[netcdf/el5] - Update to 3.6.3 - Add upstream patch to fix nofill mode data corruption bug

[Orion Poplawski]

commit 4669baf77aa0755f98f76d2202c7013efd3f14b3
Author: Orion Poplawski <orion at nwra.com>
Date:   Mon Oct 21 10:20:03 2013 -0600

    - Update to 3.6.3
    - Add upstream patch to fix nofill mode data corruption bug

 .gitignore               |    1 +
 netcdf-3.6.2-gcc43.patch |   21 ---------------------
 netcdf.spec              |   20 ++++++++++++++------
 nofill-bug.patch         |   26 ++++++++++++++++++++++++++
 sources                  |    2 +-
 5 files changed, 42 insertions(+), 28 deletions(-)
---
diff --git a/.gitignore b/.gitignore
index e49105d..5df9483 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,2 @@
 netcdf-3.6.2.tar.bz2
+/netcdf-3.6.3.tar.gz
diff --git a/netcdf.spec b/netcdf.spec
index 943b393..94bb1b2 100644
--- a/netcdf.spec
+++ b/netcdf.spec
@@ -1,13 +1,15 @@
 Name:           netcdf
-Version:        3.6.2
-Release:        7%{?dist}
+Version:        3.6.3
+Release:        1%{?dist}
 Summary:        Libraries for the Unidata network Common Data Form (NetCDF v3)
 
 Group:          Applications/Engineering
 License:        NetCDF
 URL:            http://my.unidata.ucar.edu/content/software/netcdf/index.html
-Source0:        ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-3.6.2.tar.bz2
-Patch0:         netcdf-3.6.2-gcc43.patch
+Source0:        ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-%{version}.tar.gz
+# Patch to fix nofill mode bug
+# http://www.unidata.ucar.edu/jira/browse/NCF-22
+Patch0:         http://www.unidata.ucar.edu/netcdf/patches/nofill-bug.patch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 
 BuildRequires:  gcc-gfortran, gawk
@@ -21,7 +23,7 @@ Requires:       %{name} = %{version}-%{release}
 %package static
 Summary:        Static libs for netcdf-3
 Group:          Development/Libraries
-Requires:       %{name} = %{version}-%{release}
+Requires:       %{name}-devel = %{version}-%{release}
 
 %description
 NetCDF-3 (network Common Data Form ver3) is an interface for
@@ -63,7 +65,7 @@ This package contains the netCDF-3 static libs.
 
 %prep
 %setup -q
-%patch0 -p1 -b .gcc43
+%patch0 -p0 -b .nofill
 
 %build
 export FC="gfortran"
@@ -81,6 +83,7 @@ mkdir -p ${RPM_BUILD_ROOT}%{_includedir}/netcdf-3
 /bin/mv ${RPM_BUILD_ROOT}%{_includedir}/*.* \
   ${RPM_BUILD_ROOT}%{_includedir}/netcdf-3
 /bin/rm -f ${RPM_BUILD_ROOT}%{_libdir}/*.la
+/bin/rm -f ${RPM_BUILD_ROOT}%{_infodir}/dir
 #
 #  Does the /usr/include/netcdf-3/netcdf.mod file really belong in 
 #  /usr/include/netcdf-3/ or should it go in /usr/lib/netcdf-3 ???
@@ -109,6 +112,7 @@ rm -rf ${RPM_BUILD_ROOT}
 %{_bindir}/*
 %{_libdir}/*.so.*
 %{_mandir}/man1/*
+%{_infodir}/*
 
 %files devel
 %defattr(-,root,root,-)
@@ -122,6 +126,10 @@ rm -rf ${RPM_BUILD_ROOT}
 
 
 %changelog
+* Mon Oct 21 2013 Orion Poplawski <orion at cora.nwra.com> - 3.6.3-1
+- Update to 3.6.3
+- Add upstream patch to fix nofill mode data corruption bug
+
 * Wed Apr  2 2008 Orion Poplawski <orion at cora.nwra.com> - 3.6.2-7
 - Change patch to include <cstring>
 - Remove %%{?_smp_mflags} - not parallel build safe (fortran modules)
diff --git a/nofill-bug.patch b/nofill-bug.patch
new file mode 100644
index 0000000..d77123a
--- /dev/null
+++ b/nofill-bug.patch
@@ -0,0 +1,26 @@
+Index: libsrc/posixio.c
+===================================================================
+--- libsrc/posixio.c	(revision 1125)
++++ libsrc/posixio.c	(working copy)
+@@ -505,6 +505,22 @@
+ 			/* copy upper half into lower half */
+ 			(void) memcpy(pxp->bf_base, middle, pxp->bf_cnt);
+ 		}
++		else		/* added to fix nofill bug */
++		{
++			assert(pxp->bf_extent == 2 * pxp->blksz);
++			/* still have to page out lower half, if modified */
++			if(fIsSet(pxp->bf_rflags, RGN_MODIFIED))
++			{
++				assert(pxp->bf_refcount <= 0);
++				status = px_pgout(nciop,
++					pxp->bf_offset,
++					pxp->blksz,
++					pxp->bf_base,
++					&pxp->pos);
++				if(status != ENOERR)
++					return status;
++			}
++		}
+ 		pxp->bf_offset = blkoffset;
+ 		/* pxp->bf_extent = pxp->blksz; */
diff --git a/sources b/sources
index 8ae8d16..40db926 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-1eca0ea1e81e14ebc5bb93e5dd25c364  netcdf-3.6.2.tar.bz2
+334e9bdc010b6cd03fd6531a45fe50ad  netcdf-3.6.3.tar.gz