.gitignore

+#####
+# End ignored generated files.
+#####
+
+### 'Normal' gitignore files.
 autom4te.cache
 debug.txt
 CTestConfig.cmake

.travis.yml

@@ -11,33 +11,30 @@ services:
 
 env:
     matrix:
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-netcdf-4 --disable-dap-remote-tests --enable-cdf5' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-gcc-x64-signed
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-fsigned-char --disable-netcdf-4 --disable-dap-remote-tests --enable-cdf5' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-clang-x64-signed
+# Ubuntu
+        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-netcdf-4 --disable-dap-remote-tests --enable-cdf5' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' USECP=FALSE CURHOST=docker-gcc-x64-signed TESTFILTER=FALSE
 
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-netcdf-4 --disable-dap-remote-tests' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-gcc-x86-signed
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-fsigned-char --disable-netcdf-4 --disable-dap-remote-tests' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-clang-x86-signed
+        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-netcdf-4 --disable-dap-remote-tests' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' USECP=FALSE CURHOST=docker-gcc-x86-signed TESTFILTER=FALSE
 
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-netcdf-4 --disable-dap-remote-tests --enable-cdf5' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-gcc-x64-unsigned
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-funsigned-char --disable-netcdf-4 --disable-dap-remote-tests --enable-cdf5' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-clang-x64-unsigned
+        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-netcdf-4 --disable-dap-remote-tests --enable-cdf5' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' USECP=FALSE CURHOST=docker-gcc-x64-unsigned TESTFILTER=FALSE
 
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-netcdf-4 --disable-dap-remote-tests' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-gcc-x86-unsigned
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-funsigned-char --disable-netcdf-4 --disable-dap-remote-tests' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-clang-x86-unsigned
+        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-netcdf-4 --disable-dap-remote-tests' COPTS='-DENABLE_NETCDF_4=OFF -DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' USECP=FALSE CURHOST=docker-gcc-x86-unsigned TESTFILTER=FALSE
 
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-dap-remote-tests --enable-cdf5' COPTS='-DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-gcc-x64-signed
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-fsigned-char --disable-dap-remote-tests --enable-cdf5' COPTS='-DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-clang-x64-signed
+        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-dap-remote-tests --enable-cdf5' COPTS='-DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' USECP=FALSE CURHOST=docker-gcc-x64-signed TESTFILTER=TRUE
 
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-dap-remote-tests' COPTS='-DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-gcc-x86-signed
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-fsigned-char --disable-dap-remote-tests' COPTS='-DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-clang-x86-signed
+        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-fsigned-char --disable-dap-remote-tests' COPTS='-DCMAKE_C_FLAGS=-fsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' USECP=FALSE CURHOST=docker-gcc-x86-signed TESTFILTER=TRUE
 
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-dap-remote-tests --enable-cdf5' COPTS='-DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-gcc-x64-unsigned
-        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-funsigned-char --disable-dap-remote-tests --enable-cdf5' COPTS='-DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' CURHOST=docker-clang-x64-unsigned
+        - DOCKIMG=unidata/nctests:serial   USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-dap-remote-tests --enable-cdf5' COPTS='-DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=TRUE' USECP=FALSE CURHOST=docker-gcc-x64-unsigned TESTFILTER=TRUE
 
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-dap-remote-tests' COPTS='-DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-gcc-x86-unsigned
-        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=clang AC_COPTS='CFLAGS=-funsigned-char --disable-dap-remote-tests' COPTS='-DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' CURHOST=docker-clang-x86-unsigned
+        - DOCKIMG=unidata/nctests:serial32 USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc   AC_COPTS='CFLAGS=-funsigned-char --disable-dap-remote-tests' COPTS='-DCMAKE_C_FLAGS=-funsigned-char -DENABLE_DAP_REMOTE_TESTS=OFF -DENABLE_CDF5=OFF' USECP=FALSE CURHOST=docker-gcc-x86-unsigned TESTFILTER=TRUE
+
+# Centos, Fedora
+        - DOCKIMG=unidata/nctests:serial.centos USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc AC_COPTS='--disable-dap-remote-tests' COPTS='-DENABLE_DAP_REMOTE_TESTS=OFF' USECP=TRUE CURHOST=docker-gcc-x64-centos TESTFILTER=TRUE
+        - DOCKIMG=unidata/nctests:serial.fedora USECMAKE=TRUE USEAC=TRUE DISTCHECK=TRUE USE_CC=gcc AC_COPTS='--disable-dap-remote-tests' COPTS='-DENABLE_DAP_REMOTE_TESTS=OFF' USECP=TRUE CURHOST=docker-gcc-x64-fedora TESTFILTER=TRUE
 
 before_install:
     - docker pull $DOCKIMG > /dev/null
 
 script:
 
-    - docker run --rm -it -h "$CURHOST" -e USEDASH=FALSE -e RUNF=OFF -e RUNCXX=OFF -e RUNP=OFF -e RUNNCO=OFF -e USECMAKE=$USECMAKE -e USEAC=$USEAC -e DISTCHECK=$DISTCHECK -e COPTS="$COPTS" -e AC_OPTS="$AC_OPTS" -e CTEST_OUTPUT_ON_FAILURE=1 -v $(pwd):/netcdf-c -e TESTPROC=100 $DOCKIMG
+    - docker run --rm -it -h "$CURHOST" -e USEDASH=FALSE -e RUNF=TRUE -e RUNCXX=OFF -e RUNP=OFF -e RUNNCO=OFF -e USECMAKE=$USECMAKE -e USEAC=$USEAC -e DISTCHECK=$DISTCHECK -e COPTS="$COPTS" -e AC_OPTS="$AC_OPTS" -e CTEST_OUTPUT_ON_FAILURE=1 -v $(pwd):/netcdf-c -e USE_LOCAL_CP=$USECP -e TESTPROC=100  -e ENABLE_FILTER_TESTING=$TESTFILTER $DOCKIMG

INSTALL.md

@@ -184,7 +184,7 @@ Building netCDF with Classic Library Only {#build_classic}
 ---------------------------------------
 
 It is possible to build the netCDF C libraries and utilities so that
-only the netCDF classic and 64-bit offset formats are supported, or
+only the netCDF classic, 64-bit offset, and CDF-5 formats are supported, or
 the remote data access client is not built. (See \ref netcdf_format)
 for more information about the netCDF format variants.  See the <a
 href="http://opendap.org/netCDF-DAP">netCDF-DAP site</a>
@@ -307,8 +307,8 @@ $ make check install
 ~~~
 
 
-If parallel I/O access to netCDF classic and 64-bit offset files is
-also needed, the parallel-netcdf library should also be installed.
+If parallel I/O access to netCDF classic, 64-bit offset, CDF-5 files is
+also needed, the PnetCDF library should also be installed.
 (Note: the previously recommended <a
 href=ftp://ftp.unidata.ucar.edu/pub/netcdf/contrib/pnetcdf.h>replacement
 pnetcdf.h</a> should no longer be used.)  Then configure netCDF with the
@@ -358,8 +358,7 @@ Note: --disable prefix indicates that the option is normally enabled.
 <tr><td>--enable-netcdf4<td>synonym for enable-netcdf-4
 <tr><td>--enable-hdf4<td>build netcdf-4 with HDF4 read capability<td>HDF4, HDF5 and zlib
 <tr><td>--enable-hdf4-file-tests<td>test ability to read HDF4 files<td>selected HDF4 files from Unidata ftp site
-<tr><td>--enable-pnetcdf<td>build netcdf-4 with parallel I/O for classic and
-                          64-bit offset files using parallel-netcdf
+<tr><td>--enable-pnetcdf<td>build netcdf-4 with parallel I/O for classic, 64-bit offset, and CDF-5 files using PnetCDF
 <tr><td>--enable-extra-example-tests<td>Run extra example tests<td>--enable-netcdf-4,GNU sed
 <tr><td>--enable-parallel-tests <td>run extra parallel IO tests<td>--enable-netcdf-4, parallel IO support
 <tr><td>--enable-logging<td>enable logging capability<td>--enable-netcdf-4

Makefile.am

@@ -7,9 +7,6 @@
 
 # Ed Hartnett, Ward Fisher
 
-
-
-
 # This directory stores libtool macros, put there by aclocal.
 ACLOCAL_AMFLAGS = -I m4
 
@@ -45,6 +42,7 @@ endif
 if USE_NETCDF4
 H5_TEST_DIR = h5_test
 LIBSRC4_DIR = libsrc4
+LIBHDF5 = libhdf5
 NC_TEST4 = nc_test4
 endif
 
@@ -60,7 +58,7 @@ DAP4 = libdap4
 NCDAP4TESTDIR = dap4_test
 endif #DAP4
 
-# Build pnetcdf
+# Build PnetCDF
 if USE_PNETCDF
 LIBSRCP = libsrcp
 endif
@@ -71,6 +69,11 @@ HDF4_TEST_DIR = hdf4_test
 LIBHDF4 = libhdf4
 endif
 
+# Optionally build plugins
+if ENABLE_FILTER_TESTING
+PLUGIN_DIR = plugins
+endif
+
 # Define Test directories
 if BUILD_TESTSETS
 TESTDIRS = $(V2_TEST) nc_test $(NC_TEST4) $(HDF4_TEST_DIR)	\
@@ -81,8 +84,9 @@ endif
 # and run. ncgen must come before ncdump, because their tests
 # depend on it.
 SUBDIRS = include $(H5_TEST_DIR) libdispatch libsrc $(LIBSRC4_DIR)	\
-$(LIBSRCP) $(LIBHDF4) $(OCLIB) $(DAP2) ${DAP4} liblib $(NCGEN3)		\
-$(NCGEN) $(NCDUMP) $(TESTDIRS) docs $(EXAMPLES)
+$(LIBSRCP) $(LIBHDF4) $(LIBHDF5) $(OCLIB) $(DAP2) ${DAP4} liblib	\
+$(NCGEN3) $(NCGEN) $(NCDUMP) ${PLUGIN_DIR} $(TESTDIRS) docs		\
+$(EXAMPLES)
 
 # Remove these generated files, for a distclean.
 DISTCLEANFILES = VERSION comps.txt test_prog libnetcdf.settings	\

Makefile.in

@@ -181,6 +181,10 @@ am__recursive_targets = \
   $(am__extra_recursive_targets)
 AM_RECURSIVE_TARGETS = $(am__recursive_targets:-recursive=) TAGS CTAGS \
 	cscope distdir distdir-am dist dist-all distcheck
+am__extra_recursive_targets = check-valgrind-recursive \
+	check-valgrind-memcheck-recursive \
+	check-valgrind-helgrind-recursive check-valgrind-drd-recursive \
+	check-valgrind-sgcheck-recursive
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) \
 	$(LISP)config.h.in
 # Read a list of newline-separated strings from the standard input,
@@ -203,8 +207,9 @@ ETAGS = etags
 CTAGS = ctags
 CSCOPE = cscope
 DIST_SUBDIRS = include h5_test libdispatch libsrc libsrc4 libsrcp \
-	libhdf4 oc2 libdap2 libdap4 liblib ncgen3 ncgen ncdump nctest \
-	nc_test nc_test4 hdf4_test ncdap_test dap4_test docs examples
+	libhdf4 libhdf5 oc2 libdap2 libdap4 liblib ncgen3 ncgen ncdump \
+	plugins nctest nc_test nc_test4 hdf4_test ncdap_test dap4_test \
+	docs examples
 am__DIST_COMMON = $(srcdir)/Makefile.in $(srcdir)/config.h.in \
 	$(srcdir)/libnetcdf.settings.in $(srcdir)/nc-config.in \
 	$(srcdir)/netcdf.pc.in $(srcdir)/postinstall.sh.in \
@@ -289,6 +294,11 @@ ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
+ENABLED_DOC_SECTIONS = @ENABLED_DOC_SECTIONS@
+ENABLE_VALGRIND_drd = @ENABLE_VALGRIND_drd@
+ENABLE_VALGRIND_helgrind = @ENABLE_VALGRIND_helgrind@
+ENABLE_VALGRIND_memcheck = @ENABLE_VALGRIND_memcheck@
+ENABLE_VALGRIND_sgcheck = @ENABLE_VALGRIND_sgcheck@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
@@ -330,6 +340,7 @@ MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
+MPIEXEC = @MPIEXEC@
 MSVC = @MSVC@
 NC_ENABLE_DOXYGEN_PDF_OUTPUT = @NC_ENABLE_DOXYGEN_PDF_OUTPUT@
 NC_HAS_CDF5 = @NC_HAS_CDF5@
@@ -349,6 +360,7 @@ NC_HAS_PNETCDF = @NC_HAS_PNETCDF@
 NC_HAS_SZIP = @NC_HAS_SZIP@
 NC_LIBS = @NC_LIBS@
 NC_M4 = @NC_M4@
+NC_RELAX_COORD_BOUND = @NC_RELAX_COORD_BOUND@
 NC_VERSION = @NC_VERSION@
 NC_VERSION_MAJOR = @NC_VERSION_MAJOR@
 NC_VERSION_MINOR = @NC_VERSION_MINOR@
@@ -376,6 +388,8 @@ SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 SHOW_DOXYGEN_TAG_LIST = @SHOW_DOXYGEN_TAG_LIST@
 STRIP = @STRIP@
+VALGRIND = @VALGRIND@
+VALGRIND_ENABLED = @VALGRIND_ENABLED@
 VERSION = @VERSION@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
@@ -435,6 +449,8 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+valgrind_enabled_tools = @valgrind_enabled_tools@
+valgrind_tools = @valgrind_tools@
 
 # This directory stores libtool macros, put there by aclocal.
 ACLOCAL_AMFLAGS = -I m4
@@ -464,6 +480,7 @@ pkgconfig_DATA = netcdf.pc
 # Is the user building netCDF-4?
 @USE_NETCDF4_TRUE@H5_TEST_DIR = h5_test
 @USE_NETCDF4_TRUE@LIBSRC4_DIR = libsrc4
+@USE_NETCDF4_TRUE@LIBHDF5 = libhdf5
 @USE_NETCDF4_TRUE@NC_TEST4 = nc_test4
 
 # Build the dap2 client
@@ -473,13 +490,16 @@ pkgconfig_DATA = netcdf.pc
 @ENABLE_DAP4_TRUE@DAP4 = libdap4
 @ENABLE_DAP4_TRUE@NCDAP4TESTDIR = dap4_test
 
-# Build pnetcdf
+# Build PnetCDF
 @USE_PNETCDF_TRUE@LIBSRCP = libsrcp
 
 # Build HDF4 if desired.
 @USE_HDF4_TRUE@HDF4_TEST_DIR = hdf4_test
 @USE_HDF4_TRUE@LIBHDF4 = libhdf4
 
+# Optionally build plugins
+@ENABLE_FILTER_TESTING_TRUE@PLUGIN_DIR = plugins
+
 # Define Test directories
 @BUILD_TESTSETS_TRUE@TESTDIRS = $(V2_TEST) nc_test $(NC_TEST4) $(HDF4_TEST_DIR)	\
 @BUILD_TESTSETS_TRUE@$(NCDAP2TESTDIR) $(NCDAP4TESTDIR)
@@ -489,8 +509,9 @@ pkgconfig_DATA = netcdf.pc
 # and run. ncgen must come before ncdump, because their tests
 # depend on it.
 SUBDIRS = include $(H5_TEST_DIR) libdispatch libsrc $(LIBSRC4_DIR)	\
-$(LIBSRCP) $(LIBHDF4) $(OCLIB) $(DAP2) ${DAP4} liblib $(NCGEN3)		\
-$(NCGEN) $(NCDUMP) $(TESTDIRS) docs $(EXAMPLES)
+$(LIBSRCP) $(LIBHDF4) $(LIBHDF5) $(OCLIB) $(DAP2) ${DAP4} liblib	\
+$(NCGEN3) $(NCGEN) $(NCDUMP) ${PLUGIN_DIR} $(TESTDIRS) docs		\
+$(EXAMPLES)
 
 
 # Remove these generated files, for a distclean.
@@ -695,6 +716,11 @@ $(am__recursive_targets):
 	if test "$$dot_seen" = "no"; then \
 	  $(MAKE) $(AM_MAKEFLAGS) "$$target-am" || exit 1; \
 	fi; test -z "$$fail"
+check-valgrind-local: 
+check-valgrind-memcheck-local: 
+check-valgrind-helgrind-local: 
+check-valgrind-drd-local: 
+check-valgrind-sgcheck-local: 
 
 ID: $(am__tagged_files)
 	$(am__define_uniq_tagged_files); mkid -fID $$unique
@@ -997,6 +1023,26 @@ distclean-generic:
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
 	@echo "it deletes files that may require special tools to rebuild."
+check-valgrind: check-valgrind-recursive
+
+check-valgrind-am: check-valgrind-local
+
+check-valgrind-drd: check-valgrind-drd-recursive
+
+check-valgrind-drd-am: check-valgrind-drd-local
+
+check-valgrind-helgrind: check-valgrind-helgrind-recursive
+
+check-valgrind-helgrind-am: check-valgrind-helgrind-local
+
+check-valgrind-memcheck: check-valgrind-memcheck-recursive
+
+check-valgrind-memcheck-am: check-valgrind-memcheck-local
+
+check-valgrind-sgcheck: check-valgrind-sgcheck-recursive
+
+check-valgrind-sgcheck-am: check-valgrind-sgcheck-local
+
 clean: clean-recursive
 
 clean-am: clean-generic clean-libtool mostlyclean-am
@@ -1073,7 +1119,12 @@ uninstall-am: uninstall-binSCRIPTS uninstall-pkgconfigDATA \
 	install-strip
 
 .PHONY: $(am__recursive_targets) CTAGS GTAGS TAGS all all-am \
-	am--refresh check check-am clean clean-cscope clean-generic \
+	am--refresh check check-am check-valgrind-am \
+	check-valgrind-drd-am check-valgrind-drd-local \
+	check-valgrind-helgrind-am check-valgrind-helgrind-local \
+	check-valgrind-local check-valgrind-memcheck-am \
+	check-valgrind-memcheck-local check-valgrind-sgcheck-am \
+	check-valgrind-sgcheck-local clean clean-cscope clean-generic \
 	clean-libtool cscope cscopelist-am ctags ctags-am dist \
 	dist-all dist-bzip2 dist-gzip dist-lzip dist-shar dist-tarZ \
 	dist-xz dist-zip distcheck distclean distclean-generic \

RELEASE_NOTES.md

@@ -5,6 +5,32 @@ Release Notes       {#RELEASE_NOTES}
 
 This file contains a high-level description of this package's evolution. Releases are in reverse chronological order (most recent first). Note that, as of netcdf 4.2, the `netcdf-c++` and `netcdf-fortran` libraries have been separated into their own libraries.
 
+## 4.6.2 - November 19, 2018
+
+* [Enhancement] Lazy att read - only read atts when user requests one of them.  See [GitHub #857](https://github.com/Unidata/netcdf-c/issues/857).
+* [Enhancement] Fast global att read - when global atts are read, they are read much more quickly.  See [GitHub #857](https://github.com/Unidata/netcdf-c/issues/857).
+
+## 4.6.2-rc2 November 1, 2018
+
+
+* [Enhancement] Add nccopy command options for per-variable chunk sizing, and minimum chunk size.  See [GitHub #1087](https://github.com/Unidata/netcdf-c/pull/1087).
+* [Bug Fix] Fix nccopy handling of user specified chunk sizes.  See [GitHub #725](https://github.com/Unidata/netcdf-c/issues/725),[#1087](https://github.com/Unidata/netcdf-c/issues/1087).
+* [Bug Fix] Avoid limit on number of times a netCDF4 attribute can be updated.  Not a complete fix for the HDF5 "maximum creation order" problem, but should greatly reduce occurrences in many real-world cases.  See [GitHub #350](https://github.com/Unidata/netcdf-c/issues/350).
+* [Bug Fix] The use of NC_DISKLESS has been modified to make it cleaner. This adds a new flag called NC_PERSIST that takes over the now obsolete NC_MPIPOSIX.
+* [Obsolete] Obsolete the MPIPOSIX flag.
+* [Bug Fix] When using filters with HDF5 1.10.x or later, it is necessary to utilize the HDF5 replacements for malloc, realloc, and free in the filter code.
+
+## 4.6.2-rc1 - September 19, 2018
+
+* [Enhancement] Create a new version of _NCProperties provenance attribute. This version (version 2) supports arbitrary key-value pairs. It is the default when new files are created. Version 1 continues to be accepted.
+* [Enhancement] Allow user to set http read buffersize for DAP2 and  DAP4 using the tag HTTP.READ.BUFFERSIZE in the .daprc file.
+* [Enhancement] Allow user to set http keepalive for DAP2 and  DAP4 using the tag HTTP.KEEPALIVE in the .daprc file (see the OPeNDAP documentation for details).
+* [Enhancement] Support DAP4 remote tests using a new remote test server locatedon the Unidata JetStream project.
+* [Enhancement] Improved the performance of the nc_get/put_vars operations by using the equivalent slab capabilities of hdf5. Result is a significant speedup of these operations.  See [GitHub #1001](https://github.com/Unidata/netcdf-c/pull/1001) for more information.
+* [Enhancement] Expanded the capabilities of `NC_INMEMORY` to support writing and accessing the final modified memory.  See [GitHub #879](https://github.com/Unidata/netcdf-c/pull/879) for more information.
+* [Enhancement] Made CDF5 support enabled by default.  See [Github #931](https://github.com/Unidata/netcdf-c/issues/931) for more information.
+* [Bug Fix] Corrected a number of memory issues identified in `ncgen`.  See [GitHub #558 for more information](https://github.com/Unidata/netcdf-c/pull/558).
+
 ## 4.6.1 - March 19, 2018
 
 * [Bug Fix] Corrected an issue which could result in a dap4 failure. See [Github #888](https://github.com/Unidata/netcdf-c/pull/888) for more information.
@@ -152,7 +178,7 @@ disbled until the testserver situation is resolved.
 
     This cascaded into a number of other changes.
 
-    1. Renamed libsrcp5 -> libsrcp because pnetcdf can do parallel io for CDF-1, CDF-2 and CDF-5, not just CDF-5.
+    1. Renamed libsrcp5 -> libsrcp because PnetCDF can do parallel io for CDF-1, CDF-2 and CDF-5, not just CDF-5.
     2. Given #1, then the NC_PNETCDF mode flag becomes a subset of NC_MPIIO, so made NC_PNETCDF an alias for NC_MPII.
     3. NC_FORMAT_64BIT is now deprecated.  Use NC_FORMAT_64BIT_OFFSET.
 
@@ -268,7 +294,7 @@ Example Work Flow from netcdf-c source directory:
 
 * Added an explicit check in the build systems (autotools, cmake) for the CURL-related option `CURLOPT_CHUNK_BGN_FUNCTION`.  This option was introduced in libcurl version `7.21.0`.  On installations which require libcurl and have this version, `CURLOPT_CHUNK_BGN_FUNCTION` will be available. Otherwise, it will not.
 
-* The pnetcdf support was not properly being used to provide mpi parallel io for netcdf-3 classic files. The wrong dispatch table was being used. [NCF-319](https://bugtracking.unidata.ucar.edu/browse/NCF-319)
+* The PnetCDF support was not properly being used to provide mpi parallel io for netcdf-3 classic files. The wrong dispatch table was being used. [NCF-319](https://bugtracking.unidata.ucar.edu/browse/NCF-319)
 
 * In nccopy utility, provided proper default for unlimited dimension in chunk-size specification instead of requiring explicit chunk size. Added associated test. [NCF-321](https://bugtracking.unidata.ucar.edu/browse/NCF-321)
 
@@ -596,7 +622,7 @@ subgroup getting the wrong dimension IDs for its dimensions. [NCF-247]
 [NCF-247]: https://bugtracking.unidata.ucar.edu/browse/NCF-247
 
 * Fixed bug with incorrect fixed-size variable offsets in header getting
-written when schema changed for files created by parallel-netcdf. Thanks
+written when schema changed for files created by PnetCDF Thanks
 to Wei-keng Liao for developing and contributing the fix. [NCF-234]
 
 [NCF-234]: https://bugtracking.unidata.ucar.edu/browse/NCF-234
@@ -634,7 +660,7 @@ options for specifying which groups or variables are to be copied.
 
 [NCF-216]: https://bugtracking.unidata.ucar.edu/browse/NCF-216
 
-* Merged in parallel-netcdf bugs fixes from Greg Sjaardema. [NCF-214]
+* Merged in PnetCDF bugs fixes from Greg Sjaardema. [NCF-214]
 
 [NCF-214]: https://bugtracking.unidata.ucar.edu/browse/NCF-214
 
@@ -1177,7 +1203,7 @@ definitions in the DAS, but they will be ignored.
 
 * Many documentation fixes.
 
-* Added capability to use the parallel-netcdf (a.k.a. pnetcdf) library to
+* Added capability to use the PnetCDF library to
 perform parallel I/O on classic and 32-bit offset files. Use the
 NC\_PNETCDF mode flag to get parallel I/O for non-netcdf-4 files.
 

aclocal.m4

@@ -396,6 +396,23 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS],
      [test x"$AMDEP_TRUE" != x"" || _AM_OUTPUT_DEPENDENCY_COMMANDS],
      [AMDEP_TRUE="$AMDEP_TRUE" MAKE="${MAKE-make}"])])
 
+# AM_EXTRA_RECURSIVE_TARGETS                                -*- Autoconf -*-
+
+# Copyright (C) 2012-2018 Free Software Foundation, Inc.
+#
+# This file is free software; the Free Software Foundation
+# gives unlimited permission to copy and/or distribute it,
+# with or without modifications, as long as this notice is preserved.
+
+# AM_EXTRA_RECURSIVE_TARGETS
+# --------------------------
+# Define the list of user recursive targets.  This macro exists only to
+# be traced by Automake, which will ensure that a proper definition of
+# user-defined recursive targets (and associated rules) is propagated
+# into all the generated Makefiles.
+# TODO: We should really reject non-literal arguments here...
+AC_DEFUN([AM_EXTRA_RECURSIVE_TARGETS], [])
+
 # Do all the work for Automake.                             -*- Autoconf -*-
 
 # Copyright (C) 1996-2018 Free Software Foundation, Inc.

appveyor.yml

+image: Visual Studio 2017
+
+environment:
+  matrix:
+    - TARGET_ARCH: x64
+      CONDA_INSTALL_LOCN: C:\\Miniconda-x64
+      MSYS2_INSTALL_LOCN: C:\msys64
+      MSYS2_BIN_LOCN: C:\msys64\usr\bin
+      CMAKE_GENERATOR: "Visual Studio 15 Win64"
+
+platform:
+    - x64
+
+branches:
+  except:
+    - /.*[.]dmh/
+    - /.*[.]wif/
+
+# Do not build feature branch with open Pull Requests
+skip_branch_with_pr: true
+
+install:
+  - cmd: set SRC_DIR=%cd%
+  - cmd: set INSTALL_LOC=%SRC_DIR%\install
+  - cmd: set PATH=%PATH%;%MSYS2_BIN_LOCN%;%INSTALL_LOC%\bin;%INSTALL_LOC%\lib
+  - cmd: call %CONDA_INSTALL_LOCN%\Scripts\activate.bat
+  - cmd: conda config --set always_yes yes --set changeps1 no --set show_channel_urls true
+  - cmd: conda update conda
+  - cmd: conda install hdf5=1.8.18 curl hdf4
+
+configuration: Release
+
+build: off
+
+# Run a custom script.
+build_script:
+  - cmd: mkdir build
+  - cmd: cd build
+  - cmd: cmake .. -G "%CMAKE_GENERATOR%" -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=%INSTALL_LOC% -DENABLE_BASH_SCRIPT_TESTING=OFF
+  - cmd: if errorlevel 1 exit 1
+  - cmd: cmake --build . --config Release -- /maxcpucount:4
+
+test_script:
+  - cmd: cmake --build . --config Release --target install -- /maxcpucount:4

conda.recipe/bld.bat

+set PATH=%PATH%;C:\msys64\usr\bin
+
+mkdir %SRC_DIR%\build
+cd %SRC_DIR%\build
+
+cmake -G "Visual Studio 15 Win64" ^
+      -D CMAKE_INSTALL_PREFIX=%LIBRARY_PREFIX% ^
+      -D BUILD_SHARED_LIBS=ON ^
+      -D ENABLE_TESTS=ON ^
+      -D ENABLE_HDF4=ON ^
+      -D CMAKE_PREFIX_PATH=%LIBRARY_PREFIX% ^
+      -D ZLIB_LIBRARY=%LIBRARY_LIB%\zlib.lib ^
+      -D ZLIB_INCLUDE_DIR=%LIBRARY_INC% ^
+      -D CMAKE_BUILD_TYPE=Release ^
+      %SRC_DIR%
+if errorlevel 1 exit 1
+
+cmake --build . --config Release || exit 1
+
+ctest || exit 1
+
+nmake install || exit 1

conda.recipe/meta.yaml

+
+{% set version = "dev" %}
+
+package:
+  name: netcdf-c
+  version: {{ version }}
+
+source:
+  path: ../
+
+build:
+  features:
+    - vc9  # [win and py27]
+    - vc14  # [win and py>=35]
+
+requirements:
+  build:
+    - python  # Here only to activate the `vc`s.
+    - msinttypes
+    - curl
+    - zlib 1.2.*
+    - hdf4
+    - hdf5 1.8.20
+    - vc 15  # [win and py>=35]
+  run:
+    - curl
+    - zlib 1.2.*
+    - hdf4
+    - hdf5 1.8.20
+    - vc 15  # [win and py>=35]
+
+test:
+  commands:

config.h.cmake.in

@@ -109,7 +109,6 @@ are set when opening a binary file on Windows. */
 
 /* if true, enable CDF5 Support */
 #cmakedefine ENABLE_CDF5 1
-#cmakedefine USE_CDF5 1
 
 /* if true, enable strict null byte header padding. */
 #cmakedefine USE_STRICT_NULL_BYTE_HEADER_PADDING 1
@@ -154,6 +153,12 @@ are set when opening a binary file on Windows. */
 /* Is CURLINFO_HTTP_CODE defined */
 #cmakedefine HAVE_CURLINFO_HTTP_CONNECTCODE 1
 
+/* Is CURLOPT_BUFFERSIZE defined */
+#cmakedefine HAVE_CURLOPT_BUFFERSIZE 1
+
+/* Is CURLOPT_TCP_KEEPALIVE defined */
+#cmakedefine HAVE_CURLOPT_KEEPALIVE 1
+
 /* Is CURLOPT_KEYPASSWD defined */
 #cmakedefine HAVE_CURLOPT_KEYPASSWD 1
 
@@ -367,12 +372,18 @@ are set when opening a binary file on Windows. */
 /* If true, turn on logging. */
 #cmakedefine LOGGING 1
 
+/* If true, define nc_set_log_level. */
+#cmakedefine ENABLE_SET_LOG_LEVEL 1
+
 /* max size of the default per-var chunk cache. */
 #cmakedefine MAX_DEFAULT_CACHE_SIZE ${MAX_DEFAULT_CACHE_SIZE}
 
 /* min blocksize for posixio. */
 #cmakedefine NCIO_MINBLOCKSIZE ${NCIO_MINBLOCKSIZE}
 
+/* Add extra properties to _NCProperties attribute */
+#cmakedefine NCPROPERTIES_EXTRA ${NCPROPERTIES_EXTRA}
+
 /* no IEEE float on this platform */
 #cmakedefine NO_IEEE_FLOAT 1
 
@@ -515,12 +526,6 @@ are set when opening a binary file on Windows. */
 /* if true, parallel netcdf-4 is in use */
 #cmakedefine USE_PARALLEL4 1
 
-/* if true, compile in parallel netCDF-4 based on MPI/IO */
-#cmakedefine USE_PARALLEL_MPIO 1
-
-/* if true, compile in parallel netCDF-4 based on MPI/POSIX */
-#cmakedefine USE_PARALLEL_POSIX 1
-
 /* if true, parallel netCDF is used */
 #cmakedefine USE_PNETCDF 1
 
@@ -559,6 +564,9 @@ are set when opening a binary file on Windows. */
 /* Define to `unsigned int' if <sys/types.h> does not define. */
 #cmakedefine size_t unsigned int
 
+/* Define to `int' if <sys/types.h> does not define. */
+#cmakedefine ssize_t int
+
 /* Define to `unsigned long if <sys/types.h> does not define. */
 #cmakedefine uintptr_t unsigned long
 

config.h.in

@@ -44,6 +44,9 @@
 /* if true, do remote tests */
 #undef ENABLE_DAP_REMOTE_TESTS
 
+/* If true, define nc_set_log_level. */
+#undef ENABLE_SET_LOG_LEVEL
+
 /* if true, use _FillValue for NC_ERANGE data elements */
 #undef ERANGE_FILL
 
@@ -60,6 +63,12 @@
 /* Is CURLINFO_RESPONSE_CODE defined */
 #undef HAVE_CURLINFO_RESPONSE_CODE
 
+/* Is CURLOPT_BUFFERSIZE defined */
+#undef HAVE_CURLOPT_BUFFERSIZE
+
+/* Is CURLOPT_TCP_KEEPALIVE defined */
+#undef HAVE_CURLOPT_KEEPALIVE
+
 /* Is CURLOPT_KEYPASSWD defined */
 #undef HAVE_CURLOPT_KEYPASSWD
 
@@ -111,9 +120,6 @@
 /* Define to 1 if you have the `H5Pget_fapl_mpio' function. */
 #undef HAVE_H5PGET_FAPL_MPIO
 
-/* Define to 1 if you have the `H5Pget_fapl_mpiposix' function. */
-#undef HAVE_H5PGET_FAPL_MPIPOSIX
-
 /* Define to 1 if you have the `H5Pset_all_coll_metadata_ops' function. */
 #undef HAVE_H5PSET_ALL_COLL_METADATA_OPS
 
@@ -180,9 +186,15 @@
 /* Define to 1 if you have the `mktemp' function. */
 #undef HAVE_MKTEMP
 
+/* Define to 1 if you have the `mmap' function. */
+#undef HAVE_MMAP
+
 /* Define to 1 if you have the `MPI_Comm_f2c' function. */
 #undef HAVE_MPI_COMM_F2C
 
+/* Define to 1 if you have the `MPI_Info_f2c' function. */
+#undef HAVE_MPI_INFO_F2C
+
 /* Define to 1 if you have the `mremap' function. */
 #undef HAVE_MREMAP
 
@@ -265,6 +277,9 @@
 /* Define to 1 if the system has the type `uint64'. */
 #undef HAVE_UINT64
 
+/* Define to 1 if the system has the type `uintptr_t'. */
+#undef HAVE_UINTPTR_T
+
 /* Define to 1 if you have the <unistd.h> header file. */
 #undef HAVE_UNISTD_H
 
@@ -305,6 +320,9 @@
 /* min blocksize for posixio. */
 #undef NCIO_MINBLOCKSIZE
 
+/* Extra pairs for _NCProperties */
+#undef NCPROPERTIES_EXTRA
+
 /* no IEEE float on this platform */
 #undef NO_IEEE_FLOAT
 
@@ -403,15 +421,21 @@
 /* Place to put very large netCDF test files. */
 #undef TEMP_LARGE
 
-/* if true, enable CDF5 Support */
-#undef USE_CDF5
+/* dispatch table for user-defined format 0. */
+#undef UDF0_DISPATCH
+
+/* function to get dispatch table for user-defined format 0. */
+#undef UDF0_DISPATCH_FUNC
+
+/* dispatch table for user-defined format 1. */
+#undef UDF1_DISPATCH
+
+/* function to get dispatch table for user-defined format 1. */
+#undef UDF1_DISPATCH_FUNC
 
 /* if true, build DAP Client */
 #undef USE_DAP
 
-/* if true, include NC_DISKLESS code */
-#undef USE_DISKLESS
-
 /* set this to use extreme numbers in tests */
 #undef USE_EXTREME_NUMBERS
 
@@ -428,6 +452,9 @@
    it. */
 #undef USE_HDF4_FILE_TESTS
 
+/* if true, use HDF5 */
+#undef USE_HDF5
+
 /* if true, use mmap for in-memory files */
 #undef USE_MMAP
 
@@ -437,19 +464,13 @@
 /* build the netCDF version 2 API */
 #undef USE_NETCDF_2
 
-/* if true, pnetcdf or parallel netcdf-4 is in use */
+/* if true, PnetCDF or parallel netcdf-4 is in use */
 #undef USE_PARALLEL
 
 /* if true, parallel netcdf-4 is in use */
 #undef USE_PARALLEL4
 
-/* if true, compile in parallel netCDF-4 based on MPI/IO */
-#undef USE_PARALLEL_MPIO
-
-/* if true, compile in parallel netCDF-4 based on MPI/POSIX */
-#undef USE_PARALLEL_POSIX
-
-/* if true, parallel netCDF is used */
+/* if true, PnetCDF is used */
 #undef USE_PNETCDF
 
 /* if true, use stdio instead of posixio */
@@ -461,6 +482,12 @@
 /* if true, compile in szip compression in netCDF-4 variables */
 #undef USE_SZIP
 
+/* if true, use user-defined format 0 in utilities */
+#undef USE_UDF0
+
+/* if true, use user-defined format 1 in utilities */
+#undef USE_UDF1
+
 /* Version number of package */
 #undef VERSION
 
@@ -487,6 +514,11 @@
 /* Define for large files, on AIX-style hosts. */
 #undef _LARGE_FILES
 
+/* Define to 1 if type `char' is unsigned and you are not using gcc.  */
+#ifndef __CHAR_UNSIGNED__
+# undef __CHAR_UNSIGNED__
+#endif
+
 /* Define to empty if `const' does not conform to ANSI C. */
 #undef const
 
@@ -496,6 +528,10 @@
 /* Define to `unsigned int' if <sys/types.h> does not define. */
 #undef size_t
 
+/* Define to the type of an unsigned integer type wide enough to hold a
+   pointer, if such a type exists, and if the system does not define it. */
+#undef uintptr_t
+
 /* Define strcasecmp, snprintf on Win32 systems. */
 #ifdef _WIN32
 	#define strcasecmp _stricmp

dap4_test/CMakeLists.txt

@@ -9,6 +9,7 @@ ADD_SUBDIRECTORY(cdltestfiles)
 ADD_SUBDIRECTORY(daptestfiles)
 ADD_SUBDIRECTORY(dmrtestfiles)
 ADD_SUBDIRECTORY(nctestfiles)
+ADD_SUBDIRECTORY(misctestfiles)
 
 FILE(GLOB COPY_FILES ${CMAKE_CURRENT_SOURCE_DIR}/*.sh)
 
@@ -32,7 +33,7 @@ IF(ENABLE_TESTS)
     BUILD_BIN_TEST(findtestserver4)
 
     IF(BUILD_UTILITIES)
-# disable for now       add_sh_test(dap4_test test_remote)
+      add_sh_test(dap4_test test_remote)
     ENDIF(BUILD_UTILITIES)
   ENDIF(ENABLE_DAP_REMOTE_TESTS)
 ENDIF(ENABLE_TESTS)

dap4_test/Makefile.am

@@ -6,7 +6,12 @@
 # Put together AM_CPPFLAGS and AM_LDFLAGS.
 include $(top_srcdir)/lib_flags.am
 
-TEST_EXTENSIONS = .sh
+#TEST_EXTENSIONS = .sh
+
+#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
+#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
+#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
+#TESTS_ENVIRONMENT = export SETX=1;
 	
 LDADD = ${top_builddir}/liblib/libnetcdf.la
 AM_CPPFLAGS += -I$(top_srcdir)/libdap4
@@ -30,6 +35,7 @@ if BUILD_UTILITIES
 TESTS += test_raw.sh
 TESTS += test_meta.sh
 TESTS += test_data.sh
+TESTS += test_fillmismatch.sh
 endif
 
 # Note which tests depend on other tests. Necessary for make -j check.
@@ -44,23 +50,24 @@ check_PROGRAMS += findtestserver4
 findtestserver4_SOURCES = findtestserver4.c
 if BUILD_UTILITIES
   # relies on ncdump
-  # Disabled until the testserver is stable
-#TESTS += test_remote.sh
+  TESTS += test_remote.sh
 endif
 endif
 
 endif #ENABLE_DAP4
 
 EXTRA_DIST = test_parse.sh test_meta.sh test_data.sh \
-             test_raw.sh test_remote.sh test_hyrax.sh \
-             d4test_common.sh \
-	     daptestfiles dmrtestfiles cdltestfiles nctestfiles \
+             test_raw.sh test_remote.sh test_hyrax.sh test_fillmismatch.sh \
+             tst_curlopt.sh d4test_common.sh \
+	     daptestfiles dmrtestfiles cdltestfiles nctestfiles misctestfiles \
 	     baseline baselineraw baselineremote CMakeLists.txt
 
 CLEANFILES = *.exe
 # This should only be left behind if using parallel io
 CLEANFILES += tmp_*
 
+DISTCLEANFILES = findtestserver4.c
+
 # One last thing
 BUILT_SOURCES = .daprc
 

dap4_test/Makefile.in

@@ -111,11 +111,13 @@ check_PROGRAMS = $(am__EXEEXT_1) $(am__EXEEXT_2)
 # These rely on ncdump
 @BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@am__append_4 = test_raw.sh \
 @BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@	test_meta.sh \
-@BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@	test_data.sh
+@BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@	test_data.sh \
+@BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@	test_fillmismatch.sh
 
 # Note: This program name was changed to findtestserver4
 # to avoid cmake complaint about duplicate targets.
 @ENABLE_DAP4_TRUE@@ENABLE_DAP_REMOTE_TESTS_TRUE@am__append_5 = findtestserver4
+@BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@@ENABLE_DAP_REMOTE_TESTS_TRUE@am__append_6 = test_remote.sh
 subdir = dap4_test
 ACLOCAL_M4 = $(top_srcdir)/aclocal.m4
 am__aclocal_m4_deps = $(top_srcdir)/m4/libtool.m4 \
@@ -127,7 +129,7 @@ am__configure_deps = $(am__aclocal_m4_deps) $(CONFIGURE_DEPENDENCIES) \
 DIST_COMMON = $(srcdir)/Makefile.am $(am__DIST_COMMON)
 mkinstalldirs = $(install_sh) -d
 CONFIG_HEADER = $(top_builddir)/config.h
-CONFIG_CLEAN_FILES =
+CONFIG_CLEAN_FILES = findtestserver4.c
 CONFIG_CLEAN_VPATH_FILES =
 @ENABLE_DAP4_TRUE@am__EXEEXT_1 = test_parse$(EXEEXT) \
 @ENABLE_DAP4_TRUE@	test_meta$(EXEEXT) test_data$(EXEEXT)
@@ -203,6 +205,10 @@ am__can_run_installinfo = \
     n|no|NO) false;; \
     *) (install-info --version) >/dev/null 2>&1;; \
   esac
+am__extra_recursive_targets = check-valgrind-recursive \
+	check-valgrind-memcheck-recursive \
+	check-valgrind-helgrind-recursive check-valgrind-drd-recursive \
+	check-valgrind-sgcheck-recursive
 am__tagged_files = $(HEADERS) $(SOURCES) $(TAGS_FILES) $(LISP)
 # Read a list of newline-separated strings from the standard input,
 # and print each of them once, without duplicates.  Input order is
@@ -407,11 +413,9 @@ am__set_TESTS_bases = \
 RECHECK_LOGS = $(TEST_LOGS)
 AM_RECURSIVE_TARGETS = check recheck
 TEST_SUITE_LOG = test-suite.log
-am__test_logs1 = $(TESTS:=.log)
-am__test_logs2 = $(am__test_logs1:@EXEEXT@.log=.log)
-TEST_LOGS = $(am__test_logs2:.sh.log=.log)
-SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver
-SH_LOG_COMPILE = $(SH_LOG_COMPILER) $(AM_SH_LOG_FLAGS) $(SH_LOG_FLAGS)
+TEST_EXTENSIONS = @EXEEXT@ .test
+LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver
+LOG_COMPILE = $(LOG_COMPILER) $(AM_LOG_FLAGS) $(LOG_FLAGS)
 am__set_b = \
   case '$@' in \
     */*) \
@@ -422,8 +426,16 @@ am__set_b = \
     *) \
       b='$*';; \
   esac
+am__test_logs1 = $(TESTS:=.log)
+am__test_logs2 = $(am__test_logs1:@EXEEXT@.log=.log)
+TEST_LOGS = $(am__test_logs2:.test.log=.log)
+TEST_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver
+TEST_LOG_COMPILE = $(TEST_LOG_COMPILER) $(AM_TEST_LOG_FLAGS) \
+	$(TEST_LOG_FLAGS)
 am__DIST_COMMON = $(srcdir)/Makefile.in $(top_srcdir)/depcomp \
-	$(top_srcdir)/lib_flags.am $(top_srcdir)/test-driver
+	$(top_srcdir)/lib_flags.am \
+	$(top_srcdir)/ncdap_test/findtestserver.c.in \
+	$(top_srcdir)/test-driver
 DISTFILES = $(DIST_COMMON) $(DIST_SOURCES) $(TEXINFOS) $(EXTRA_DIST)
 ACLOCAL = @ACLOCAL@
 ALLOCA = @ALLOCA@
@@ -463,6 +475,11 @@ ECHO_C = @ECHO_C@
 ECHO_N = @ECHO_N@
 ECHO_T = @ECHO_T@
 EGREP = @EGREP@
+ENABLED_DOC_SECTIONS = @ENABLED_DOC_SECTIONS@
+ENABLE_VALGRIND_drd = @ENABLE_VALGRIND_drd@
+ENABLE_VALGRIND_helgrind = @ENABLE_VALGRIND_helgrind@
+ENABLE_VALGRIND_memcheck = @ENABLE_VALGRIND_memcheck@
+ENABLE_VALGRIND_sgcheck = @ENABLE_VALGRIND_sgcheck@
 EXEEXT = @EXEEXT@
 FGREP = @FGREP@
 GREP = @GREP@
@@ -504,6 +521,7 @@ MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
 MANIFEST_TOOL = @MANIFEST_TOOL@
 MKDIR_P = @MKDIR_P@
+MPIEXEC = @MPIEXEC@
 MSVC = @MSVC@
 NC_ENABLE_DOXYGEN_PDF_OUTPUT = @NC_ENABLE_DOXYGEN_PDF_OUTPUT@
 NC_HAS_CDF5 = @NC_HAS_CDF5@
@@ -523,6 +541,7 @@ NC_HAS_PNETCDF = @NC_HAS_PNETCDF@
 NC_HAS_SZIP = @NC_HAS_SZIP@
 NC_LIBS = @NC_LIBS@
 NC_M4 = @NC_M4@
+NC_RELAX_COORD_BOUND = @NC_RELAX_COORD_BOUND@
 NC_VERSION = @NC_VERSION@
 NC_VERSION_MAJOR = @NC_VERSION_MAJOR@
 NC_VERSION_MINOR = @NC_VERSION_MINOR@
@@ -550,6 +569,8 @@ SET_MAKE = @SET_MAKE@
 SHELL = @SHELL@
 SHOW_DOXYGEN_TAG_LIST = @SHOW_DOXYGEN_TAG_LIST@
 STRIP = @STRIP@
+VALGRIND = @VALGRIND@
+VALGRIND_ENABLED = @VALGRIND_ENABLED@
 VERSION = @VERSION@
 abs_builddir = @abs_builddir@
 abs_srcdir = @abs_srcdir@
@@ -609,25 +630,33 @@ target_vendor = @target_vendor@
 top_build_prefix = @top_build_prefix@
 top_builddir = @top_builddir@
 top_srcdir = @top_srcdir@
+valgrind_enabled_tools = @valgrind_enabled_tools@
+valgrind_tools = @valgrind_tools@
 AM_TESTS_ENVIRONMENT = export TOPSRCDIR=${abs_top_srcdir}; export TOPBUILDDIR=${abs_top_builddir}; 
 
 # Put together AM_CPPFLAGS and AM_LDFLAGS.
-TEST_EXTENSIONS = .sh
+
+#TEST_EXTENSIONS = .sh
+
+#SH_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
+#sh_LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
+#LOG_DRIVER = $(SHELL) $(top_srcdir)/test-driver-verbose
+#TESTS_ENVIRONMENT = export SETX=1;
 LDADD = ${top_builddir}/liblib/libnetcdf.la
-TESTS = $(am__append_3) $(am__append_4)
+TESTS = $(am__append_3) $(am__append_4) $(am__append_6)
 @ENABLE_DAP4_TRUE@test_parse_SOURCES = test_parse.c test_common.h
 @ENABLE_DAP4_TRUE@test_meta_SOURCES = test_meta.c test_common.h
 @ENABLE_DAP4_TRUE@test_data_SOURCES = test_data.c test_common.h
 @ENABLE_DAP4_TRUE@@ENABLE_DAP_REMOTE_TESTS_TRUE@findtestserver4_SOURCES = findtestserver4.c
-#TESTS += test_remote.sh
 EXTRA_DIST = test_parse.sh test_meta.sh test_data.sh \
-             test_raw.sh test_remote.sh test_hyrax.sh \
-             d4test_common.sh \
-	     daptestfiles dmrtestfiles cdltestfiles nctestfiles \
+             test_raw.sh test_remote.sh test_hyrax.sh test_fillmismatch.sh \
+             tst_curlopt.sh d4test_common.sh \
+	     daptestfiles dmrtestfiles cdltestfiles nctestfiles misctestfiles \
 	     baseline baselineraw baselineremote CMakeLists.txt
 
 # This should only be left behind if using parallel io
 CLEANFILES = *.exe tmp_*
+DISTCLEANFILES = findtestserver4.c
 
 # One last thing
 BUILT_SOURCES = .daprc
@@ -635,7 +664,7 @@ all: $(BUILT_SOURCES)
 	$(MAKE) $(AM_MAKEFLAGS) all-am
 
 .SUFFIXES:
-.SUFFIXES: .c .lo .log .o .obj .sh .sh$(EXEEXT) .trs
+.SUFFIXES: .c .lo .log .o .obj .test .test$(EXEEXT) .trs
 $(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am $(top_srcdir)/lib_flags.am $(am__configure_deps)
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
@@ -666,6 +695,8 @@ $(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
 $(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
 	cd $(top_builddir) && $(MAKE) $(AM_MAKEFLAGS) am--refresh
 $(am__aclocal_m4_deps):
+findtestserver4.c: $(top_builddir)/config.status $(top_srcdir)/ncdap_test/findtestserver.c.in
+	cd $(top_builddir) && $(SHELL) ./config.status $(subdir)/$@
 
 clean-checkPROGRAMS:
 	@list='$(check_PROGRAMS)'; test -n "$$list" || exit 0; \
@@ -738,6 +769,11 @@ mostlyclean-libtool:
 
 clean-libtool:
 	-rm -rf .libs _libs
+check-valgrind-local: 
+check-valgrind-memcheck-local: 
+check-valgrind-helgrind-local: 
+check-valgrind-drd-local: 
+check-valgrind-sgcheck-local: 
 
 ID: $(am__tagged_files)
 	$(am__define_uniq_tagged_files); mkid -fID $$unique
@@ -932,19 +968,61 @@ recheck: all $(check_PROGRAMS)
 	        am__force_recheck=am--force-recheck \
 	        TEST_LOGS="$$log_list"; \
 	exit $$?
-.sh.log:
+test_parse.sh.log: test_parse.sh
+	@p='test_parse.sh'; \
+	b='test_parse.sh'; \
+	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+test_raw.sh.log: test_raw.sh
+	@p='test_raw.sh'; \
+	b='test_raw.sh'; \
+	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+test_meta.sh.log: test_meta.sh
+	@p='test_meta.sh'; \
+	b='test_meta.sh'; \
+	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+test_data.sh.log: test_data.sh
+	@p='test_data.sh'; \
+	b='test_data.sh'; \
+	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+test_fillmismatch.sh.log: test_fillmismatch.sh
+	@p='test_fillmismatch.sh'; \
+	b='test_fillmismatch.sh'; \
+	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+test_remote.sh.log: test_remote.sh
+	@p='test_remote.sh'; \
+	b='test_remote.sh'; \
+	$(am__check_pre) $(LOG_DRIVER) --test-name "$$f" \
+	--log-file $$b.log --trs-file $$b.trs \
+	$(am__common_driver_flags) $(AM_LOG_DRIVER_FLAGS) $(LOG_DRIVER_FLAGS) -- $(LOG_COMPILE) \
+	"$$tst" $(AM_TESTS_FD_REDIRECT)
+.test.log:
 	@p='$<'; \
 	$(am__set_b); \
-	$(am__check_pre) $(SH_LOG_DRIVER) --test-name "$$f" \
+	$(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
 	--log-file $$b.log --trs-file $$b.trs \
-	$(am__common_driver_flags) $(AM_SH_LOG_DRIVER_FLAGS) $(SH_LOG_DRIVER_FLAGS) -- $(SH_LOG_COMPILE) \
+	$(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
 	"$$tst" $(AM_TESTS_FD_REDIRECT)
-@am__EXEEXT_TRUE@.sh$(EXEEXT).log:
+@am__EXEEXT_TRUE@.test$(EXEEXT).log:
 @am__EXEEXT_TRUE@	@p='$<'; \
 @am__EXEEXT_TRUE@	$(am__set_b); \
-@am__EXEEXT_TRUE@	$(am__check_pre) $(SH_LOG_DRIVER) --test-name "$$f" \
+@am__EXEEXT_TRUE@	$(am__check_pre) $(TEST_LOG_DRIVER) --test-name "$$f" \
 @am__EXEEXT_TRUE@	--log-file $$b.log --trs-file $$b.trs \
-@am__EXEEXT_TRUE@	$(am__common_driver_flags) $(AM_SH_LOG_DRIVER_FLAGS) $(SH_LOG_DRIVER_FLAGS) -- $(SH_LOG_COMPILE) \
+@am__EXEEXT_TRUE@	$(am__common_driver_flags) $(AM_TEST_LOG_DRIVER_FLAGS) $(TEST_LOG_DRIVER_FLAGS) -- $(TEST_LOG_COMPILE) \
 @am__EXEEXT_TRUE@	"$$tst" $(AM_TESTS_FD_REDIRECT)
 
 distdir: $(BUILT_SOURCES)
@@ -1018,11 +1096,32 @@ clean-generic:
 distclean-generic:
 	-test -z "$(CONFIG_CLEAN_FILES)" || rm -f $(CONFIG_CLEAN_FILES)
 	-test . = "$(srcdir)" || test -z "$(CONFIG_CLEAN_VPATH_FILES)" || rm -f $(CONFIG_CLEAN_VPATH_FILES)
+	-test -z "$(DISTCLEANFILES)" || rm -f $(DISTCLEANFILES)
 
 maintainer-clean-generic:
 	@echo "This command is intended for maintainers to use"
 	@echo "it deletes files that may require special tools to rebuild."
 	-test -z "$(BUILT_SOURCES)" || rm -f $(BUILT_SOURCES)
+check-valgrind: check-valgrind-am
+
+check-valgrind-am: check-valgrind-local
+
+check-valgrind-drd: check-valgrind-drd-am
+
+check-valgrind-drd-am: check-valgrind-drd-local
+
+check-valgrind-helgrind: check-valgrind-helgrind-am
+
+check-valgrind-helgrind-am: check-valgrind-helgrind-local
+
+check-valgrind-memcheck: check-valgrind-memcheck-am
+
+check-valgrind-memcheck-am: check-valgrind-memcheck-local
+
+check-valgrind-sgcheck: check-valgrind-sgcheck-am
+
+check-valgrind-sgcheck-am: check-valgrind-sgcheck-local
+
 clean: clean-am
 
 clean-am: clean-checkPROGRAMS clean-generic clean-libtool clean-local \
@@ -1103,19 +1202,23 @@ uninstall-am:
 .MAKE: all check check-am install install-am install-strip
 
 .PHONY: CTAGS GTAGS TAGS all all-am am--depfiles check check-TESTS \
-	check-am clean clean-checkPROGRAMS clean-generic clean-libtool \
-	clean-local cscopelist-am ctags ctags-am distclean \
-	distclean-compile distclean-generic distclean-libtool \
-	distclean-tags distdir dvi dvi-am html html-am info info-am \
-	install install-am install-data install-data-am install-dvi \
-	install-dvi-am install-exec install-exec-am install-html \
-	install-html-am install-info install-info-am install-man \
-	install-pdf install-pdf-am install-ps install-ps-am \
-	install-strip installcheck installcheck-am installdirs \
-	maintainer-clean maintainer-clean-generic mostlyclean \
-	mostlyclean-compile mostlyclean-generic mostlyclean-libtool \
-	pdf pdf-am ps ps-am recheck tags tags-am uninstall \
-	uninstall-am
+	check-am check-valgrind-am check-valgrind-drd-am \
+	check-valgrind-drd-local check-valgrind-helgrind-am \
+	check-valgrind-helgrind-local check-valgrind-local \
+	check-valgrind-memcheck-am check-valgrind-memcheck-local \
+	check-valgrind-sgcheck-am check-valgrind-sgcheck-local clean \
+	clean-checkPROGRAMS clean-generic clean-libtool clean-local \
+	cscopelist-am ctags ctags-am distclean distclean-compile \
+	distclean-generic distclean-libtool distclean-tags distdir dvi \
+	dvi-am html html-am info info-am install install-am \
+	install-data install-data-am install-dvi install-dvi-am \
+	install-exec install-exec-am install-html install-html-am \
+	install-info install-info-am install-man install-pdf \
+	install-pdf-am install-ps install-ps-am install-strip \
+	installcheck installcheck-am installdirs maintainer-clean \
+	maintainer-clean-generic mostlyclean mostlyclean-compile \
+	mostlyclean-generic mostlyclean-libtool pdf pdf-am ps ps-am \
+	recheck tags tags-am uninstall uninstall-am
 
 .PRECIOUS: Makefile
 
@@ -1125,7 +1228,6 @@ uninstall-am:
 @ENABLE_DAP4_TRUE@test_meta.log: test_raw.log
 @ENABLE_DAP4_TRUE@test_data.log: test_meta.log
 @BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@@ENABLE_DAP_REMOTE_TESTS_TRUE@  # relies on ncdump
-@BUILD_UTILITIES_TRUE@@ENABLE_DAP4_TRUE@@ENABLE_DAP_REMOTE_TESTS_TRUE@  # Disabled until the testserver is stable
 
 .daprc:
 	echo "#DAPRC" >.daprc

dap4_test/baseline/test_atomic_array.5.nc.d4d

 netcdf test_atomic_array.5.nc {
 types:
-  ubyte(*) _bytestring ;
+  opaque(16) opaque16_t ;
 dimensions:
 	_Anonymous1 = 1 ;
 	_Anonymous2 = 2 ;
@@ -8,7 +8,7 @@ variables:
 	ubyte vu8(_Anonymous1, _Anonymous2) ;
 	double vd(_Anonymous1) ;
 	string vs(_Anonymous1, _Anonymous1) ;
-	_bytestring vo(_Anonymous1, _Anonymous1) ;
+	opaque16_t vo(_Anonymous1, _Anonymous1) ;
 
 // global attributes:
 		string :_dap4.ce = "/vu8[1][0:2:2];/vd[1];/vs[1][0];/vo[0][1]" ;
@@ -24,5 +24,6 @@ data:
   "Καλημέα" ;
 
  vo =
-  {171, 205, 239, 0, 0, 0, 0, 0} ;
+  0XABCDEF00000000000000000000000000 ;
+
 }