Merge branch 'master' of https://github.com/Unidata/netcdf-c

CMakeLists.txt

@@ -568,7 +568,6 @@ ENDIF()
 IF (USE_HDF5 OR ENABLE_NETCDF_4)
   SET(USE_HDF5 ON)
   SET(USE_NETCDF4 ON)
-
   # Accomodate developers who have hdf5 libraries and
   # headers on their system, but do not have a the hdf
   # .cmake files.  If this is the case, they should
@@ -576,6 +575,13 @@ IF (USE_HDF5 OR ENABLE_NETCDF_4)
   IF(HDF5_LIB AND HDF5_HL_LIB AND HDF5_INCLUDE_DIR)
     SET(HDF5_LIBRARIES ${HDF5_LIB} ${HDF5_HL_LIB})
     SET(HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIR})
+    # Find out if HDF5 was built with parallel support.
+    # Do that by checking for the targets H5Pget_fapl_mpiposx and
+    # H5Pget_fapl_mpio in ${HDF5_LIB}.
+    CHECK_LIBRARY_EXISTS(${HDF5_LIB} H5Pget_fapl_mpioposix "" HDF5_IS_PARALLEL)
+    IF(NOT HDF5_IS_PARALLEL)
+      CHECK_LIBRARY_EXISTS(${HDF5_LIB} H5Pget_fapl_mpio "" HDF5_IS_PARALLEL)
+    ENDIF()
   ELSE()
     IF(MSVC)
       FIND_PACKAGE(HDF5 COMPONENTS C HL NO_MODULE REQUIRED)
@@ -583,7 +589,6 @@ IF (USE_HDF5 OR ENABLE_NETCDF_4)
     ELSE()
       FIND_PACKAGE(HDF5 COMPONENTS C HL REQUIRED)
     ENDIF()
-
   ENDIF()
 
   INCLUDE_DIRECTORIES(${HDF5_INCLUDE_DIRS})
@@ -730,20 +735,13 @@ SET(STATUS_PARALLEL "OFF")
 OPTION(ENABLE_PARALLEL "Build netCDF-4 with parallel IO" OFF)
 IF(ENABLE_PARALLEL AND ENABLE_NETCDF_4)
   SET(USE_PARALLEL ON CACHE BOOL "")
-	# Check for H5Pget_fapl_mpiposx, define USE_PARALLEL_POSIX
-	CHECK_LIBRARY_EXISTS(${HDF5_LIB} H5Pget_fapl_mpioposix "" USE_PARALLEL_POSIX)	
-		
-	# Else Check for H5Pget_fapl_mpio, define USE_PARALLEL_MPIO
-	IF(NOT USE_PARALLEL_POSIX)
-	       CHECK_LIBRARY_EXISTS(${HDF5_LIB} H5Pget_fapl_mpio "" USE_PARALLEL_MPIO)
-	ENDIF()
-	
-	IF(NOT USE_PARALLEL_POSIX AND NOT USE_PARALLEL_MPIO)
+  IF(NOT HDF5_IS_PARALLEL)
     SET(USE_PARALLEL OFF CACHE BOOL "")
     MESSAGE(STATUS "Cannot find HDF5 library built with parallel support. Disabling parallel build.")
-	ENDIF()
+  ELSE()
     SET(STATUS_PARALLEL "ON")
   ENDIF()
+ENDIF()
 
 # Options to enable parallel IO, tests.
 SET(STATUS_PNETCDF "OFF")

cf

@@ -16,6 +16,8 @@ DAP=1
 #M32=1
 #M64=1
 
+FORCE="-i"
+
 #INSTALL=1
 PREFIX=/usr/local
 
@@ -153,6 +155,7 @@ FLAGS="$FLAGS --disable-examples"
 #FLAGS="$FLAGS --enable-large-file-tests"
 #FLAGS="$FLAGS --disable-testsets"
 #FLAGS="$FLAGS --disable-dap-remote-tests"
+#FLAGS="$FLAGS --enable-dap-auth-tests"
 #FLAGS="$FLAGS --enable-doxygen"
 #FLAGS="$FLAGS --enable-logging"
 #FLAGS="$FLAGS --disable-diskless"
@@ -215,6 +218,6 @@ export DISTCHECK_CONFIGURE_FLAGS
 if test -f Makefile ; then ${MAKE} distclean >/dev/null 2>&1 ; fi
 sh $X ./configure ${FLAGS}
 for c in $cmds; do
-  ${MAKE} $c
+  ${MAKE} ${FORCE} $c
 done
 exit 0

configure.ac

@@ -304,6 +304,22 @@ if test "x$enable_dap" = "xno" ; then
 fi
 AC_MSG_RESULT($enable_dap_remote_tests)
 
+# Default is now to do the remote authorization tests
+AC_MSG_CHECKING([whether dap remote authorization testing should be enabled (default off)])
+AC_ARG_ENABLE([dap-auth-test],
+              [AS_HELP_STRING([--enable-dap-auth-tests],
+                                 [enable dap remote authorization tests])])
+test "x$enable_dap_auth_tests" = xyes || enable_dap_auth_tests=no
+# dap must be enabled
+if test "x$enable_dap" = "xno" ; then
+  enable_dap_auth_tests=no
+fi
+# if remote tests are disabled, then so is this
+if test "x$enable_dap_remote_tests" = "xno" ; then
+  enable_dap_remote_tests=no
+fi
+AC_MSG_RESULT($enable_dap_auth_tests)
+
 # Control if groups are supported in [netcdf4]dap2 code
 AC_MSG_CHECKING([whether [netcdf4] group names should be enabled (default on)])
 AC_ARG_ENABLE([dap-groups],
@@ -811,6 +827,7 @@ AM_CONDITIONAL(TEST_PARALLEL, [test "x$enable_parallel" = xyes -a "x$enable_para
 AM_CONDITIONAL(BUILD_DAP, [test "x$enable_dap" = xyes])
 AM_CONDITIONAL(USE_DAP, [test "x$enable_dap" = xyes]) # Alias
 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])

include/nc.h

@@ -28,6 +28,7 @@ typedef struct NC {
 	char* path;
 	int   mode; /* as provided to nc_open/nc_create */
 	int   substrate;
+	int   refcount; /* To enable multiple name-based opens */
 } NC;
 
 /*
@@ -76,6 +77,7 @@ extern int nc_get_default_format(void);
 extern int add_to_NCList(NC*);
 extern void del_from_NCList(NC*);/* does not free object */
 extern NC* find_in_NCList(int ext_ncid);
+extern NC* find_in_NCList_by_name(const char*);
 extern void free_NCList(void);/* reclaim whole list */
 extern int count_NCList(void); /* return # of entries in NClist */
 

libdispatch/ddispatch.c

@@ -31,15 +31,10 @@ static struct NCPROTOCOLLIST {
    against future changes.
 */
 static const char* servers[] = {
-"http://thredds-test.ucar.edu",
-"http://thredds.ucar.edu",
-"http://motherlode.ucar.edu:8081",
-"http://motherlode.ucar.edu:8080",
-"http://motherlode.ucar.edu",
 "http://remotetest.unidata.ucar.edu",
+"http://thredds-test.unidata.ucar.edu",
 "http://remotetest.ucar.edu",
-"http://remotetests.unidata.ucar.edu",
-"http://remotetests.ucar.edu",
+"http://thredds-test.ucar.edu",
 NULL
 };
 

libdispatch/dfile.c

@@ -1033,6 +1033,11 @@ nc_abort(int ncid)
    NC* ncp;
    int stat = NC_check_id(ncid, &ncp);
    if(stat != NC_NOERR) return stat;
+
+   /* What to do if refcount > 0? */
+   /* currently, forcibly abort */
+   ncp->refcount = 0;
+
    stat = ncp->dispatch->abort(ncid);
    del_from_NCList(ncp);
    free_NC(ncp);
@@ -1085,10 +1090,15 @@ nc_close(int ncid)
    NC* ncp;
    int stat = NC_check_id(ncid, &ncp);
    if(stat != NC_NOERR) return stat;
+
+   ncp->refcount--;
+   if(ncp->refcount <= 0)
+   {
        stat = ncp->dispatch->close(ncid);
        /* Remove from the nc list */
        del_from_NCList(ncp);
        free_NC(ncp);
+   }
    return stat;
 }
 
@@ -1505,6 +1515,11 @@ NC_create(const char *path, int cmode, size_t initialsz,
       nc_initialized = 1;
    }
 
+   /* If this path is already open, then fail */
+   ncp = find_in_NCList_by_name(path);
+   if(ncp != NULL)
+	return NC_ENFILE;   
+
    if((isurl = NC_testurl(path)))
 	model = NC_urlmodel(path);
 
@@ -1636,6 +1651,14 @@ NC_open(const char *path, int cmode,
       nc_initialized = 1;
    }
 
+   /* If this path is already open, then bump the refcount and return it */
+   ncp = find_in_NCList_by_name(path);
+   if(ncp != NULL) {
+	ncp->refcount++;
+	if(ncidp) *ncidp = ncp->ext_ncid;	
+	return NC_NOERR;
+   }
+
    isurl = NC_testurl(path);
    if(isurl)
       model = NC_urlmodel(path);

libdispatch/nclistmgr.c

@@ -42,6 +42,10 @@ add_to_NCList(NC* ncp)
 	    return NC_ENOMEM;
 	numfiles = 0;
     }
+    /* Check the refcount */
+    if(ncp->refcount > 0)
+	return NC_NOERR;
+
     new_id = 0; /* id's begin at 1 */
     for(i=1; i < NCFILELISTLENGTH; i++) {
 	if(nc_filelist[i] == NULL) {new_id = i; break;}
@@ -60,6 +64,10 @@ del_from_NCList(NC* ncp)
    unsigned int ncid = ((unsigned int)ncp->ext_ncid) >> ID_SHIFT;
    if(numfiles == 0 || ncid == 0 || nc_filelist == NULL) return;
    if(nc_filelist[ncid] != ncp) return;
+   /* Check the refcount */
+   if(ncp->refcount > 0)
+	return; /* assume caller has decrecmented */
+
    nc_filelist[ncid] = NULL;
    numfiles--;
 
@@ -78,3 +86,25 @@ find_in_NCList(int ext_ncid)
    return f;
 }
 
+/*
+Added to support open by name
+*/
+NC*
+find_in_NCList_by_name(const char* path)
+{
+   int i;
+   NC* f = NULL;
+   if(nc_filelist == NULL)
+	return NULL;
+   for(i=1; i < NCFILELISTLENGTH; i++) {
+	if(nc_filelist[i] != NULL) {
+	    if(strcmp(nc_filelist[i]->path,path)==0) {
+		f = nc_filelist[i];
+		break;
+	    }				
+	}
+   }
+   return f;
+}
+
+

ncdap_test/CMakeLists.txt

@@ -40,10 +40,16 @@ IF(ENABLE_TESTS)
 	ENDIF()
 	add_bin_test(ncdap test_nstride_cached)
 	add_bin_test(ncdap test_partvar)
-	add_bin_test(ncdap test_varm3)
 	add_bin_test(ncdap t_auth)
 	add_bin_test(ncdap t_misc)
 	
+# test_varm3 did not survive the transition
+# to remotetest.unidata.ucar.edu; the
+# coads_climatology.nc file cannot be found.
+# Can restore if/when we find that file
+# and put it in testdods directory on remotetest.
+#	add_bin_test(ncdap test_varm3)
+
 ENDIF()
 ADD_SUBDIRECTORY(testdata3)
 ADD_SUBDIRECTORY(expected3)

ncdap_test/Makefile.am

@@ -34,26 +34,35 @@ endif
 test_cvt3_SOURCES = test_cvt.c
 test_vara_SOURCES = test_vara.c
 test_partvar_SOURCES = test_partvar.c
-test_varm3_SOURCES = test_varm3.c
 t_dap3a_SOURCES = t_dap3a.c
 test_nstride_cached_SOURCE = test_nstride_cached.c
 t_auth_SOURCES = t_auth.c
 t_misc_SOURCES = t_misc.c
 
 TESTS += t_dap3a test_cvt3 test_vara test_partvar
-TESTS += test_varm3
 TESTS += t_dap3a
 TESTS += test_nstride_cached
-TESTS += t_auth
 TESTS += t_misc
 
 check_PROGRAMS += t_dap3a test_cvt3 test_vara test_partvar
-check_PROGRAMS += test_varm3
 check_PROGRAMS += t_dap3a
 check_PROGRAMS += test_nstride_cached
-check_PROGRAMS += t_auth
 check_PROGRAMS += t_misc
 
+# test_varm3 did not survive the transition
+# to remotetest.unidata.ucar.edu; the
+# coads_climatology.nc file cannot be found.
+# Can restore if/when we find that file
+# and put it in testdods directory on remotetest.
+# test_varm3_SOURCES = test_varm3.c
+# check_PROGRAMS += test_varm3
+# TESTS += test_varm3
+
+if ENABLE_DAP_AUTH_TESTS
+check_PROGRAMS += t_auth
+TESTS += t_auth
+endif
+
 endif #ENABLE_DAP_REMOTE_TESTS
 
 

ncdap_test/t_misc.c

@@ -5,7 +5,7 @@
 #include <netcdf.h>
 
 
-#define URL1 "http://thredds-test.ucar.edu" /* test that no trailing / is ok */
+#define URL1 "http://remotetest.unidata.ucar.edu" /* test that no trailing / is ok */
 
 static void
 CHECK(int e, const char* msg)

ncdump/env

@@ -0,0 +1,6 @@
+F="tst_small.nc"
+
+alias q0="./ncdump $F"
+alias qh="./ncdump -h $F"
+alias qq="gdb --args ./ncdump $F"
+alias qqh="gdb --args ./ncdump -h $F"