Merge pull request #2036 from Unidata/gh1983.wif

Address optimization issue

CMakeLists.txt

@@ -118,11 +118,6 @@ MACRO(CHECK_C_LINKER_FLAG M_FLAG M_RESULT)
   SET(CMAKE_REQUIRED_FLAGS "${T_REQ_FLAG}")
 ENDMACRO()
 
-# Enable 'dist and distcheck'.
-# File adapted from http://ensc.de/cmake/FindMakeDist.cmake
-FIND_PACKAGE(MakeDist)
-# End 'enable dist and distcheck'
-
 # Set the build type.
 IF(NOT CMAKE_BUILD_TYPE)
   SET(CMAKE_BUILD_TYPE DEBUG CACHE STRING "Choose the type of build, options are: None, Debug, Release."
@@ -199,6 +194,15 @@ ENDIF()
 
 OPTION(NC_FIND_SHARED_LIBS "Find dynamically-built versions of dependent libraries" ${BUILD_SHARED_LIBS})
 
+##
+# Check to see if C compiler supports -fno-strict-aliasing, in support of
+# https://github.com/Unidata/netcdf-c/issues/1983
+##
+CHECK_C_COMPILER_FLAG(-fno-strict-aliasing CC_SUPPORTS_NO_STRICT_ALIASING)
+IF(CC_SUPPORTS_NO_STRICT_ALIASING)
+  SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fno-strict-aliasing")
+ENDIF(CC_SUPPORTS_NO_STRICT_ALIASING)
+
 ##
 # We've had a request to allow for non-versioned shared libraries.
 # This seems reasonable enough to accommodate.  See
@@ -861,7 +865,7 @@ int main() {
 }" HAVE_LIBCURL_766)
 
 IF (HAVE_LIBCURL_766)
-  # If libcurl version is >= 7.66, then can skip tests 
+  # If libcurl version is >= 7.66, then can skip tests
   # for these symbols which were added in an earlier version
   set(HAVE_CURLOPT_USERNAME TRUE)
   set(HAVE_CURLOPT_PASSWORD TRUE)
@@ -977,9 +981,9 @@ IF(MSVC)
     FILE(COPY ${netCDF_SOURCE_DIR}/libsrc/XGetopt.c
          DESTINATION ${netCDF_BINARY_DIR}/ncdump/)
     FILE(COPY ${netCDF_SOURCE_DIR}/libsrc/XGetopt.c
-         DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/) 
+         DESTINATION ${netCDF_BINARY_DIR}/nczarr_test/)
     FILE(COPY ${netCDF_SOURCE_DIR}/libsrc/XGetopt.c
-         DESTINATION ${netCDF_BINARY_DIR}/ncdap_test/) 
+         DESTINATION ${netCDF_BINARY_DIR}/ncdap_test/)
   ENDIF()
 ENDIF()
 
@@ -2122,9 +2126,6 @@ INSTALL(PROGRAMS ${netCDF_BINARY_DIR}/nc-config
 ##
 print_conf_summary()
 
-# Enable Makedist files.
-ADD_MAKEDIST()
-ENABLE_MAKEDIST(README.md COPYRIGHT RELEASE_NOTES.md INSTALL INSTALL.cmake test_prog.c lib_flags.am cmake CMakeLists.txt COMPILE.cmake.txt config.h.cmake.in cmake_uninstall.cmake.in netcdf-config-version.cmake.in netcdf-config.cmake.in FixBundle.cmake.in nc-config.cmake.in configure configure.ac install-sh config.h.in config.sub CTestConfig.cmake.in)
 
 #####
 # Configure and print the libnetcdf.settings file.

configure.ac

@@ -54,6 +54,25 @@ AC_CANONICAL_TARGET
 
 AC_CONFIG_HEADERS([config.h])
 
+
+##
+# Check to see if the compiler supports -fno-strict-aliasing and, if so,
+# add that to the C compiler flags.  This is in support of https://github.com/Unidata/netcdf-c/issues/1983.
+##
+SAVE_CFLAGS="${CFLAGS}"
+AC_LANG_PUSH([C])
+CFLAGS="${CFLAGS} -fno-strict-aliasing"
+
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([
+        [int i = 0;]])],
+        [have_no_strict_aliasing=yes],
+        [have_no_strict_aliasing=no])
+AC_MSG_CHECKING([whether compiler supports -fno-strict-aliasing])
+AC_MSG_RESULT([$have_no_strict_aliasing])
+AC_LANG_POP([C])
+if test $have_no_strict_aliasing = no; then
+   CFLAGS=$SAVE_CFLAGS
+fi
 ##
 # Some files need to exist in build directories
 # that do not correspond to their source directory, or

include/netcdf.h

@@ -293,11 +293,14 @@ NOTE: The NC_MAX_DIMS, NC_MAX_ATTRS, and NC_MAX_VARS limits
 
 /** In HDF5 files you can set storage for each variable to be either
  * contiguous or chunked, with nc_def_var_chunking().  This define is
- * used there. */
+ * used there. Unknown storage is used for further extensions of HDF5
+ * storage models, which should be handled transparently by netcdf */
 /**@{*/
-#define NC_CHUNKED    0
-#define NC_CONTIGUOUS 1
-#define NC_COMPACT    2
+#define NC_CHUNKED         0
+#define NC_CONTIGUOUS      1
+#define NC_COMPACT         2
+#define NC_UNKNOWN_STORAGE 3
+#define NC_VIRTUAL         4
 /**@}*/
 
 /** In HDF5 files you can set check-summing for each variable.

libhdf5/hdf5create.c

@@ -118,11 +118,12 @@ nc4_create_file(const char *path, int cmode, size_t initialsz,
     }
 
     /* Need this access plist to control how HDF5 handles open objects
-     * on file close. Setting H5F_CLOSE_SEMI will cause H5Fclose to
-     * fail if there are any open objects in the file. */
+     * on file close. (Setting H5F_CLOSE_WEAK will cause H5Fclose not to
+     * fail if there are any open objects in the file. This may happen when virtual
+     * datasets are opened). */
     if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
         BAIL(NC_EHDFERR);
-    if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI))
+    if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_WEAK))
         BAIL(NC_EHDFERR);
 
 #ifdef USE_PARALLEL4

libhdf5/hdf5open.c

@@ -764,12 +764,13 @@ nc4_open_file(const char *path, int mode, void* parameters, int ncid)
 #endif /* !USE_PARALLEL4 */
 
     /* Need this access plist to control how HDF5 handles open objects
-     * on file close. (Setting H5F_CLOSE_SEMI will cause H5Fclose to
-     * fail if there are any open objects in the file). */
+     * on file close. (Setting H5F_CLOSE_WEAK will cause H5Fclose not to
+     * fail if there are any open objects in the file. This may happen when virtual
+     * datasets are opened). */
     if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0)
         BAIL(NC_EHDFERR);
 
-    if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI) < 0)
+    if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_WEAK) < 0)
         BAIL(NC_EHDFERR);
 
 #ifdef USE_PARALLEL4
@@ -1190,6 +1191,16 @@ get_chunking_info(hid_t propid, NC_VAR_INFO_T *var)
     {
 	var->storage = NC_COMPACT;
     }
+#ifdef H5D_VIRTUAL
+    else if (layout == H5D_VIRTUAL)
+    {
+	var->storage = NC_VIRTUAL;
+    }
+#endif
+    else
+    {
+    var->storage = NC_UNKNOWN_STORAGE;
+    }
 
     return NC_NOERR;
 }

libsrc4/nc4internal.c

@@ -1694,8 +1694,12 @@ rec_print_metadata(NC_GRP_INFO_T *grp, int tab_count)
             strcat(storage_str, "contiguous");
         else if (var->storage == NC_COMPACT)
             strcat(storage_str, "compact");
-        else
+        else if (var->storage == NC_CHUNKED)
             strcat(storage_str, "chunked");
+        else if (var->storage == NC_VIRTUAL)
+            strcat(storage_str, "virtual");
+        else
+            strcat(storage_str, "unknown");
         LOG((2, "%s VARIABLE - varid: %d name: %s ndims: %d "
              "dimids:%s storage: %s", tabs, var->hdr.id, var->hdr.name,
              var->ndims,

nc_perf/tst_attsperf.c

@@ -137,7 +137,7 @@ readfile_hdf5(char *file_name, long long *delta, int do_inq, int num_vars)
 
    /* Open and close the root group. */
    if ((fapl_id = H5Pcreate(H5P_FILE_ACCESS)) < 0) ERR;
-   if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_SEMI)) ERR;
+   if (H5Pset_fclose_degree(fapl_id, H5F_CLOSE_WEAK)) ERR;
    if ((hdfid = H5Fopen(file_name, H5F_ACC_RDONLY, fapl_id)) < 0) ERR;
    if ((hdf_grpid = H5Gopen2(hdfid, "/", H5P_DEFAULT)) < 0) ERR;
 

nc_test/nc_test.c

@@ -98,7 +98,7 @@ main(int argc, char *argv[])
      */
     (void) signal(SIGFPE, SIG_IGN);
 
-    verbose = 0;
+    verbose = 1;
     max_nmpt = 8;
 
     /* If you uncomment the nc_set_log_level line, you will get a lot

nc_test/test_get.m4

@@ -98,11 +98,11 @@ define(`TEST_NC_GET_VAR1',dnl
 int
 TestFunc(var1)_$1(VarArgs)
 {
-    int i, err, ncid, cdf_format;
+    int i=0, err=0, ncid=0, cdf_format=0;
     int nok = 0;        /* count of valid comparisons */
-    int canConvert;     /* Both text or both numeric */
-    IntType j, index[MAX_RANK];
-    double expect;
+    int canConvert=0;     /* Both text or both numeric */
+    IntType j=0, index[MAX_RANK];
+    double expect=0;
     $1 value[1];
 
     err = FileOpen(testfile, NC_NOWRITE);
@@ -253,6 +253,10 @@ TestFunc(var)_$1(VarArgs)
     double expect[MAX_NELS];
     $1 value[MAX_NELS];
 
+    for(j = 0; j < MAX_NELS; j++) {
+          expect[j] = 0;
+    }
+
     err = FileOpen(testfile, NC_NOWRITE);
     IF (err != NC_NOERR) error("open: %s", APIFunc(strerror)(err));
 
@@ -376,6 +380,10 @@ TestFunc(vara)_$1(VarArgs)
     double expect[MAX_NELS];
     $1 value[MAX_NELS];
 
+    for(j = 0; j < MAX_NELS; j++) {
+          expect[j] = 0;
+    }
+
     err = FileOpen(testfile, NC_NOWRITE);
     IF (err != NC_NOERR) error("open: %s", APIFunc(strerror)(err));
 
@@ -635,6 +643,10 @@ TestFunc(vars)_$1(VarArgs)
     double expect[MAX_NELS];
     $1 value[MAX_NELS];
 
+    for(j = 0; j < MAX_NELS; j++) {
+          expect[j] = 0;
+    }
+
     err = FileOpen(testfile, NC_NOWRITE);
     IF (err != NC_NOERR) error("open: %s", APIFunc(strerror)(err));
 
@@ -814,7 +826,7 @@ ifelse(`$1',`uchar',`ifdef(`PNETCDF',,``#'endif')')
                 IF (err != 0) error("error in toMixedBase");
                 nels = 1;
                 for (j = 0; j < var_rank[i]; j++) {
-                    count[j] = 1 + (edge[j]-index[j]-1) / (IntType)stride[j];
+                    count[j] = 1 + (edge[j]-index[j]-1) / ( (IntType)stride[j] == 0 ? 1 : (IntType)stride[j]);
                     nels *= count[j];
                     index[j] += start[j];
                 }
@@ -928,6 +940,10 @@ TestFunc(varm)_$1(VarArgs)
     double expect[MAX_NELS];
     $1 value[MAX_NELS];
 
+    for(j = 0; j < MAX_NELS; j++) {
+          expect[j] = 0;
+    }
+
     err = FileOpen(testfile, NC_NOWRITE);
     IF (err != NC_NOERR) error("open: %s", APIFunc(strerror)(err));
 
@@ -1107,7 +1123,7 @@ ifelse(`$1',`uchar',`ifdef(`PNETCDF',,``#'endif')')
                 IF (err != 0) error("error in toMixedBase");
                 nels = 1;
                 for (j = 0; j < var_rank[i]; j++) {
-                    count[j] = 1 + (edge[j]-index[j]-1) / (IntType)stride[j];
+                    count[j] = 1 + (edge[j]-index[j]-1) / ( (IntType)stride[j] == 0 ? 1 : (IntType)stride[j]);
                     nels *= count[j];
                     index[j] += start[j];
                 }
@@ -1221,6 +1237,10 @@ TestFunc(att)_$1(AttVarArgs)
     double expect[MAX_NELS];
     $1 value[MAX_NELS];
 
+    for(j = 0; j < MAX_NELS; j++) {
+          expect[j] = 0;
+    }
+
     err = FileOpen(testfile, NC_NOWRITE);
     IF (err != NC_NOERR) error("open: %s", APIFunc(strerror)(err));
 
@@ -1348,4 +1368,3 @@ TEST_NC_GET_ATT(ushort)
 TEST_NC_GET_ATT(uint)
 TEST_NC_GET_ATT(longlong)
 TEST_NC_GET_ATT(ulonglong)
-