[netcdfgroup] Patches for netcdf-4.1.1

• To: netcdf@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] Patches for netcdf-4.1.1
• From: Kacper Kowalik <xarthisius@xxxxxxxxxx>
• Date: Fri, 17 Dec 2010 21:26:44 +0100

Hi,
I would like to submit a couple of patches to fix issue I found in
netcdf-4.1.1. Namely:
 * fix building with openmpi-1.4.3[1]
 * fix implicit function declaration
 * fix parallel build failure for fortran part[2]
I hope you'll accept it before final 4.1.2 release.
Best regards,
Kacper Kowalik

[1] http://bugs.gentoo.org/show_bug.cgi?id=347893
[2] http://bugs.gentoo.org/show_bug.cgi?id=296174

Fix implicit function declarations

--- libsrc/nc.c
+++ libsrc/nc.c
@@ -15,7 +15,7 @@
 #  include <mpp/shmem.h>
 #  include <intrinsics.h>
 #endif
-#ifdef HAVE_UNISTD
+#ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
 
--- fortran/fort-nc4.c
+++ fortran/fort-nc4.c
@@ -30,6 +30,14 @@
 /* These are in libsrc4/nc4vars.c... */
 int nc_inq_var_chunking_ints(int ncid, int varid, int *contiguousp, int 
*chunksizesp);
 int nc_def_var_chunking_ints(int ncid, int varid, int contiguous, int 
*chunksizes);
+int nc_set_var_chunk_cache_ints(int ncid, int varid, int size, int nelems, int 
preemption);
+int nc_get_var_chunk_cache_ints(int ncid, int varid, int *sizep, int *nelemsp, 
int *preemptionp);
+
+/* These are in libsrc4/nc4file.c... */
+int nc_set_chunk_cache_ints(int size, int nelems, int preemption);
+int nc_get_chunk_cache_ints(int *sizep, int *nelemsp, int *preemptionp);
+int nc_create_par_fortran(const char *path, int cmode, int comm, int info, int 
*ncidp);
+int nc_open_par_fortran(const char *path, int mode, int comm, int info, int 
*ncidp);
 
 FCALLSCFUN5(NF_INT, nc_create_par_fortran, NF_CREATE_PAR, nf_create_par,
            STRING, FINT2CINT, FINT2CINT, FINT2CINT, PCINT2FINT)
--- libncdap3/oc/daplex.c
+++ libncdap3/oc/daplex.c
@@ -86,6 +86,8 @@
 SCAN_PROG
 };
 
+int daperror(DAPparsestate* state, const char* msg);
+
 /**************************************************/
 
 int
--- libncdap3/oc/ocinternal.c
+++ libncdap3/oc/ocinternal.c
@@ -37,6 +37,8 @@
 #endif
 
 extern OCnode* makeunlimiteddimension(void);
+int occurlopen(CURL** curlp);
+void occurlclose(CURL* curl);
 
 #ifdef WIN32
 #include <fcntl.h>
--- libncdap3/oc/dapparse.c
+++ libncdap3/oc/dapparse.c
@@ -11,6 +11,7 @@
 static OCtype octypefor(Object etype);
 static char* scopeduplicates(OClist* list);
 static int check_int32(char* val, long* value);
+void setwordchars(DAPlexstate* lexstate, int kind);
 
 /****************************************************/
 
--- libncdap3/ncdap3.c
+++ libncdap3/ncdap3.c
@@ -4,6 +4,7 @@
  *   $Header: 
/var/cvsroot/gentoo-x86/sci-libs/netcdf/files/netcdf-4.1.1-implicits.patch,v 
1.2 2010/12/05 11:38:45 xarthisius Exp $
  *********************************************************************/
 #include "config.h"
+#include "netcdf3.h"
 #include "ncdap3.h"
 #include "dispatch3.h"
 #include "dapdispatch3.h"
--- libncdap3/oc/dapparselex.h
+++ libncdap3/oc/dapparselex.h
@@ -88,4 +88,5 @@
 extern void daplexinit(char* input, DAPlexstate** lexstatep);
 extern void daplexcleanup(DAPlexstate** lexstatep);
 
+void dassetup(DAPparsestate* state);
 #endif /*DAPPARSELEX_H*/

Ensure hdf5.h is included before netcdf.h to avoid build error with openmpi >= 
1.4.1

--- libsrc4/nc4internal.h
+++ libsrc4/nc4internal.h
@@ -8,13 +8,13 @@
 
 #include <config.h>
 #include <stdio.h>
+#include <hdf5.h>
 #include "error.h"
 #include <stdlib.h>
 #include <ctype.h>
 #include <stdarg.h>
 #include <string.h>
 #include "netcdf3.h"
-#include <hdf5.h>
 #include <netcdf.h>
 
 #ifdef USE_PARALLEL
--- libncdap4/ncdap4.h
+++ libncdap4/ncdap4.h
@@ -12,9 +12,9 @@
 #include <stdio.h>
 
 #include "config.h"
+#include "nc4internal.h"
 #include "netcdf.h"
 #include "nc.h"
-#include "nc4internal.h"
 #include "ncdap.h"
 #include "getvara.h"
 #include "constraints3.h"

Avoid building fortran modules twice, just install them instead.

https://bugs.gentoo.org/296174

--- netcdf-4.1.1/f90/Makefile.am
+++ netcdf-4.1.1/f90/Makefile.am
@@ -101,17 +101,23 @@
 # Some fortran compilers change the file names of .mod files to all
 # uppercase. Just to be special.
 if UPPER_CASE_MOD
-nodist_include_HEADERS = TYPESIZES.mod NETCDF.mod
-TYPESIZES.mod: typeSizes.o
-NETCDF.mod: $(NETCDF_O)
-BUILT_SOURCES = TYPESIZES.mod
+NETCDF_MODULES = TYPESIZES.mod NETCDF.mod
 else
-nodist_include_HEADERS = typesizes.mod netcdf.mod 
-typesizes.mod: typeSizes.o
-netcdf.mod: $(NETCDF_O)
-BUILT_SOURCES = typesizes.mod
+NETCDF_MODULES = typesizes.mod netcdf.mod 
 endif
 
+install-data-local:
+       test -z "$(includedir)" || $(MKDIR_P) "$(DESTDIR)$(includedir)"
+       @list='$(NETCDF_MODULES)'; test -n "$(includedir)" || list=; \
+       for p in $$list; do \
+         if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
+         echo "$$d$$p"; \
+       done | $(am__base_list) | \
+       while read files; do \
+         echo " $(INSTALL_HEADER) $$files '$(DESTDIR)$(includedir)'"; \
+         $(INSTALL_HEADER) $$files "$(DESTDIR)$(includedir)" || exit $$?; \
+       done
+
 # This is what we are building: a convenience library of F90 functions.
 noinst_LTLIBRARIES = libnetcdff90.la
 

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