Merge branch 'master' into addfilter.dmh

CMakeLists.txt

@@ -25,8 +25,8 @@ set(PACKAGE "netCDF" CACHE STRING "")
 #####
 
 SET(NC_VERSION_MAJOR 4)
-SET(NC_VERSION_MINOR 6)
-SET(NC_VERSION_PATCH 4)
+SET(NC_VERSION_MINOR 7)
+SET(NC_VERSION_PATCH 1)
 SET(NC_VERSION_NOTE "-development")
 SET(netCDF_VERSION ${NC_VERSION_MAJOR}.${NC_VERSION_MINOR}.${NC_VERSION_PATCH}${NC_VERSION_NOTE})
 SET(VERSION ${netCDF_VERSION})
@@ -315,7 +315,7 @@ SET(CHUNK_CACHE_PREEMPTION 0.75 CACHE STRING "Default file chunk cache preemptio
 SET(MAX_DEFAULT_CACHE_SIZE 67108864 CACHE STRING "Default maximum cache size.")
 SET(NETCDF_LIB_NAME "" CACHE STRING "Default name of the netcdf library.")
 SET(TEMP_LARGE "." CACHE STRING "Where to put large temp files if large file tests are run.")
-SET(NCPROPERTIES_EXTRA "" CACHE STRNG "Specify extra pairs for _NCProperties.")
+SET(NCPROPERTIES_EXTRA "" CACHE STRING "Specify extra pairs for _NCProperties.")
 SET(MPIEXEC "mpiexec" CACHE STRING "Command to run MPI programs if parallel tests are run.")
 
 IF(NOT NETCDF_LIB_NAME STREQUAL "")
@@ -1008,14 +1008,14 @@ IF(ENABLE_PARALLEL4 AND ENABLE_NETCDF_4)
     SET(STATUS_PARALLEL "ON")
     configure_file("${netCDF_SOURCE_DIR}/nc_test4/run_par_test.sh.in"
       "${netCDF_BINARY_DIR}/tmp/run_par_test.sh" @ONLY NEWLINE_STYLE LF)
-    configure_file("${netCDF_SOURCE_DIR}/nc_test4/run_par_test2.sh.in"
-      "${netCDF_BINARY_DIR}/tmp/run_par_test2.sh" @ONLY NEWLINE_STYLE LF)
+    #configure_file("${netCDF_SOURCE_DIR}/nc_test4/run_par_test2.sh.in"
+    #  "${netCDF_BINARY_DIR}/tmp/run_par_test2.sh" @ONLY NEWLINE_STYLE LF)
     FILE(COPY "${netCDF_BINARY_DIR}/tmp/run_par_test.sh"
       DESTINATION ${netCDF_BINARY_DIR}/nc_test4
       FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
-    FILE(COPY "${netCDF_BINARY_DIR}/tmp/run_par_test2.sh"
-      DESTINATION ${netCDF_BINARY_DIR}/nc_test4
-      FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
+    #FILE(COPY "${netCDF_BINARY_DIR}/tmp/run_par_test2.sh"
+    #  DESTINATION ${netCDF_BINARY_DIR}/nc_test4
+    #  FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
 
   ENDIF()
 ENDIF()
@@ -1418,6 +1418,7 @@ CHECK_FUNCTION_EXISTS(getrlimit HAVE_GETRLIMIT)
 CHECK_FUNCTION_EXISTS(_filelengthi64 HAVE_FILE_LENGTH_I64)
 CHECK_FUNCTION_EXISTS(mmap HAVE_MMAP)
 CHECK_FUNCTION_EXISTS(mremap HAVE_MREMAP)
+CHECK_FUNCTION_EXISTS(fileno HAVE_FILENO)
 
 # Check to see if MAP_ANONYMOUS is defined.
 CHECK_C_SOURCE_COMPILES("
@@ -1783,6 +1784,9 @@ IF(ENABLE_TESTS)
   IF(USE_NETCDF4)
     INCLUDE_DIRECTORIES(h5_test)
     ADD_SUBDIRECTORY(nc_test4)
+    IF(BUILD_BENCHMARKS)
+      ADD_SUBDIRECTORY(nc_perf)
+    ENDIF()
     ADD_SUBDIRECTORY(h5_test)
   ENDIF()
   IF(ENABLE_DAP2)
@@ -1856,6 +1860,8 @@ SET(CC ${CMAKE_C_COMPILER})
 # Process all dependency libraries and create a string
 # used when parsing netcdf.pc.in
 
+SET(NC_LIBS "")
+
 FOREACH(_LIB ${ALL_TLL_LIBS})
   GET_FILENAME_COMPONENT(_LIB_NAME ${_LIB} NAME_WE)
   STRING(REGEX REPLACE "^lib" "" _NAME ${_LIB_NAME})
@@ -1865,13 +1871,13 @@ FOREACH(_LIB ${ALL_TLL_LIBS})
 ENDFOREACH()
 
 #SET(NC_LIBS "-lnetcdf ${NC_LIBS}")
-
-STRING(REPLACE ";" " " NC_LIBS "${NC_LIBS}")
-STRING(REPLACE "-lhdf5::hdf5-shared" "-lhdf5" NC_LIBS ${NC_LIBS})
-STRING(REPLACE "-lhdf5::hdf5_hl-shared" "-lhdf5_hl" NC_LIBS ${NC_LIBS})
-STRING(REPLACE "-lhdf5::hdf5-static" "-lhdf5" NC_LIBS ${NC_LIBS})
-STRING(REPLACE "-lhdf5::hdf5_hl-static" "-lhdf5_hl" NC_LIBS ${NC_LIBS})
-
+IF(NC_LIBS)
+  STRING(REPLACE ";" " " NC_LIBS "${NC_LIBS}")
+  STRING(REPLACE "-lhdf5::hdf5-shared" "-lhdf5" NC_LIBS ${NC_LIBS})
+  STRING(REPLACE "-lhdf5::hdf5_hl-shared" "-lhdf5_hl" NC_LIBS ${NC_LIBS})
+  STRING(REPLACE "-lhdf5::hdf5-static" "-lhdf5" NC_LIBS ${NC_LIBS})
+  STRING(REPLACE "-lhdf5::hdf5_hl-static" "-lhdf5_hl" NC_LIBS ${NC_LIBS})
+ENDIF()
 
 STRING(REPLACE ";" " " LINKFLAGS "${LINKFLAGS}")
 

Makefile.am

@@ -78,10 +78,15 @@ if ENABLE_FILTER_TESTING
 PLUGIN_DIR = plugins
 endif
 
+# If benchmarks were turned on, build and run a bunch more tests.
+if BUILD_BENCHMARKS
+BENCHMARKS_DIR = nc_perf
+endif # BUILD_BENCHMARKS
+
 # Define Test directories
 if BUILD_TESTSETS
-TESTDIRS = $(V2_TEST) nc_test $(NC_TEST4) $(HDF4_TEST_DIR)	\
-$(NCDAP2TESTDIR) $(NCDAP4TESTDIR)
+TESTDIRS = $(V2_TEST) nc_test $(NC_TEST4) $(BENCHMARKS_DIR)	\
+$(HDF4_TEST_DIR) $(NCDAP2TESTDIR) $(NCDAP4TESTDIR)
 endif
 
 # This is the list of subdirs for which Makefiles will be constructed

RELEASE_NOTES.md

@@ -5,8 +5,11 @@ 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.
 
+## 4.7.1 - TBD
 
-## 4.6.4 - TBD
+## 4.7.0 - April 29, 2019
+
+* [Enhancement] Updated behavior of `pkgconfig` and `nc-config` to allow the use of the `--static` flags, e.g. `nc-config --libs --static`, which will show information for linking against `libnetcdf` statically. See [Github #1360](https://github.com/Unidata/netcdf-c/issues/1360) and [Github #1257](https://github.com/Unidata/netcdf-c/issues/1257) for more information.
 
 * [Enhancement] Provide byte-range reading of remote datasets. This allows
 read-only access to, for example, Amazon S3 objects and also Thredds Server

config.h.cmake.in

@@ -199,6 +199,8 @@ are set when opening a binary file on Windows. */
 /* Define if we have filelengthi64. */
 #cmakedefine HAVE_FILE_LENGTH_I64 @HAVE_FILE_LENGTH_I64@
 
+/* Define to 1 if you have the `fileno' function. */
+#cmakedefine HAVE_FILENO 1
 
 /* Define to 1 if you have the `fsync' function. */
 #cmakedefine HAVE_FSYNC 1

configure.ac

@@ -5,15 +5,12 @@
 # the COPYRIGHT file for more information.
 # Ed Hartnett, Ward Fisher, Dennis Heimbigner
 
-# Recall that ${VAR-exp} expands to $VAR if var is set (even to null),
-# and to exp otherwise.
-
 # Running autoconf on this file will trigger a warning if
 # autoconf is not at least the specified version.
 AC_PREREQ([2.59])
 
 # Initialize with name, version, and support email address.
-AC_INIT([netCDF], [4.6.4-development], [support-netcdf@unidata.ucar.edu], [netcdf-c])
+AC_INIT([netCDF], [4.7.1-development], [support-netcdf@unidata.ucar.edu], [netcdf-c])
 
 ##
 # Prefer an empty CFLAGS variable instead of the default -g -O2.
@@ -23,8 +20,8 @@ AC_INIT([netCDF], [4.6.4-development], [support-netcdf@unidata.ucar.edu], [netcd
 : ${CFLAGS=""}
 
 AC_SUBST([NC_VERSION_MAJOR]) NC_VERSION_MAJOR=4
-AC_SUBST([NC_VERSION_MINOR]) NC_VERSION_MINOR=6
-AC_SUBST([NC_VERSION_PATCH]) NC_VERSION_PATCH=4
+AC_SUBST([NC_VERSION_MINOR]) NC_VERSION_MINOR=7
+AC_SUBST([NC_VERSION_PATCH]) NC_VERSION_PATCH=1
 AC_SUBST([NC_VERSION_NOTE]) NC_VERSION_NOTE="-development"
 
 #####
@@ -249,15 +246,6 @@ AC_ARG_ENABLE([remote-fortran-bootstrap], [AS_HELP_STRING([--enable-remote-fortr
 test "x$enable_remote_fortran_bootstrap" = xyes || enable_remote_fortran_bootstrap=no
 AC_MSG_RESULT([$enable_remote_fortran_bootstrap])
 
-# Does the user want to run extra example tests
-AC_MSG_CHECKING([whether extra example tests should be run])
-AC_ARG_ENABLE([extra-example-tests],
-              [AS_HELP_STRING([--enable-extra-example-tests],
-                              [Run extra example tests; requires GNU sed. Ignored if \
-                               netCDF-4 is not enabled.])])
-test "x$enable_extra_example_tests" = xyes || enable_extra_example_tests=no
-AC_MSG_RESULT($enable_extra_example_tests)
-
 # Does the user want to run extra parallel tests when parallel netCDF-4 is built?
 AC_MSG_CHECKING([whether parallel IO tests should be run])
 AC_ARG_ENABLE([parallel-tests],
@@ -368,7 +356,7 @@ fi
 
 # --enable-dap => enable-dap4
 enable_dap4=$enable_dap
-# Default is now to always do the short remote tests
+# Default is to do the short remote tests.
 AC_MSG_CHECKING([whether dap remote testing should be enabled (default on)])
 AC_ARG_ENABLE([dap-remote-tests],
               [AS_HELP_STRING([--disable-dap-remote-tests],
@@ -379,7 +367,7 @@ if test "x$enable_dap" = "xno" ; then
 fi
 AC_MSG_RESULT($enable_dap_remote_tests)
 
-# Default is now to do the remote authorization tests
+# Default is not to do the remote authorization tests.
 AC_MSG_CHECKING([whether dap remote authorization testing should be enabled (default off)])
 AC_ARG_ENABLE([dap-auth-tests],
               [AS_HELP_STRING([--enable-dap-auth-tests],
@@ -543,6 +531,9 @@ AC_ARG_ENABLE([benchmarks],
                               are timed. We use these tests to check netCDF performance.])])
 test "x$enable_benchmarks" = xyes || enable_benchmarks=no
 AC_MSG_RESULT($enable_benchmarks)
+if test "x$enable_netcdf4" = xno -a "x$enable_benchmarks" = xyes; then
+AC_MSG_ERROR([Can't use benchmarks if netCDF-4 is disabled.])
+fi
 AM_CONDITIONAL(BUILD_BENCHMARKS, [test x$enable_benchmarks = xyes])
 
 # Does the user want to use extreme numbers in testing.
@@ -639,15 +630,6 @@ AC_ARG_WITH([udf1-magic-number],
             [UDF1_MAGIC_NUMBER=$with_udf1_magic_number])
 AC_MSG_RESULT([$UDF1_MAGIC_NUMBER])
 
-# Did the user specify a default cache preemption?
-AC_MSG_CHECKING([whether a default cache preemption for HDF5 was specified])
-AC_ARG_WITH([chunk-cache-preemption],
-              [AS_HELP_STRING([--with-chunk-cache-preemption=<float between 0 and 1 inclusive>],
-                              [Specify default file chunk cache preemption policy for HDF5 files (a number between 0 and 1, inclusive).])],
-            [CHUNK_CACHE_PREEMPTION=$with_chunk_cache_preemption], [CHUNK_CACHE_PREEMPTION=0.75])
-AC_MSG_RESULT([$CHUNK_CACHE_PREEMPTION])
-AC_DEFINE_UNQUOTED([CHUNK_CACHE_PREEMPTION], [$CHUNK_CACHE_PREEMPTION], [default file chunk cache preemption policy.])
-
 # According to the autoconf mailing list gurus, we must test for
 # compilers unconditionally. That is, we can't skip looking for the
 # fortran compilers, just because the user doesn't want fortran. This
@@ -1015,7 +997,6 @@ if test "x$enable_netcdf_4" = xyes || test "x$enable_dap" = xyes; then
    AC_SEARCH_LIBS([deflate], [zlibwapi zlibstat zlib zlib1 z], [], [
      AC_MSG_ERROR([Can't find or link to the z library. Turn off netCDF-4 and \
      DAP clients with --disable-netcdf-4 --disable-dap, or see config.log for errors.])])
-   AC_SEARCH_LIBS([SZ_Compress], [szip sz], [], [])
    AC_SEARCH_LIBS([dlopen], [dl dld], [], [])
 fi
 
@@ -1041,11 +1022,10 @@ if test "x$enable_hdf5" = xyes; then
    [AC_MSG_ERROR([Can't find or link to the hdf5 high-level. Use --disable-netcdf-4, or see config.log for errors.])])
 
    AC_CHECK_HEADERS([hdf5.h], [], [AC_MSG_ERROR([Compiling a test with HDF5 failed.  Either hdf5.h cannot be found, or config.log should be checked for other reason.])])
-   AC_CHECK_FUNCS([H5Z_SZIP])
 
    # H5Pset_fapl_mpiposix and H5Pget_fapl_mpiposix have been removed since HDF5 1.8.12.
    # Use H5Pset_fapl_mpio and H5Pget_fapl_mpio, instead.
-   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5resize_memory H5allocate_memory H5Pset_libver_bounds H5Pset_all_coll_metadata_ops])
+   AC_CHECK_FUNCS([H5Pget_fapl_mpio H5Pset_deflate H5Z_SZIP H5free_memory H5resize_memory H5allocate_memory H5Pset_libver_bounds H5Pset_all_coll_metadata_ops H5Z_SZIP])
 
    # Check to see if HDF5 library has collective metadata APIs, (HDF5 >= 1.10.0)
    if test "x$ac_cv_func_H5Pset_all_coll_metadata_ops" = xyes; then
@@ -1060,6 +1040,13 @@ if test "x$enable_hdf5" = xyes; then
    AC_MSG_CHECKING([whether parallel io is enabled in hdf5])
    AC_MSG_RESULT([$hdf5_parallel])
 
+   # Check to see if we need to search for and link against szlib.
+   if test "x$ac_cv_func_H5Z_SZIP" = xyes; then
+      AC_SEARCH_LIBS([SZ_Compress], [szip sz], [],
+      [AC_MSG_ERROR([libhdf5 installed with szip support, but cannot find or link to the szip library.])])
+   fi
+
+
    if test "x$hdf5_parallel" = "xno"; then
       if test "x$enable_parallel_tests" = "xyes"; then
          AC_MSG_ERROR([Parallel tests requested, but no parallel HDF5 installation detected.])
@@ -1293,7 +1280,6 @@ AM_CONDITIONAL(ENABLE_CDF5, [test "x$enable_cdf5" = xyes])
 AM_CONDITIONAL(ENABLE_DAP_REMOTE_TESTS, [test "x$enable_dap_remote_tests" = xyes])
 AM_CONDITIONAL(ENABLE_DAP_AUTH_TESTS, [test "x$enable_dap_auth_tests" = xyes])
 AM_CONDITIONAL(ENABLE_DAP_LONG_TESTS, [test "x$enable_dap_long_tests" = xyes])
-AM_CONDITIONAL(EXTRA_EXAMPLE_TESTS, [test "x$enable_extra_example_tests" = xyes])
 AM_CONDITIONAL(USE_SZIP, [test "x$ac_cv_func_H5Z_SZIP" = xyes])
 AM_CONDITIONAL(USE_PNETCDF_DIR, [test ! "x$PNETCDFDIR" = x])
 AM_CONDITIONAL(USE_LOGGING, [test "x$enable_logging" = xyes])
@@ -1398,14 +1384,6 @@ if test "x$enable_jna" = xyes ; then
 AC_DEFINE([JNA], [1], [if true, include JNA bug fix])
 fi
 
-# Control large metadata performance test
-AC_MSG_CHECKING([whether large metadata performance testing should be run])
-AC_ARG_ENABLE([metadata-perf],
-              [AS_HELP_STRING([--enable-metadata-perf],
-                              [Test performance of nc_create and nc_open on large metadata])])
-test "x$enable_metadata_perf" = xyes || enable_metadata_perf=no
-AC_MSG_RESULT($enable_metadata_perf)
-
 # Control filter test/example
 AC_MSG_CHECKING([whether filter testing should be run])
 AC_ARG_ENABLE([filter-testing],
@@ -1514,36 +1492,25 @@ AX_SET_META([NC_HAS_CDF5],[$enable_cdf5],[yes])
 AX_SET_META([NC_HAS_ERANGE_FILL], [$enable_erange_fill],[yes])
 AX_SET_META([NC_RELAX_COORD_BOUND], [$enable_zero_length_coord_bound],[yes])
 AX_SET_META([NC_HAS_BYTERANGE],[$enable_byterange],[yes])
+#####
+# End netcdf_meta.h definitions.
+#####
 
-# Automake says that this is always run in top_builddir
-# and that srcdir is defined (== top_srcdir)
-abs_top_builddir=`pwd`
-cd $srcdir
-abs_top_srcdir=`pwd`
-cd $abs_top_builddir
-
-# test_common.sh setup
-AC_CONFIG_FILES(test_common.sh:test_common.in)
-#rm -f ${abs_top_builddir}/test_common.sh
-#sed -e "s|@TOPSRCDIR@|${abs_top_srcdir}|" -e "s|@TOPBUILDDIR@|${abs_top_builddir}|" <${abs_top_srcdir}/test_common.in >${abs_top_builddir}/test_common.sh
-
-# nc_test4/findplugin.sh setup
+# This would be true for a cmake build.
 AC_SUBST([ISCMAKE], [])
+
+# This would be true for a visual studio build.
 AC_SUBST([MSVC], [])
+
+AC_MSG_NOTICE([generating header files and makefiles])
+AC_CONFIG_FILES(test_common.sh:test_common.in)
 AC_CONFIG_FILES(nc_test4/findplugin.sh:nc_test4/findplugin.in)
 AC_CONFIG_FILES(examples/C/findplugin.sh:nc_test4/findplugin.in)
-
-# DAP 2/4 findtestserver[4].c setup
 AC_CONFIG_FILES(ncdap_test/findtestserver.c:ncdap_test/findtestserver.c.in)
 AC_CONFIG_FILES(dap4_test/findtestserver4.c:ncdap_test/findtestserver.c.in)
-
-#####
-# End netcdf_meta.h definitions.
-#####
-
-AC_MSG_NOTICE([generating header files and makefiles])
 AC_CONFIG_FILES([nc_test4/run_par_test.sh], [chmod ugo+x nc_test4/run_par_test.sh])
-AC_CONFIG_FILES([nc_test4/run_par_bm_test.sh], [chmod ugo+x nc_test4/run_par_bm_test.sh])
+AC_CONFIG_FILES([nc_perf/run_par_bm_test.sh], [chmod ugo+x nc_perf/run_par_bm_test.sh])
+AC_CONFIG_FILES([examples/C/run_par_test.sh], [chmod ugo+x examples/C/run_par_test.sh])
 AC_CONFIG_FILES([nc-config], [chmod 755 nc-config])
 AC_CONFIG_FILES([Makefile
                  netcdf.pc
@@ -1575,6 +1542,7 @@ AC_CONFIG_FILES([Makefile
                  docs/images/Makefile
                  nctest/Makefile
                  nc_test4/Makefile
+                 nc_perf/Makefile
                  nc_test/Makefile
                  ncdap_test/Makefile
                  ncdap_test/testdata3/Makefile

docs/Doxyfile.developer

@@ -38,7 +38,7 @@ PROJECT_NAME           = netCDF-C
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 4.6.4-development
+PROJECT_NUMBER         = 4.7.1-development
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

examples/C/Makefile.am

@@ -11,7 +11,8 @@
 
 LDADD = -lm
 AM_CPPFLAGS = -I$(top_srcdir)/include
-AM_LDFLAGS =
+AM_CPPFLAGS += -I$(top_builddir)/liblib
+AM_LDFLAGS = ${top_builddir}/liblib/libnetcdf.la
 
 # These are the netCDF-3 examples.
 check_PROGRAMS = simple_xy_wr simple_xy_rd sfc_pres_temp_wr	\
@@ -21,7 +22,7 @@ TESTS = run_examples.sh
 
 # To build netcdf-4, or not to build netcdf-4, that is the question...
 if USE_HDF5
-# These are the extra netCDF-4 examples.
+# These are the netCDF-4 examples.
 check_PROGRAMS += simple_nc4_wr simple_nc4_rd simple_xy_nc4_wr	\
 simple_xy_nc4_rd
 
@@ -33,14 +34,13 @@ endif
 
 endif #USE_HDF5
 
+if TEST_PARALLEL4
 if USE_PNETCDF
-# These are the extra netCDF-4 examples.
+# This is a pnetcdf example.
 check_PROGRAMS += parallel_vara
-TESTS += parallel_vara
+TESTS += run_par_test.sh
 endif #USE_PNETCDF
-
-AM_CPPFLAGS += -I$(top_builddir)/liblib
-AM_LDFLAGS += ${top_builddir}/liblib/libnetcdf.la
+endif # TEST_PARALLEL4
 
 if USE_HDF5
 TESTS += run_examples4.sh