---
 CMakeLists.txt     | 3 ++-
 include/netcdf.h   | 4 ++++
 libsrc/Makefile.am | 2 +-
 libsrc/putget.c    | 3 +++
 ncdump/Makefile.am | 2 +-
 ncgen/Makefile.am  | 2 +-
 ncgen3/Makefile.am | 2 +-
 oc2/ocinternal.h   | 5 +++++
 8 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index a29d9f6a2..80effbf4d 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -19,6 +19,7 @@ ENDIF()
 
 # Get system configuration
 find_program(UNAME NAMES uname)
+IF(UNAME)
 macro(getuname name flag)
         exec_program("${UNAME}" ARGS "${flag}" OUTPUT_VARIABLE "${name}")
 endmacro(getuname)
@@ -26,7 +27,7 @@ getuname(osname -s)
 getuname(osrel  -r)
 getuname(cpu    -m)
 set(BUILDNAME        "${osname}-${osrel}-${cpu}" CACHE STRING "Build name variable for CDash")
-
+ENDIF()
 ENABLE_TESTING()
 INCLUDE(CTest)
 
diff --git a/include/netcdf.h b/include/netcdf.h
index c644310f3..8891d4074 100644
--- a/include/netcdf.h
+++ b/include/netcdf.h
@@ -14,6 +14,10 @@ for more info.
 #include <stddef.h> /* size_t, ptrdiff_t */
 #include <errno.h>  /* netcdf functions sometimes return system errors */
 
+/* Required for alloca on Windows */ 
+#if defined(_WIN32) || defined(_WIN64)
+#include <malloc.h>
+#endif
 
 #ifdef _WIN64
 #include <sys/stat.h>
diff --git a/libsrc/Makefile.am b/libsrc/Makefile.am
index d5bb2bafd..1320f9968 100644
--- a/libsrc/Makefile.am
+++ b/libsrc/Makefile.am
@@ -39,7 +39,7 @@ noinst_LTLIBRARIES = libnetcdf3.la
 # with m4), but they are included in the distribution so that the user
 # does not have to have m4.
 MAINTAINERCLEANFILES = attr.c ncx.c putget.c $(man_MANS) attrx.c putgetx.c
-EXTRA_DIST = attr.m4 ncx.m4 putget.m4 $(man_MANS) CMakeLists.txt 
+EXTRA_DIST = attr.m4 ncx.m4 putget.m4 $(man_MANS) CMakeLists.txt XGetopt.c 
 
 # This tells make how to turn .m4 files into .c files.
 .m4.c:
diff --git a/libsrc/putget.c b/libsrc/putget.c
index 3add44aaf..f72a65b57 100644
--- a/libsrc/putget.c
+++ b/libsrc/putget.c
@@ -23,6 +23,9 @@
 #endif
 #include "nc3dispatch.h"
 
+#if defined(_WIN32) || defined(_WIN64)
+#include <malloc.h>
+#endif
 
 #undef MIN  /* system may define MIN somewhere and complain */
 #define MIN(mm,nn) (((mm) < (nn)) ? (mm) : (nn))
diff --git a/ncdump/Makefile.am b/ncdump/Makefile.am
index 795955930..2bab7937d 100644
--- a/ncdump/Makefile.am
+++ b/ncdump/Makefile.am
@@ -123,7 +123,7 @@ ref_nc_test_netcdf4.cdl ref_tst_special_atts3.cdl tst_brecs.cdl         \
 ref_tst_grp_spec0.cdl ref_tst_grp_spec.cdl tst_grp_spec.sh              \
 ref_tst_charfill.cdl tst_charfill.cdl tst_charfill.sh                   \
 tst_iter.sh tst_mud.sh ref_tst_mud4.cdl                                 \
-ref_tst_ncf213.cdl CMakeLists.txt
+ref_tst_ncf213.cdl CMakeLists.txt XGetopt.c
 
 # NCGEN4 additions
 SUBDIRS=cdl4 expected4
diff --git a/ncgen/Makefile.am b/ncgen/Makefile.am
index 998da4714..14daed1a6 100644
--- a/ncgen/Makefile.am
+++ b/ncgen/Makefile.am
@@ -22,7 +22,7 @@ man_MANS = ncgen.1
 # These files all need to be distributed.
 EXTRA_DIST = ncgen.y ncgenyy.c ncgen.l $(man_MANS) internals.html	\
 run_tests.sh run_nc4_tests.sh c0.cdl ref_camrun.cdl \
-ncf199.cdl CMakeLists.txt
+ncf199.cdl CMakeLists.txt XGetopt.c
 
 # This shell script causes ncgen to build a classic and a 64-bit
 # offset file from a cdl file shipped with the distribution.
diff --git a/ncgen3/Makefile.am b/ncgen3/Makefile.am
index 2112d2d0f..a1485abf7 100644
--- a/ncgen3/Makefile.am
+++ b/ncgen3/Makefile.am
@@ -30,7 +30,7 @@ endif # USE_NETCDF4
 
 CLEANFILES = c0.nc c0_64.nc c0_4.nc c0_4c.nc
 
-EXTRA_DIST += CMakeLists.txt
+EXTRA_DIST += CMakeLists.txt XGetopt.c
 
 # This is used if someone wants to rebuild ncgenyy.c or ncgentab.c
 # Otherwise never invoked, but records how to do it. Don't forget to
diff --git a/oc2/ocinternal.h b/oc2/ocinternal.h
index 42ec1e6ab..bf1a960a0 100644
--- a/oc2/ocinternal.h
+++ b/oc2/ocinternal.h
@@ -6,6 +6,11 @@
 
 #include "config.h"
 
+
+#if defined(_WIN32) || defined(_WIN64)
+#include <malloc.h>
+#endif
+
 #ifdef _AIX
 #include <netinet/in.h>
 #endif

From 9b4db7a039bcfb71e1c1eb607ba9e8f6209311c2 Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Sun, 24 Mar 2013 17:33:17 +0000
Subject: [PATCH 04/14] Make some things static that do not need to be
 externally visible

---
 libdap2/dceconstraints.c |  6 +++---
 libdap2/getvara3.c       |  2 +-
 libdap2/ncd3dispatch.c   |  4 ++--
 libdap2/ncdap3.c         | 10 +++++-----
 libdap2/ncdap3.h         |  1 -
 libdispatch/dstring.c    |  2 +-
 libsrc/nc3dispatch.c     |  2 +-
 libsrc/putget.c          |  3 ---
 libsrc4/nc4dispatch.c    |  2 +-
 libsrc4/nc4internal.c    |  6 +++---
 oc2/occompile.c          |  4 ++--
 oc2/ocdebug.c            |  2 +-
 oc2/ocnode.c             |  2 +-
 oc2/ocutil.c             |  6 +++---
 oc2/ocutil.h             |  1 -
 oc2/xxdr.c               |  2 +-
 16 files changed, 25 insertions(+), 30 deletions(-)

diff --git a/libdap2/dceconstraints.c b/libdap2/dceconstraints.c
index 0b47142ad..0f12befcd 100644
--- a/libdap2/dceconstraints.c
+++ b/libdap2/dceconstraints.c
@@ -245,7 +245,7 @@ dcemergeprojections(DCEprojection* merged, DCEprojection* addition)
    that can be used with the url
 */
 
-char*
+static char*
 buildprojectionstring(NClist* projections)
 {
     char* pstring;
@@ -256,7 +256,7 @@ buildprojectionstring(NClist* projections)
     return pstring;
 }
 
-char*
+static char*
 buildselectionstring(NClist* selections)
 {
     NCbytes* buf = ncbytesnew();
@@ -267,7 +267,7 @@ buildselectionstring(NClist* selections)
     return sstring;
 }
 
-char*
+static char*
 buildconstraintstring(DCEconstraint* constraints)
 {
     NCbytes* buf = ncbytesnew();
diff --git a/libdap2/getvara3.c b/libdap2/getvara3.c
index f1bb72446..e23089947 100644
--- a/libdap2/getvara3.c
+++ b/libdap2/getvara3.c
@@ -695,7 +695,7 @@ findfield(CDFnode* node, CDFnode* field)
 }
 
 
-int
+static int
 nc3d_getvarmx(int ncid, int varid,
 	    const size_t *start,
 	    const size_t *edges,
diff --git a/libdap2/ncd3dispatch.c b/libdap2/ncd3dispatch.c
index 0227cff1d..0263ca37f 100644
--- a/libdap2/ncd3dispatch.c
+++ b/libdap2/ncd3dispatch.c
@@ -42,7 +42,7 @@ static int NCD3_get_vars(int ncid, int varid,
 	    const size_t *start, const size_t *edges, const ptrdiff_t* stride,
             void *value, nc_type memtype);
 
-NC_Dispatch NCD3_dispatch_base = {
+static NC_Dispatch NCD3_dispatch_base = {
 
 NC_DISPATCH_NC3 | NC_DISPATCH_NCD,
 
@@ -133,7 +133,7 @@ NULL, /*get_var_chunk_cache*/
 
 NC_Dispatch* NCD3_dispatch_table = NULL; /* moved here from ddispatch.c */
 
-NC_Dispatch NCD3_dispatcher; /* overlay result */
+static NC_Dispatch NCD3_dispatcher; /* overlay result */
 
 int
 NCD3_initialize(void)
diff --git a/libdap2/ncdap3.c b/libdap2/ncdap3.c
index 04785fd5d..bf95fdf35 100644
--- a/libdap2/ncdap3.c
+++ b/libdap2/ncdap3.c
@@ -32,7 +32,7 @@ static NCerror buildattribute3a(NCDAPCOMMON*, NCattribute*, nc_type, int);
 
 static char* getdefinename(CDFnode* node);
 
-int nc3dinitialized = 0;
+static int ncd3initialized = 0;
 
 size_t dap_one[NC_MAX_VAR_DIMS];
 size_t dap_zero[NC_MAX_VAR_DIMS];
@@ -46,8 +46,8 @@ int nc__opendap(void) {return 0;}
 /**************************************************/
 /* Do local initialization */
 
-int
-nc3dinitialize(void)
+static int
+ncd3initialize(void)
 {
     int i;
     compute_nccalignments();
@@ -55,7 +55,7 @@ nc3dinitialize(void)
 	dap_one[i] = 1;
 	dap_zero[i] = 0;
     }
-    nc3dinitialized = 1;
+    ncd3initialized = 1;
 #ifdef DEBUG
     /* force logging to go to stderr */
     nclogclose();
@@ -79,7 +79,7 @@ NCD3_open(const char * path, int mode,
     NCDAPCOMMON* dapcomm = NULL;
     const char* value;
 
-    if(!nc3dinitialized) nc3dinitialize();
+    if(!ncd3initialized) ncd3initialize();
 
     if(path == NULL)
 	return NC_EDAPURL;
diff --git a/libdap2/ncdap3.h b/libdap2/ncdap3.h
index 45b6fcca0..09db76d11 100644
--- a/libdap2/ncdap3.h
+++ b/libdap2/ncdap3.h
@@ -130,7 +130,6 @@ extern size_t dap_zero[NC_MAX_VAR_DIMS];
 
 extern NCerror nc3d_open(const char* path, int mode, int* ncidp);
 extern int nc3d_close(int ncid);
-extern int nc3dinitialize(void);
 extern NCerror restruct3(CDFnode* ddsroot, CDFnode* template, NClist*);
 extern void setvisible(CDFnode* root, int visible);
 extern NCerror mapnodes3(CDFnode* dstroot, CDFnode* srcroot);
diff --git a/libdispatch/dstring.c b/libdispatch/dstring.c
index e8bb00869..32f21d21e 100644
--- a/libdispatch/dstring.c
+++ b/libdispatch/dstring.c
@@ -35,7 +35,7 @@ free_NC_string(NC_string *ncstrp)
 }
 
 
-int 
+static int 
 nextUTF8(const char* cp)
 {
     /*  The goal here is to recognize the length of each
diff --git a/libsrc/nc3dispatch.c b/libsrc/nc3dispatch.c
index 10c4087f9..95cb0a5e9 100644
--- a/libsrc/nc3dispatch.c
+++ b/libsrc/nc3dispatch.c
@@ -76,7 +76,7 @@ static int NC3_set_var_chunk_cache(int,int,size_t,size_t,float);
 static int NC3_get_var_chunk_cache(int,int,size_t*,size_t*,float*);
 #endif /*USE_NETCDF4*/
 
-NC_Dispatch NC3_dispatcher = {
+static NC_Dispatch NC3_dispatcher = {
 
 NC_DISPATCH_NC3,
 
diff --git a/libsrc/putget.c b/libsrc/putget.c
index f72a65b57..3add44aaf 100644
--- a/libsrc/putget.c
+++ b/libsrc/putget.c
@@ -23,9 +23,6 @@
 #endif
 #include "nc3dispatch.h"
 
-#if defined(_WIN32) || defined(_WIN64)
-#include <malloc.h>
-#endif
 
 #undef MIN  /* system may define MIN somewhere and complain */
 #define MIN(mm,nn) (((mm) < (nn)) ? (mm) : (nn))
diff --git a/libsrc4/nc4dispatch.c b/libsrc4/nc4dispatch.c
index d0e0160e4..7d0839f69 100644
--- a/libsrc4/nc4dispatch.c
+++ b/libsrc4/nc4dispatch.c
@@ -10,7 +10,7 @@
 #include "ncdispatch.h"
 #include "nc4dispatch.h"
 
-NC_Dispatch NC4_dispatcher = {
+static NC_Dispatch NC4_dispatcher = {
 
 NC_DISPATCH_NC4,
 
diff --git a/libsrc4/nc4internal.c b/libsrc4/nc4internal.c
index 1595f63e5..8c5adcf4e 100644
--- a/libsrc4/nc4internal.c
+++ b/libsrc4/nc4internal.c
@@ -668,7 +668,7 @@ nc4_dim_list_add(NC_DIM_INFO_T **list)
 }
 
 /* Add to the beginning of a dim list. */
-int
+static int
 nc4_dim_list_add2(NC_DIM_INFO_T **list, NC_DIM_INFO_T **new_dim)
 {
    NC_DIM_INFO_T *dim;
@@ -1012,7 +1012,7 @@ field_list_del(NC_FIELD_INFO_T **list, NC_FIELD_INFO_T *field)
 }
 
 /* Delete a type from a type list, and nc_free the memory. */
-int
+static int
 type_list_del(NC_TYPE_INFO_T **list, NC_TYPE_INFO_T *type)
 {
    NC_FIELD_INFO_T *field, *f;
@@ -1071,7 +1071,7 @@ type_list_del(NC_TYPE_INFO_T **list, NC_TYPE_INFO_T *type)
 }
 
 /* Delete a del from a var list, and nc_free the memory. */
-int
+static int
 nc4_dim_list_del(NC_DIM_INFO_T **list, NC_DIM_INFO_T *dim)
 {
    /* Take this dimension out of the list. */
diff --git a/oc2/occompile.c b/oc2/occompile.c
index 866d9f59e..d74633af4 100644
--- a/oc2/occompile.c
+++ b/oc2/occompile.c
@@ -26,8 +26,8 @@ static int ocerrorstring(XXDR* xdrs);
 static int istoplevel(OCnode* node);
 
 /* Sequence tag constant */
-const char StartOfSequence = '\x5A';
-const char EndOfSequence = '\xA5';
+static const char StartOfSequence = '\x5A';
+static const char EndOfSequence = '\xA5';
 
 /*
 Provide an option that makes a single pass over 
diff --git a/oc2/ocdebug.c b/oc2/ocdebug.c
index aedf3bb59..a22703266 100644
--- a/oc2/ocdebug.c
+++ b/oc2/ocdebug.c
@@ -24,7 +24,7 @@ octhrow(int err)
 #endif
 
 int
-xdrerror(void)
+xxdrerror(void)
 {
     oclog(OCLOGERR,"xdr failure");
     return OCTHROW(OC_EDATADDS);
diff --git a/oc2/ocnode.c b/oc2/ocnode.c
index 929bd9dc4..11a88cd57 100644
--- a/oc2/ocnode.c
+++ b/oc2/ocnode.c
@@ -122,7 +122,7 @@ ocnode_new(char* name, OCtype ptype, OCnode* root)
     return cdf;
 }
 
-OCattribute*
+static OCattribute*
 makeattribute(char* name, OCtype ptype, OClist* values)
 {
     OCattribute* att = (OCattribute*)ocmalloc(sizeof(OCattribute)); /* ocmalloc zeros*/
diff --git a/oc2/ocutil.c b/oc2/ocutil.c
index 42854e916..932ae8408 100644
--- a/oc2/ocutil.c
+++ b/oc2/ocutil.c
@@ -46,7 +46,7 @@ ocstrncmp(const char* s1, const char* s2, size_t len)
 }
 
 
-void
+static void
 makedimlist(OClist* path, OClist* dims)
 {
     unsigned int i,j;
@@ -94,7 +94,7 @@ freeAttributes(OClist* attset)
     }
 }
 
-void
+static void
 freeOCnode(OCnode* cdf, int deep)
 {
     unsigned int i;
@@ -516,7 +516,7 @@ oc_ispacked(OCnode* node)
 /* Must be consistent with ocx.h.OCDT */
 #define NMODES 6
 #define MAXMODENAME 8 /*max (strlen(modestrings[i])) */
-char* modestrings[NMODES+1] = {
+static char* modestrings[NMODES+1] = {
 "FIELD", /* ((OCDT)(1<<0)) field of a container */
 "ELEMENT", /* ((OCDT)(1<<1)) element of a structure array */
 "RECORD", /* ((OCDT)(1<<2)) record of a sequence */
diff --git a/oc2/ocutil.h b/oc2/ocutil.h
index acdc02b21..a8e1f69e6 100644
--- a/oc2/ocutil.h
+++ b/oc2/ocutil.h
@@ -38,7 +38,6 @@ extern void ocmakedimlist(OClist* path, OClist* dims);
 extern int ocfindbod(OCbytes* buffer, size_t*, size_t*);
 
 /* Reclaimers*/
-extern void freeOCnode(OCnode*,int);
 extern void ocfreeprojectionclause(OCprojectionclause* clause);
 
 /* Misc. */
diff --git a/oc2/xxdr.c b/oc2/xxdr.c
index 17ba5c41d..aa26c01ff 100644
--- a/oc2/xxdr.c
+++ b/oc2/xxdr.c
@@ -240,7 +240,7 @@ xxdr_skip_strings(XXDR* xdrs, off_t n)
 }
 
 unsigned int
-xdr_roundup(unsigned int n)
+xxdr_roundup(off_t n)
 {
     unsigned int rounded;
     rounded = RNDUP(n);

From 8d993d58d8fc72a27efb18dee55b1a1f96535af3 Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Mon, 25 Mar 2013 16:29:19 +0000
Subject: [PATCH 05/14] undo a conversion to static

---
 cf                    | 22 ++++++++++++++++------
 libsrc4/nc4internal.c |  2 +-
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/cf b/cf
index 6164378d0..4d4d55d26 100644
--- a/cf
+++ b/cf
@@ -9,6 +9,7 @@ fi
 HDF5=1
 DAP=1
 #PNETCDF=1
+#HDF4=1
 #RPC=1
 #PGI=1
 #M32=1
@@ -25,6 +26,11 @@ cmds=""
 #cmds="$cmds install"
 fi
 
+# HDF4=>HDF5
+if test "x$HDF4" = x1 ; then
+HDF5=1
+fi
+
 # Test pgi compiler
 if test "x$PGI" = x1 ; then
 PATH="/opt/pgi/linux86/11.1/bin:$PATH"
@@ -97,11 +103,16 @@ MAKE=make
 IGNORE="test 0 = 1"
 
 if test "x$HDF5" = "x1" ; then
-CPPFLAGS="-I${stddir}/include -I${stddir}/include $CPPFLAGS"
-LDFLAGS="-L${stddir}/lib -lhdf5_hl -lhdf5 -L${stddir}/lib -lz $LDFLAGS"
+CPPFLAGS="-I${stddir}/include $CPPFLAGS"
+LDFLAGS="-L${stddir}/lib -lhdf5_hl -lhdf5 -lz $LDFLAGS"
 LD_LIBRARY_PATH="${stddir}/lib:$LD_LIBRARY_PATH"
 fi
 
+#if test "x$HDF4" = "x1" ; then
+#CPPFLAGS="-I/machine/local/include $CPPFLAGS"
+#LDFLAGS="-L/machine/local/lib $LDFLAGS"
+#fi
+
 if test "x$DAP" = "x1" -o "x$CDMR" = "x1" -o "x$RPC" = "x1" ; then
 if curl-config --version >/dev/null ; then
 TMP=`curl-config --cflags`
@@ -146,10 +157,6 @@ FLAGS="$FLAGS --enable-logging"
 #FLAGS="$FLAGS --with-libcf"
 #valgrind => not shared
 #FLAGS="$FLAGS --enable-valgrind-tests"
-# hdf4 requires adding to paths
-#FLAGS="$FLAGS --enable-hdf4 --enable-hdf4-file-tests"
-#CPPFLAGS="$CPPFLAGS -I/machine/local/include"
-#LDFLAGS="$LDFLAGS -L/machine/local/lib -L/usr/local/lib"
 
 FLAGS="$FLAGS --disable-shared"
 #FLAGS="$FLAGS --enable-shared"
@@ -157,6 +164,9 @@ FLAGS="$FLAGS --disable-shared"
 if test "x$HDF5" = "x" ; then
 FLAGS="$FLAGS --disable-netcdf-4"
 fi
+if test "x$HDF4" = x1 ; then
+FLAGS="$FLAGS --enable-hdf4 --enable-hdf4-file-tests"
+fi
 if test "x$DAP" = "x" ; then
 FLAGS="$FLAGS --disable-dap"
 fi
diff --git a/libsrc4/nc4internal.c b/libsrc4/nc4internal.c
index 8c5adcf4e..1f7cca7f1 100644
--- a/libsrc4/nc4internal.c
+++ b/libsrc4/nc4internal.c
@@ -1071,7 +1071,7 @@ type_list_del(NC_TYPE_INFO_T **list, NC_TYPE_INFO_T *type)
 }
 
 /* Delete a del from a var list, and nc_free the memory. */
-static int
+int
 nc4_dim_list_del(NC_DIM_INFO_T **list, NC_DIM_INFO_T *dim)
 {
    /* Take this dimension out of the list. */

From 4e41843740edbecbdda24a8809d20a3bebe1dc3a Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Mon, 25 Mar 2013 17:12:50 +0000
Subject: [PATCH 06/14] 1) fix some minor bugs when pnetcdf is enabled
 2)Comment out some apparently unused procedures

---
 cf                       |  2 +-
 libdap2/dceconstraints.c |  6 +++---
 libdap2/dceconstraints.h |  8 ++++++++
 libdap2/getvara3.c       |  4 +++-
 libsrc4/nc4internal.c    |  4 +++-
 nc_test/tst_atts3.c      |  4 ++--
 oc2/oc.c                 |  4 ----
 oc2/ocutil.c             | 12 +++++++++---
 8 files changed, 29 insertions(+), 15 deletions(-)

diff --git a/cf b/cf
index 4d4d55d26..5c4a2ccd1 100644
--- a/cf
+++ b/cf
@@ -8,7 +8,7 @@ fi
 
 HDF5=1
 DAP=1
-#PNETCDF=1
+PNETCDF=1
 #HDF4=1
 #RPC=1
 #PGI=1
diff --git a/libdap2/dceconstraints.c b/libdap2/dceconstraints.c
index 0f12befcd..0b47142ad 100644
--- a/libdap2/dceconstraints.c
+++ b/libdap2/dceconstraints.c
@@ -245,7 +245,7 @@ dcemergeprojections(DCEprojection* merged, DCEprojection* addition)
    that can be used with the url
 */
 
-static char*
+char*
 buildprojectionstring(NClist* projections)
 {
     char* pstring;
@@ -256,7 +256,7 @@ buildprojectionstring(NClist* projections)
     return pstring;
 }
 
-static char*
+char*
 buildselectionstring(NClist* selections)
 {
     NCbytes* buf = ncbytesnew();
@@ -267,7 +267,7 @@ buildselectionstring(NClist* selections)
     return sstring;
 }
 
-static char*
+char*
 buildconstraintstring(DCEconstraint* constraints)
 {
     NCbytes* buf = ncbytesnew();
diff --git a/libdap2/dceconstraints.h b/libdap2/dceconstraints.h
index 64783a41c..1fb4982e0 100644
--- a/libdap2/dceconstraints.h
+++ b/libdap2/dceconstraints.h
@@ -136,6 +136,14 @@ extern size_t dcesafeindex(DCEsegment* seg, size_t start, size_t stop);
 /* Compute segment size for start upto stop */
 extern size_t dcesegmentsize(DCEsegment*, size_t start, size_t stop);
 
+/* Convert a DCE projection/selection/constraint instance into a string
+   that can be used with a url. Caller must free returned string.
+*/
+
+extern char* buildprojectionstring(NClist* projections);
+extern char* buildselectionstring(NClist* selections);
+extern char* buildconstraintstring(DCEconstraint* constraints);
+
 extern int dceverbose;
 
 #endif /*DCECONSTRAINTS_H*/
diff --git a/libdap2/getvara3.c b/libdap2/getvara3.c
index e23089947..fd4b7cf6b 100644
--- a/libdap2/getvara3.c
+++ b/libdap2/getvara3.c
@@ -695,7 +695,8 @@ findfield(CDFnode* node, CDFnode* field)
 }
 
 
-static int
+#ifdef EXTERN_UNUSED
+int
 nc3d_getvarmx(int ncid, int varid,
 	    const size_t *start,
 	    const size_t *edges,
@@ -879,6 +880,7 @@ fprintf(stderr,"old: %lu -> %lu  %f\n",
 done:
     return ncstat;
 }
+#endif /*EXTERN_UNUSED*/
 
 static int
 conversionrequired(nc_type t1, nc_type t2)
diff --git a/libsrc4/nc4internal.c b/libsrc4/nc4internal.c
index 1f7cca7f1..6c48147ab 100644
--- a/libsrc4/nc4internal.c
+++ b/libsrc4/nc4internal.c
@@ -668,7 +668,8 @@ nc4_dim_list_add(NC_DIM_INFO_T **list)
 }
 
 /* Add to the beginning of a dim list. */
-static int
+#ifdef EXTERN_UNUSED
+int
 nc4_dim_list_add2(NC_DIM_INFO_T **list, NC_DIM_INFO_T **new_dim)
 {
    NC_DIM_INFO_T *dim;
@@ -684,6 +685,7 @@ nc4_dim_list_add2(NC_DIM_INFO_T **list, NC_DIM_INFO_T **new_dim)
       *new_dim = dim;
    return NC_NOERR;
 }
+#endif
 
 /* Add to the end of an att list. */
 int
diff --git a/nc_test/tst_atts3.c b/nc_test/tst_atts3.c
index e3fc49a34..25c66d4e8 100644
--- a/nc_test/tst_atts3.c
+++ b/nc_test/tst_atts3.c
@@ -120,8 +120,6 @@ 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};
@@ -136,6 +134,8 @@ main(int argc, char **argv)
     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};
 
+    (void) signal(SIGFPE, SIG_IGN);
+
    printf("\n*** Testing netcdf-3 attribute functions.\n");
    printf("*** testing really simple global atts...");
 #define NUM_SIMPLE_ATTS 9
diff --git a/oc2/oc.c b/oc2/oc.c
index 55b560fd1..c8f5f5758 100644
--- a/oc2/oc.c
+++ b/oc2/oc.c
@@ -963,14 +963,10 @@ OCerror
 oc_data_fieldbyname(OCobject link, OCobject datanode, const char* name, OCobject* fieldp)
 {
     OCerror err = OC_NOERR;
-    OCstate* state;
-    OCdata* data;
     size_t count,i;
     OCobject ddsnode;
     OCVERIFY(OC_State,link);
-    OCDEREF(OCstate*,state,link);
     OCVERIFY(OC_Data,datanode);
-    OCDEREF(OCdata*,data,datanode);
 
     /* Get the dds node for this datanode */
     err = oc_data_ddsnode(link,datanode,&ddsnode);
diff --git a/oc2/ocutil.c b/oc2/ocutil.c
index 932ae8408..21699a7af 100644
--- a/oc2/ocutil.c
+++ b/oc2/ocutil.c
@@ -46,7 +46,8 @@ ocstrncmp(const char* s1, const char* s2, size_t len)
 }
 
 
-static void
+#ifdef EXTERN_UNUSEd
+void
 makedimlist(OClist* path, OClist* dims)
 {
     unsigned int i,j;
@@ -59,6 +60,7 @@ makedimlist(OClist* path, OClist* dims)
         }
     }
 }
+#endif
 
 void
 ocfreeprojectionclause(OCprojectionclause* clause)
@@ -76,7 +78,8 @@ ocfreeprojectionclause(OCprojectionclause* clause)
     free(clause);
 }
 
-static void
+#ifdef EXTERN_UNUSED
+void
 freeAttributes(OClist* attset)
 {
     unsigned int i,j;
@@ -93,8 +96,10 @@ freeAttributes(OClist* attset)
 	}
     }
 }
+#endif
 
-static void
+#ifdef EXTERN_UNUSED
+void
 freeOCnode(OCnode* cdf, int deep)
 {
     unsigned int i;
@@ -113,6 +118,7 @@ freeOCnode(OCnode* cdf, int deep)
     }
     free(cdf);
 }
+#endif
 
 int
 ocfindbod(OCbytes* buffer, size_t* bodp, size_t* ddslenp)

From b15a7b1191c16bcdc1734aec167c3d4e8d7c47f7 Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Mon, 25 Mar 2013 17:44:08 +0000
Subject: [PATCH 07/14] Make some initial changes to support move to
 thredds.ucar.edu

---
 libdispatch/ddispatch.c  | 5 +++--
 ncdap_test/tst_remote.sh | 2 +-
 ncdap_test/tst_tds.sh    | 4 ++--
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/libdispatch/ddispatch.c b/libdispatch/ddispatch.c
index cd5a0119d..e2a5b9891 100644
--- a/libdispatch/ddispatch.c
+++ b/libdispatch/ddispatch.c
@@ -32,10 +32,11 @@ static struct NCPROTOCOLLIST {
 */
 static const char* servers[] = {
 "http://motherlode.ucar.edu:8081", /* try this first */
-"http://remotetest.unidata.ucar.edu",
-"http://remotetest.ucar.edu",
+"http://thredds.ucar.edu", /* Eventually, this will work */
 "http://motherlode.ucar.edu:8080",
 "http://motherlode.ucar.edu",
+"http://remotetest.unidata.ucar.edu",
+"http://remotetest.ucar.edu",
 "http://remotetests.unidata.ucar.edu",
 "http://remotetests.ucar.edu",
 NULL
diff --git a/ncdap_test/tst_remote.sh b/ncdap_test/tst_remote.sh
index 0a5fdea57..0956752f4 100755
--- a/ncdap_test/tst_remote.sh
+++ b/ncdap_test/tst_remote.sh
@@ -124,7 +124,7 @@ argo_all.cdp;1;&location.LATITUDE<1&location.LATITUDE>-1\
 # Test string access 
 # this test cannot be used because the
 # dataset has a limited lifetime
-#REMOTEURLC4="http://motherlode.ucar.edu:$PORT/thredds/dodsC/station/metar"
+#REMOTEURLC4="http://thredds.ucar.edu/thredds/dodsC/station/metar"
 #REMOTETESTSC4="\
 #Surface_METAR_20120101_0000.nc;1;weather[0:10]"
 
diff --git a/ncdap_test/tst_tds.sh b/ncdap_test/tst_tds.sh
index 4a2647b59..b81a253af 100755
--- a/ncdap_test/tst_tds.sh
+++ b/ncdap_test/tst_tds.sh
@@ -42,9 +42,9 @@ EXPECTED="${srcdir}/expecttds3"
 # Special test info
 ##################################################
 # TDS files under 10 megabytes
-# TDS Catalog: http://motherlode.ucar.edu:8080/thredds/catalog/public/dataset/catalog.html
+# TDS Catalog: http://thredds.ucar.edu/thredds/catalog/public/dataset/catalog.html
 
-TDSURL1="http://motherlode.ucar.edu:8080/thredds/dodsC/public/dataset"
+TDSURL1="http://thredds.ucar.edu/thredds/dodsC/public/dataset"
 TDSTESTS1="\
 tst-striped.nc \
 tst-PROFILER_RASS.nc \

From ab17dded899dd6facf7678e07a3a0e881265dd66 Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Mon, 25 Mar 2013 18:01:32 +0000
Subject: [PATCH 08/14] Caron says to use thredds-test as the default test
 server.

---
 cf                       | 2 +-
 libdap2/Make0            | 2 +-
 libdap2/test_vara.c      | 5 +++--
 libdispatch/ddispatch.c  | 5 +++--
 libdispatch/defcheck.c   | 2 +-
 ncdap_test/tst_remote.sh | 2 +-
 6 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/cf b/cf
index 5c4a2ccd1..4d4d55d26 100644
--- a/cf
+++ b/cf
@@ -8,7 +8,7 @@ fi
 
 HDF5=1
 DAP=1
-PNETCDF=1
+#PNETCDF=1
 #HDF4=1
 #RPC=1
 #PGI=1
diff --git a/libdap2/Make0 b/libdap2/Make0
index 0b341f758..45507c451 100755
--- a/libdap2/Make0
+++ b/libdap2/Make0
@@ -258,7 +258,7 @@ fix::
 	done
 
 ##################################################
-T=civ2
+T=test_vara
 
 v::
 	cc -g -c ${T}.c ${INCL}
diff --git a/libdap2/test_vara.c b/libdap2/test_vara.c
index bd34940ac..90ed90e50 100644
--- a/libdap2/test_vara.c
+++ b/libdap2/test_vara.c
@@ -79,14 +79,15 @@ main()
     size_t start[RANK];
     size_t count[RANK];
     char URL[4096];
-    const char* svc = NULL:
+    const char* svc = NULL;
     
-    /* Find Test Server *.
+    /* Find Test Server */
     svc = NC_findtestserver("dts");
     if(svc == NULL) {
 	fprintf(stderr,"Cannot locate test server\n");
 	exit(1);
     }
+    printf("Using test server: %s\n",svc);
     strcpy(URL,svc);
     strcat(URL,DTSTEST);
 
diff --git a/libdispatch/ddispatch.c b/libdispatch/ddispatch.c
index e2a5b9891..c2e36dbf8 100644
--- a/libdispatch/ddispatch.c
+++ b/libdispatch/ddispatch.c
@@ -31,8 +31,9 @@ static struct NCPROTOCOLLIST {
    against future changes.
 */
 static const char* servers[] = {
-"http://motherlode.ucar.edu:8081", /* try this first */
-"http://thredds.ucar.edu", /* Eventually, this will work */
+"http://thredds-test.ucar.edu",
+"http://thredds.ucar.edu",
+"http://motherlode.ucar.edu:8081",
 "http://motherlode.ucar.edu:8080",
 "http://motherlode.ucar.edu",
 "http://remotetest.unidata.ucar.edu",
diff --git a/libdispatch/defcheck.c b/libdispatch/defcheck.c
index 9108bd279..5facde137 100644
--- a/libdispatch/defcheck.c
+++ b/libdispatch/defcheck.c
@@ -4,7 +4,7 @@
 #include <string.h>
 #include <netcdf.h>
 
-#define URL "http://motherlode.ucar.edu:8081/dts/test.02"
+#define URL "http://thredds-test.ucar.edu/dts/test.02"
 #define VAR "i32"
 
 #define ERRCODE 2
diff --git a/ncdap_test/tst_remote.sh b/ncdap_test/tst_remote.sh
index 0956752f4..cd2dc3a01 100755
--- a/ncdap_test/tst_remote.sh
+++ b/ncdap_test/tst_remote.sh
@@ -124,7 +124,7 @@ argo_all.cdp;1;&location.LATITUDE<1&location.LATITUDE>-1\
 # Test string access 
 # this test cannot be used because the
 # dataset has a limited lifetime
-#REMOTEURLC4="http://thredds.ucar.edu/thredds/dodsC/station/metar"
+#REMOTEURLC4="http://thredds-test.ucar.edu/thredds/dodsC/station/metar"
 #REMOTETESTSC4="\
 #Surface_METAR_20120101_0000.nc;1;weather[0:10]"
 

From 2071ca9bf3719753ea365c2d98122d451bf9583b Mon Sep 17 00:00:00 2001
From: Russ Rew <russ@unidata.ucar.edu>
Date: Mon, 25 Mar 2013 18:06:19 +0000
Subject: [PATCH 09/14] Fixed NCF-244, a netCDF-4 bug resulting in two
 dimensions with the same dimension ID

---
 include/nc4internal.h |  2 +-
 libsrc4/nc4file.c     |  3 ++-
 libsrc4/nc4hdf.c      | 22 ++++++++++++++--------
 libsrc4/nc4var.c      |  5 -----
 4 files changed, 17 insertions(+), 15 deletions(-)

diff --git a/include/nc4internal.h b/include/nc4internal.h
index c655817de..f38c5e8b2 100644
--- a/include/nc4internal.h
+++ b/include/nc4internal.h
@@ -317,7 +317,7 @@ int nc4_pg_varm(NC_PG_T pg, NC *nc, int ncid, int varid, const size_t *startp,
 		const size_t *countp, const ptrdiff_t *stridep,
 		const ptrdiff_t *imapp, nc_type xtype, int is_long, void *op);
 int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp);
-int nc4_rec_write_metadata(NC_GRP_INFO_T *grp);
+int nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order);
 int nc4_rec_write_types(NC_GRP_INFO_T *grp);
 int nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5);
 int nc4_reopen_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var);
diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c
index ddb182079..15993532e 100644
--- a/libsrc4/nc4file.c
+++ b/libsrc4/nc4file.c
@@ -2961,9 +2961,10 @@ sync_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
    /* Write any metadata that has changed. */
    if (!(h5->cmode & NC_NOWRITE))
    {
+      int bad_coord_order = 0;	/* if detected, propagate to all groups to consistently store dimids */
       if ((retval = nc4_rec_write_types(h5->root_grp)))
 	 return retval;
-      if ((retval = nc4_rec_write_metadata(h5->root_grp)))
+      if ((retval = nc4_rec_write_metadata(h5->root_grp, bad_coord_order)))
 	 return retval;
    }
 
diff --git a/libsrc4/nc4hdf.c b/libsrc4/nc4hdf.c
index 3ba0d95fa..40cf9b061 100644
--- a/libsrc4/nc4hdf.c
+++ b/libsrc4/nc4hdf.c
@@ -1420,9 +1420,12 @@ var_create_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, int write_dimid)
       maxdimsize[d] = var->dim[d]->unlimited ? H5S_UNLIMITED : (hsize_t)var->dim[d]->len;
       chunksize[d] = var->chunksizes[d];*/
    
-         for (d = 0; d < var->ndims; d++)
-         for (g = grp; g && (dims_found < var->ndims); g = g->parent)
-            for (dim = g->dim; dim; dim = dim->next)
+      for (d = 0; d < var->ndims; d++)
+      {
+	 for (g = grp; g && (dims_found < var->ndims); g = g->parent) 
+	 {
+	    for (dim = g->dim; dim; dim = dim->next)
+	    {
                if (dim->dimid == var->dimids[d])
                {
                   dimsize[d] = dim->unlimited ? NC_HDF5_UNLIMITED_DIMSIZE : dim->len;
@@ -1456,6 +1459,9 @@ var_create_dataset(NC_GRP_INFO_T *grp, NC_VAR_INFO_T *var, int write_dimid)
                   dims_found++;
                   break;
                }
+	    }
+	 }
+      }
       
       if (var->contiguous)
       {
@@ -2420,20 +2426,20 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, int write_dimid)
 }
 
 /* Recursively write all the metadata in a group. Groups and types
- * have all already been written. */
+ * have all already been written.  Propagate bad cooordinate order to
+ * subgroups, if detected. */
 int
-nc4_rec_write_metadata(NC_GRP_INFO_T *grp)
+nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order)
 {
    NC_DIM_INFO_T *dim;
    NC_VAR_INFO_T *var;
    NC_GRP_INFO_T *child_grp;
    int found_coord, coord_varid = -1, wrote_coord;
-   int bad_coord_order = 0;
    int last_dimid = -1;
    int retval;
 
    assert(grp && grp->name && grp->hdf_grpid);
-   LOG((3, "nc4_rec_write_metadata: grp->name %s", grp->name));
+   LOG((3, "nc4_rec_write_metadata: grp->name %s, bad_coord_order %d", grp->name, bad_coord_order));
 
    /* Write global attributes for this group. */
    if ((retval = write_attlist(grp->att, NC_GLOBAL, grp)))
@@ -2516,7 +2522,7 @@ nc4_rec_write_metadata(NC_GRP_INFO_T *grp)
    
    /* If there are any child groups, write their metadata. */
    for (child_grp = grp->children; child_grp; child_grp = child_grp->next)
-      if ((retval = nc4_rec_write_metadata(child_grp)))
+      if ((retval = nc4_rec_write_metadata(child_grp, bad_coord_order)))
          return retval;
       
    return NC_NOERR;
diff --git a/libsrc4/nc4var.c b/libsrc4/nc4var.c
index 075fc0d02..537a25d06 100644
--- a/libsrc4/nc4var.c
+++ b/libsrc4/nc4var.c
@@ -361,7 +361,6 @@ nc_def_var_nc4(int ncid, const char *name, nc_type xtype,
    NC_HDF5_FILE_INFO_T *h5;
    NC_TYPE_INFO_T *type_info;
    char norm_name[NC_MAX_NAME + 1];
-   int new_varid = 0;
    int num_unlim = 0;
    int d;
    size_t num_values = 1;
@@ -415,10 +414,6 @@ nc_def_var_nc4(int ncid, const char *name, nc_type xtype,
    if (h5->no_write)
      return NC_EPERM;
 
-   /* Get the new varid. */
-   for (var = grp->var; var; var = var->next)
-      new_varid++;
-
    /* Check all the dimids to make sure they exist. */
    for (d = 0; d < ndims; d++)
    {

From 6e5e794e896db692723005ea50c0afe3956ae768 Mon Sep 17 00:00:00 2001
From: Ward Fisher <wfisher@unidata.ucar.edu>
Date: Mon, 25 Mar 2013 20:28:40 +0000
Subject: [PATCH 10/14] Merged latest changes from netcdf-cmake branch in
 preparation for next release candidate (4.3.0 rc4).

---
 CMakeLists.txt | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 80effbf4d..a4510d1ca 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -69,8 +69,9 @@ INCLUDE (${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
 INCLUDE (${CMAKE_ROOT}/Modules/CheckCXXSourceCompiles.cmake)
 INCLUDE (${CMAKE_ROOT}/Modules/TestBigEndian.cmake)
 INCLUDE (${CMAKE_ROOT}/Modules/CheckSymbolExists.cmake)
-INCLUDE (${CMAKE_ROOT}/Modules/FindPkgConfig.cmake)
 INCLUDE (${CMAKE_ROOT}/Modules/GetPrerequisites.cmake)
+
+FIND_PACKAGE(PkgConfig QUIET)
 # Only necessary for Windows
 IF(MSVC)
 	INCLUDE (${CMAKE_SOURCE_DIR}/cmake/modules/windows/FindHDF5.cmake)
@@ -376,11 +377,24 @@ IF (USE_HDF5 OR ENABLE_NETCDF_4)
   #FIND_PACKAGE(HDF5 COMPONENTS C HL REQUIRED)
   FIND_LIBRARY(HDF5_LIB NAMES hdf5 libhdf5 hdf5dll)
   FIND_LIBRARY(HDF5_HL_LIB NAMES hdf5_hl libhdf5_hl hdf5_hldll)
+
+  IF(NOT HDF5_LIB) 
+	MESSAGE(FATAL_ERROR "netCDF-4 support specified, but hdf5 libraries not found.")
+  ELSEIF(NOT HDF5_HL_LIB)
+	MESSAGE(FATAL_ERROR "netCDF-4 support specified, but hdf5 high-level libraries not found.")
+  ENDIF()
  
   SET(HDF5_LIBRARIES ${HDF5_LIB} ${HDF5_HL_LIB})  
   FIND_PATH(HDF5_INCLUDE_DIR H5public.h)
 
-  MESSAGE(STATUS "${HDF5_LIB}, ${HDF5_HL_LIB}, ${HDF5_INCLUDE_DIR}")
+  IF(NOT HDF5_INCLUDE_DIR) 
+	MESSAGE(FATAL_ERROR "netCDF-4 support specified, but hdf5 include directories not found.")
+  ENDIF()
+
+  MESSAGE(STATUS "Found HDF5: ${HDF5_LIB}")
+  MESSAGE(STATUS "Found HDF5_HL: ${HDF5_HL_LIB}")
+  MESSAGE(STATUS "Found HDF5 Includes: ${HDF5_INCLUDE_DIR}")
+
 
   INCLUDE_DIRECTORIES(${HDF5_INCLUDE_DIR})
   

From 89ea9a46312c68347617a0429a363dbebf2ce02a Mon Sep 17 00:00:00 2001
From: Ward Fisher <wfisher@unidata.ucar.edu>
Date: Mon, 25 Mar 2013 21:02:11 +0000
Subject: [PATCH 11/14] Added include for Windows in order to make use of
 alloca.

---
 libsrc/putget.c | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/libsrc/putget.c b/libsrc/putget.c
index 3add44aaf..f72a65b57 100644
--- a/libsrc/putget.c
+++ b/libsrc/putget.c
@@ -23,6 +23,9 @@
 #endif
 #include "nc3dispatch.h"
 
+#if defined(_WIN32) || defined(_WIN64)
+#include <malloc.h>
+#endif
 
 #undef MIN  /* system may define MIN somewhere and complain */
 #define MIN(mm,nn) (((mm) < (nn)) ? (mm) : (nn))

From b36dc5b5fb92c335b5384b57b1b0e4e68bdbd62b Mon Sep 17 00:00:00 2001
From: Russ Rew <russ@unidata.ucar.edu>
Date: Tue, 26 Mar 2013 15:14:19 +0000
Subject: [PATCH 12/14] Fix NCF-244 bug for case where using different order
 for defining coordinate variables and their associated dimensions occurs in
 any subgroup, rather than just the root group.  If this occurs, the variable
 attribute "_Netcdf4Dimid" is created for every dimension scale.

Also add a test for this bug fix in tst_dims3.nc, based on Pedro
Vicente's demo.
---
 include/nc4internal.h |   1 +
 libsrc4/nc4file.c     |   2 +
 libsrc4/nc4hdf.c      |  52 +++++++++++++++-------
 nc_test4/tst_dims3.c  | 101 ++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 141 insertions(+), 15 deletions(-)

diff --git a/include/nc4internal.h b/include/nc4internal.h
index f38c5e8b2..69e5df087 100644
--- a/include/nc4internal.h
+++ b/include/nc4internal.h
@@ -317,6 +317,7 @@ int nc4_pg_varm(NC_PG_T pg, NC *nc, int ncid, int varid, const size_t *startp,
 		const size_t *countp, const ptrdiff_t *stridep,
 		const ptrdiff_t *imapp, nc_type xtype, int is_long, void *op);
 int nc4_rec_match_dimscales(NC_GRP_INFO_T *grp);
+int nc4_rec_detect_bad_coord_order(NC_GRP_INFO_T *grp, int *bad_coord_orderp);
 int nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order);
 int nc4_rec_write_types(NC_GRP_INFO_T *grp);
 int nc4_enddef_netcdf4_file(NC_HDF5_FILE_INFO_T *h5);
diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c
index 15993532e..09b1befbb 100644
--- a/libsrc4/nc4file.c
+++ b/libsrc4/nc4file.c
@@ -2964,6 +2964,8 @@ sync_netcdf4_file(NC_HDF5_FILE_INFO_T *h5)
       int bad_coord_order = 0;	/* if detected, propagate to all groups to consistently store dimids */
       if ((retval = nc4_rec_write_types(h5->root_grp)))
 	 return retval;
+      if ((retval = nc4_rec_detect_bad_coord_order(h5->root_grp, &bad_coord_order)))
+	 return retval;
       if ((retval = nc4_rec_write_metadata(h5->root_grp, bad_coord_order)))
 	 return retval;
    }
diff --git a/libsrc4/nc4hdf.c b/libsrc4/nc4hdf.c
index 40cf9b061..419558ece 100644
--- a/libsrc4/nc4hdf.c
+++ b/libsrc4/nc4hdf.c
@@ -2425,26 +2425,18 @@ write_dim(NC_DIM_INFO_T *dim, NC_GRP_INFO_T *grp, int write_dimid)
    return retval;
 }
 
-/* Recursively write all the metadata in a group. Groups and types
- * have all already been written.  Propagate bad cooordinate order to
- * subgroups, if detected. */
+/* Recursively determine if there is a mismatch between order of
+ * coordinate creation and associated dimensions in this group or any
+ * subgroups, to find out if we have to handle that situation. */
 int
-nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order)
+nc4_rec_detect_bad_coord_order(NC_GRP_INFO_T *grp, int *bad_coord_orderp)
 {
    NC_DIM_INFO_T *dim;
    NC_VAR_INFO_T *var;
    NC_GRP_INFO_T *child_grp;
-   int found_coord, coord_varid = -1, wrote_coord;
    int last_dimid = -1;
    int retval;
 
-   assert(grp && grp->name && grp->hdf_grpid);
-   LOG((3, "nc4_rec_write_metadata: grp->name %s, bad_coord_order %d", grp->name, bad_coord_order));
-
-   /* Write global attributes for this group. */
-   if ((retval = write_attlist(grp->att, NC_GLOBAL, grp)))
-      return retval;
-
    /* If the user writes coord vars in a different order then he
     * defined their dimensions, then, when the file is reopened, the
     * order of the dimids will change to match the order of the coord
@@ -2456,8 +2448,8 @@ nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order)
       {
 	 if (var->dimids[0] < last_dimid)
 	 {
-	    bad_coord_order++;
-	    break;
+	     *bad_coord_orderp = 1;
+	     return NC_NOERR;
 	 }
 	 last_dimid = var->dimids[0];
       }
@@ -2472,9 +2464,39 @@ nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order)
 	    if (!strcmp(dim->name, var->name) && !dim->dirty)
 	    {
 	       LOG((5, "coord var defined after enddef/redef"));
-	       bad_coord_order++;
+	       *bad_coord_orderp = 1;
+	       return NC_NOERR;
 	    }
    
+   /* If there are any child groups, check them also for this condition. */
+   for (child_grp = grp->children; child_grp; child_grp = child_grp->next)
+      if ((retval = nc4_rec_detect_bad_coord_order(child_grp, bad_coord_orderp)))
+         return retval;
+
+   return NC_NOERR;
+}
+
+
+/* Recursively write all the metadata in a group. Groups and types
+ * have all already been written.  Propagate bad cooordinate order to
+ * subgroups, if detected. */
+int
+nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order)
+{
+   NC_DIM_INFO_T *dim;
+   NC_VAR_INFO_T *var;
+   NC_GRP_INFO_T *child_grp;
+   int found_coord, coord_varid = -1, wrote_coord;
+
+   int last_dimid = -1;
+   int retval;
+
+   assert(grp && grp->name && grp->hdf_grpid);
+   LOG((3, "nc4_rec_write_metadata: grp->name %s, bad_coord_order %d", grp->name, bad_coord_order));
+
+   /* Write global attributes for this group. */
+   if ((retval = write_attlist(grp->att, NC_GLOBAL, grp)))
+      return retval;
       
    /* For some stupid reason, the dim list is stored backwards! Get to
     * the back of the list. */
diff --git a/nc_test4/tst_dims3.c b/nc_test4/tst_dims3.c
index 6a38fb814..f29f8ea17 100644
--- a/nc_test4/tst_dims3.c
+++ b/nc_test4/tst_dims3.c
@@ -20,10 +20,18 @@ nc_set_log_level(0);
 #define FILE_NAME "tst_dims3.nc"
 #define RANK_time 1
 #define GRP_NAME  "G"
+#define GRP2_NAME "G2"
 #define TIME_NAME "time"
 #define VAR2_NAME "z"
 #define TIME_RANK 1
 #define NUM_TIMES 2
+#define LEV_NAME "level"     
+#define VRT_NAME "vert_number"
+#define LEV_NUM  3
+#define LEV_RANK 1
+#define VRT_RANK 1
+#define VAR2_RANK 2
+#define NUM_VRT 3
       int ncid, grpid;
       int time_dim, time_dim_in;
       int time_var, z_var;
@@ -97,5 +105,98 @@ nc_set_log_level(0);
 	ERR_RET;
    }
    SUMMARIZE_ERR;
+   printf("*** testing defining dimensions and coord variables in different orders in root group...");
+   {
+       int ncid, grpid, grp2id;
+       int time_dimid, lev_dimid, vrt_dimid, g2lev_dimid, g2vrt_dimid;
+       int time_dimid_in, lev_dimid_in, vrt_dimid_in, g2lev_dimid_in, g2vrt_dimid_in;
+       int time_varid, lev_varid, gvar2_varid, g2lev_varid, g2vrt_varid;
+       int var2_dims[VAR2_RANK];
+      /* Create test for fix of bug that resulted in two dimensions
+       * having the same dimid, which violates the Pauli exclusion
+       * principle for dimensions. */
+      if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR_RET;
+      if (nc_def_grp(ncid, GRP_NAME, &grpid)) ERR;
+      if (nc_def_dim(ncid, TIME_NAME, NC_UNLIMITED, &time_dimid)) ERR_RET;
+      if (nc_def_dim(ncid, LEV_NAME, LEV_NUM, &lev_dimid)) ERR_RET;
+      var2_dims[0] = time_dimid;
+      var2_dims[1] = lev_dimid;
+      if (nc_def_var(grpid, VAR2_NAME, NC_FLOAT, VAR2_RANK, var2_dims, &gvar2_varid)) ERR;
+      /* define coord vars in opposite order of coord dims */
+      if (nc_def_var(ncid, LEV_NAME, NC_FLOAT, LEV_RANK, &lev_dimid, &lev_varid)) ERR;
+      if (nc_def_var(ncid, TIME_NAME, NC_FLOAT, TIME_RANK, &time_dimid, &time_varid)) ERR;
+
+      if (nc_def_grp(ncid, GRP2_NAME, &grp2id)) ERR;
+      if (nc_def_dim(grp2id, LEV_NAME, LEV_NUM, &g2lev_dimid)) ERR_RET;
+      if (nc_def_dim(grp2id, VRT_NAME, NUM_VRT, &g2vrt_dimid)) ERR_RET;
+      if (nc_def_var(grp2id, LEV_NAME, NC_FLOAT, LEV_RANK, &g2lev_dimid, &g2lev_varid)) ERR;
+      if (nc_def_var(grp2id, VRT_NAME, NC_FLOAT, VRT_RANK, &g2vrt_dimid, &g2vrt_varid)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Re-open, in which dimids may get reassigned */
+      if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
+      if (nc_inq_dimid(ncid, TIME_NAME, &time_dimid_in)) ERR;
+      if (nc_inq_dimid(ncid, LEV_NAME, &lev_dimid_in)) ERR;
+      if (nc_inq_ncid(ncid, GRP2_NAME, &grp2id)) ERR;
+      if (nc_inq_dimid(grp2id, LEV_NAME, &g2lev_dimid_in)) ERR;
+      if (nc_inq_dimid(grp2id, VRT_NAME, &g2vrt_dimid_in)) ERR;
+      /* dimids must still all be distinct */
+      if (time_dimid_in == lev_dimid_in ||
+	  time_dimid_in == g2lev_dimid_in ||
+	  time_dimid_in == g2vrt_dimid_in ||
+	  lev_dimid_in == g2lev_dimid_in ||
+	  lev_dimid_in == g2vrt_dimid_in ||
+	  g2lev_dimid_in == g2vrt_dimid_in) ERR;
+
+      if (nc_close(ncid))
+	ERR_RET;
+   }
+   SUMMARIZE_ERR;
+   printf("*** testing defining dimensions and coord variables in different orders in subgroup...");
+   {
+       int ncid, grpid, grp2id;
+       int time_dimid, lev_dimid, vrt_dimid, g2lev_dimid, g2vrt_dimid;
+       int time_dimid_in, lev_dimid_in, vrt_dimid_in, g2lev_dimid_in, g2vrt_dimid_in;
+       int time_varid, lev_varid, gvar2_varid, g2lev_varid, g2vrt_varid;
+       int var2_dims[VAR2_RANK];
+      /* Create test for fix of bug inside a subgroup that results in two dimensions
+       * having the same dimid. */
+      if (nc_create(FILE_NAME, NC_NETCDF4, &ncid)) ERR_RET;
+      if (nc_def_grp(ncid, GRP_NAME, &grpid)) ERR;
+      if (nc_def_dim(ncid, TIME_NAME, NC_UNLIMITED, &time_dimid)) ERR_RET;
+      if (nc_def_dim(ncid, LEV_NAME, LEV_NUM, &lev_dimid)) ERR_RET;
+      var2_dims[0] = time_dimid;
+      var2_dims[1] = lev_dimid;
+      if (nc_def_var(grpid, VAR2_NAME, NC_FLOAT, VAR2_RANK, var2_dims, &gvar2_varid)) ERR;
+      if (nc_def_var(ncid, TIME_NAME, NC_FLOAT, TIME_RANK, &time_dimid, &time_varid)) ERR;
+      if (nc_def_var(ncid, LEV_NAME, NC_FLOAT, LEV_RANK, &lev_dimid, &lev_varid)) ERR;
+
+      if (nc_def_grp(ncid, GRP2_NAME, &grp2id)) ERR;
+      if (nc_def_dim(grp2id, LEV_NAME, LEV_NUM, &g2lev_dimid)) ERR_RET;
+      if (nc_def_dim(grp2id, VRT_NAME, NUM_VRT, &g2vrt_dimid)) ERR_RET;
+      /* define coord vars in opposite order of coord dims */
+      if (nc_def_var(grp2id, VRT_NAME, NC_FLOAT, VRT_RANK, &g2vrt_dimid, &g2vrt_varid)) ERR;
+      if (nc_def_var(grp2id, LEV_NAME, NC_FLOAT, LEV_RANK, &g2lev_dimid, &g2lev_varid)) ERR;
+      if (nc_close(ncid)) ERR;
+
+      /* Re-open, in which dimids may get reassigned */
+      if (nc_open(FILE_NAME, NC_NOWRITE, &ncid)) ERR;
+      if (nc_inq_dimid(ncid, TIME_NAME, &time_dimid_in)) ERR;
+      if (nc_inq_dimid(ncid, LEV_NAME, &lev_dimid_in)) ERR;
+      if (nc_inq_ncid(ncid, GRP2_NAME, &grp2id)) ERR;
+      if (nc_inq_dimid(grp2id, LEV_NAME, &g2lev_dimid_in)) ERR;
+      if (nc_inq_dimid(grp2id, VRT_NAME, &g2vrt_dimid_in)) ERR;
+      /* dimids must still all be distinct */
+      if (time_dimid_in == lev_dimid_in ||
+	  time_dimid_in == g2lev_dimid_in ||
+	  time_dimid_in == g2vrt_dimid_in ||
+	  lev_dimid_in == g2lev_dimid_in ||
+	  lev_dimid_in == g2vrt_dimid_in ||
+	  g2lev_dimid_in == g2vrt_dimid_in) ERR;
+
+      if (nc_close(ncid))
+	ERR_RET;
+   }
+   SUMMARIZE_ERR;
    FINAL_RESULTS;
 }

From 86eab350c22d23889bbd99b802882e5719bb1f3d Mon Sep 17 00:00:00 2001
From: Russ Rew <russ@unidata.ucar.edu>
Date: Tue, 26 Mar 2013 15:17:44 +0000
Subject: [PATCH 13/14] Added entry for NCF-244 fix.

---
 RELEASE_NOTES | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/RELEASE_NOTES b/RELEASE_NOTES
index aa4bfee0c..c7e6b7481 100644
--- a/RELEASE_NOTES
+++ b/RELEASE_NOTES
@@ -8,6 +8,11 @@ VERSION		COMMENTS
 -------		--------
 4.3		Released 201?-??-??
 
+		Fixed netCDF-4 bug with particular order of
+		creation of dimensions, coordinate variables, and
+		subgroups resulting in two dimensions with the same
+		dimension ID. [NCF-244]
+
 		Fixed bug with incorrect fixed-size variable offsets in header
 		getting written when schema changed for files created
 		by parallel-netcdf.  Thanks to Wei-keng Liao for

From 4b7817e69e4168541b100d5732f69cd9e6704a2e Mon Sep 17 00:00:00 2001
From: Dennis Heimbigner <dmh@unidata.ucar.edu>
Date: Tue, 26 Mar 2013 16:31:56 +0000
Subject: [PATCH 14/14] Return EACCES instead of NC_EMETADATA when failing to
 create an HDF5 file

---
 cf                |  5 ++---
 libsrc/putget.c   |  3 ---
 libsrc4/nc4file.c | 14 +++++++++-----
 libsrc4/nc4hdf.c  |  1 -
 4 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/cf b/cf
index 4d4d55d26..383b6dd5b 100644
--- a/cf
+++ b/cf
@@ -144,13 +144,12 @@ FLAGS="$FLAGS --disable-examples"
 #FLAGS="$FLAGS --enable-dap-long-tests"
 #FLAGS="$FLAGS --enable-ffio"
 #FLAGS="$FLAGS --enable-benchmarks"
-FLAGS="$FLAGS --enable-extra-tests"
-FLAGS="$FLAGS --enable-logging"
+#FLAGS="$FLAGS --enable-extra-tests"
 #FLAGS="$FLAGS --enable-large-file-tests"
 #FLAGS="$FLAGS --disable-testsets"
 #FLAGS="$FLAGS --disable-dap-remote-tests"
 #FLAGS="$FLAGS --enable-doxygen"
-FLAGS="$FLAGS --enable-logging"
+#FLAGS="$FLAGS --enable-logging"
 #FLAGS="$FLAGS --disable-diskless"
 #FLAGS="$FLAGS --enable-mmap"
 #FLAGS="$FLAGS --with-udunits"
diff --git a/libsrc/putget.c b/libsrc/putget.c
index f72a65b57..3add44aaf 100644
--- a/libsrc/putget.c
+++ b/libsrc/putget.c
@@ -23,9 +23,6 @@
 #endif
 #include "nc3dispatch.h"
 
-#if defined(_WIN32) || defined(_WIN64)
-#include <malloc.h>
-#endif
 
 #undef MIN  /* system may define MIN somewhere and complain */
 #define MIN(mm,nn) (((mm) < (nn)) ? (mm) : (nn))
diff --git a/libsrc4/nc4file.c b/libsrc4/nc4file.c
index 09b1befbb..2e6c5ec28 100644
--- a/libsrc4/nc4file.c
+++ b/libsrc4/nc4file.c
@@ -8,12 +8,14 @@ Copyright 2003, University Corporation for Atmospheric Research. See
 COPYRIGHT file for copying and redistribution conditions.  
 */
 
-#include "nc4internal.h"
-#include "nc.h"
-#include <H5DSpublic.h>
+#include "config.h"
+#include <errno.h>  /* netcdf functions sometimes return system errors */
 
+#include "nc.h"
+#include "nc4internal.h"
 #include "nc4dispatch.h"
-#include "ncdispatch.h"
+
+#include <H5DSpublic.h>
 
 #ifdef USE_HDF4
 #include <mfhdf.h>
@@ -326,7 +328,9 @@ nc4_create_file(const char *path, int cmode, MPI_Comm comm, MPI_Info info,
 
    /* Create the file. */
    if ((nc4_info->hdfid = H5Fcreate(path, flags, fcpl_id, fapl_id)) < 0) 
-      BAIL(NC_EFILEMETA);
+        /*Change the return error from NC_EFILEMETADATA to
+          System error EACCES because that is the more likely problem */
+      BAIL(EACCES);
 
    /* Open the root group. */
    if ((nc4_info->root_grp->hdf_grpid = H5Gopen2(nc4_info->hdfid, "/", 
diff --git a/libsrc4/nc4hdf.c b/libsrc4/nc4hdf.c
index 419558ece..ede5e957b 100644
--- a/libsrc4/nc4hdf.c
+++ b/libsrc4/nc4hdf.c
@@ -2488,7 +2488,6 @@ nc4_rec_write_metadata(NC_GRP_INFO_T *grp, int bad_coord_order)
    NC_GRP_INFO_T *child_grp;
    int found_coord, coord_varid = -1, wrote_coord;
 
-   int last_dimid = -1;
    int retval;
 
    assert(grp && grp->name && grp->hdf_grpid);