Merge pull request #8 from NCAR/master

Updating master
E3SM-Project · Aug 12, 2016 · 418c9ad · 418c9ad
2 parents ea39095 + 04f17b2
commit 418c9ad
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Showing 9 changed files with 195 additions and 25 deletions.
diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
@@ -5,17 +5,30 @@
 #==============================================================================
 
 find_package(Doxygen)
+
+# This supports the build with/witout async code. Once async code is
+# fully merged, remove the definition of C_SRC_FILES and its mention
+# in Doxyfile.in for simplicity.
+if (PIO_ENABLE_ASYNC)
+  SET(C_SRC_FILES "@CMAKE_CURRENT_SOURCE_DIR@/../src/clib/bget.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pioc.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pioc_sc.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_darray_async.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_get_nc_async.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_internal.h @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_nc4.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_put_nc_async.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_spmd.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/bget.h @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pioc_support.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_lists.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_nc_async.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_varm.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/dtypes.h  @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_file.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio.h @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_msg.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_rearrange.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/topology.c")
+else ()
+  SET(C_SRC_FILES "@CMAKE_CURRENT_SOURCE_DIR@/../src/clib/bget.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pioc.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pioc_sc.c  @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_internal.h @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_nc4.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_spmd.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/bget.h @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pioc_support.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_darray.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_get_nc.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_lists.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_put_nc.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_varm.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/dtypes.h @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_file.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio.h @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_msg.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_nc.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/pio_rearrange.c @CMAKE_CURRENT_SOURCE_DIR@/../src/clib/topology.c")
+endif ()
+
 if(DOXYGEN_FOUND)
-    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in 
-                   ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
-    add_custom_target(doc
-        COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/customdoxygen.css 
-                                         ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/DoxygenLayout.xml 
-                                         ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/doxygen.sty 
-                                         ${CMAKE_CURRENT_BINARY_DIR}
-        COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
-        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-        COMMENT "Generating API documentation with Doxygen" VERBATIM)
+  # Process the Doxyfile using options set during configure.
+  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in 
+    ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY)
+
+  # Copy necessary files.
+  add_custom_target(doc
+    COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/customdoxygen.css 
+    ${CMAKE_CURRENT_BINARY_DIR}
+    COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/DoxygenLayout.xml 
+    ${CMAKE_CURRENT_BINARY_DIR}
+    COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/doxygen.sty 
+    ${CMAKE_CURRENT_BINARY_DIR}
+    COMMAND ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    COMMENT "Generating API documentation with Doxygen" VERBATIM)
 endif(DOXYGEN_FOUND)
diff --git a/doc/Doxyfile.in b/doc/Doxyfile.in
@@ -769,11 +769,15 @@ WARN_LOGFILE           =
 # Note: If this tag is empty the current directory is searched.
 
 INPUT                  = @CMAKE_CURRENT_SOURCE_DIR@/source \
-                         @CMAKE_CURRENT_SOURCE_DIR@/../src/clib \
                          @CMAKE_CURRENT_SOURCE_DIR@/../src/flib \
                          @CMAKE_CURRENT_SOURCE_DIR@/../examples/c \
                          @CMAKE_CURRENT_SOURCE_DIR@/../examples/f03 \
-                         @CMAKE_BINARY_DIR@/src/flib
+                         @CMAKE_BINARY_DIR@/src/clib \
+                         @CMAKE_BINARY_DIR@/src/flib \
+			 @C_SRC_FILES@
+
+# Uncomment this after the async code is fully merged into PIO.
+#                         @CMAKE_CURRENT_SOURCE_DIR@/../src/clib 
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses

diff --git a/src/clib/pio.h b/src/clib/pio.h
@@ -325,6 +325,7 @@ enum PIO_ERROR_HANDLERS
     PIO_RETURN_ERROR = (-53)  
 };
 
+/** Define the netCDF-based error codes. */
 #if defined( _PNETCDF) || defined(_NETCDF)
 #define PIO_GLOBAL NC_GLOBAL
 #define PIO_UNLIMITED NC_UNLIMITED
@@ -417,25 +418,29 @@ enum PIO_ERROR_HANDLERS
 #define PIO_EBADCHUNK NC_EBADCHUNK
 #define PIO_ENOTBUILT NC_ENOTBUILT
 #define PIO_EDISKLESS NC_EDISKLESS
-
 #define PIO_FILL_DOUBLE NC_FILL_DOUBLE
 #define PIO_FILL_FLOAT NC_FILL_FLOAT
 #define PIO_FILL_INT NC_FILL_INT
 #define PIO_FILL_CHAR NC_FILL_CHAR
+#endif /*  defined( _PNETCDF) || defined(_NETCDF) */
 
-#endif
+/** Define the extra error codes for the parallel-netcdf library. */
 #ifdef _PNETCDF
 #define PIO_EINDEP  NC_EINDEP
-#else
+#else  /* _PNETCDF */
 #define PIO_EINDEP  (-203) 
-#endif
+#endif /* _PNETCDF */
 
+/** Define error codes for PIO. */
 #define PIO_EBADIOTYPE  -255
+
+/** ??? */
 #define PIO_REQ_NULL (NC_REQ_NULL-1)
 
 #if defined(__cplusplus)
 extern "C" {
 #endif
+    int PIOc_strerror(int pioerr, char *errstr);
     int PIOc_freedecomp(int iosysid, int ioid);
     int PIOc_inq_att (int ncid, int varid, const char *name, nc_type *xtypep, PIO_Offset *lenp); 
     int PIOc_inq_format (int ncid, int *formatp); 

diff --git a/src/clib/pio_darray_async.c b/src/clib/pio_darray_async.c
@@ -1577,15 +1577,15 @@ int pio_read_darray_nc(file_desc_t *file, io_desc_t *iodesc, const int vid,
 }
 
 /** Read an array of data from a file to the (serial) IO library.
- *  @ingroup PIO_read_darray
  *
  * @param file a pointer to the open file descriptor for the file
  * that will be written to
  * @param iodesc a pointer to the defined iodescriptor for the buffer
  * @param vid the variable id to be read.
- * @param IOBUF
+ * @param IOBUF the buffer to be read into from this mpi task
  *
  * @returns
+ * @ingroup PIO_read_darray
  */
 int pio_read_darray_nc_serial(file_desc_t *file, io_desc_t *iodesc,
 			      const int vid, void *IOBUF)
@@ -1813,7 +1813,7 @@ int pio_read_darray_nc_serial(file_desc_t *file, io_desc_t *iodesc,
  * processor.
  *
  * @return 0 for success, error code otherwise.
- * @ingroup PIO_write_darray
+ * @ingroup PIO_read_darray
  */
 int PIOc_read_darray(const int ncid, const int vid, const int ioid,
 		     const PIO_Offset arraylen, void *array)

diff --git a/src/clib/pioc_support.c b/src/clib/pioc_support.c
@@ -17,6 +17,55 @@ int pio_log_level = 0;
 int my_rank;
 #endif /* PIO_ENABLE_LOGGING */
 
+/** Return a string description of an error code. If zero is passed, a
+ * null is returned.
+ *
+ * @param pioerr the error code returned by a PIO function call. 
+ * @param errmsg Pointer that will get the error message. It will be
+ * PIO_MAX_NAME chars or less.
+ *
+ * @return 0 on success
+ */
+int
+PIOc_strerror(int pioerr, char *errmsg)
+{
+
+    /* System error? */
+    if(pioerr > 0)
+    {
+	const char *cp = (const char *)strerror(pioerr);
+	if (cp)
+	    strncpy(errmsg, cp, PIO_MAX_NAME);
+	else
+	    strcpy(errmsg, "Unknown Error");
+    }
+    else if (pioerr == PIO_NOERR)
+    {
+	strcpy(errmsg, "No error");
+    }
+    else if (pioerr <= NC2_ERR && pioerr >= NC4_LAST_ERROR)     /* NetCDF error? */
+    {
+#if defined( _PNETCDF) || defined(_NETCDF)
+	strncpy(errmsg, nc_strerror(pioerr), NC_MAX_NAME);
+#else /* defined( _PNETCDF) || defined(_NETCDF) */
+	strcpy(errmsg, "NetCDF error code, PIO not built with netCDF.");
+#endif /* defined( _PNETCDF) || defined(_NETCDF) */
+    }
+    else
+    {
+	/* Handle PIO errors. */
+	switch(pioerr) {
+	case PIO_EBADIOTYPE:
+	    strcpy(errmsg, "Bad IO type");
+	    break;
+	default:
+	    strcpy(errmsg, "unknown PIO error");
+	}
+    }
+
+    return PIO_NOERR;
+}
+
 /** Set the logging level. Set to -1 for nothing, 0 for errors only, 1
  * for important logging, and so on. Log levels below 1 are only
  * printed on the io/component root. If the library is not built with

diff --git a/src/flib/pio.F90 b/src/flib/pio.F90
@@ -59,7 +59,8 @@ module pio
        PIO_set_chunk_cache, &
        PIO_get_chunk_cache, &
        PIO_set_var_chunk_cache, &
-       PIO_get_var_chunk_cache
+       PIO_get_var_chunk_cache, &
+       PIO_strerror
 
   use pionfatt_mod, only : PIO_put_att   => put_att,        &
        PIO_get_att   => get_att

diff --git a/src/flib/pio_nf.F90 b/src/flib/pio_nf.F90
@@ -37,7 +37,8 @@ module pio_nf
        pio_set_var_chunk_cache                              , &
        pio_get_var_chunk_cache                              , &
        pio_redef                                            , &
-       pio_set_log_level
+       pio_set_log_level                                    , &
+       pio_strerror
 !       pio_copy_att    to be done
 
   interface pio_def_var
@@ -194,6 +195,11 @@ module pio_nf
           set_log_level                                      
   end interface pio_set_log_level
 
+  interface pio_strerror
+     module procedure &
+          strerror
+  end interface pio_strerror
+
   interface pio_inquire
      module procedure &
           inquire_desc                                      , &
@@ -678,6 +684,34 @@ end function PIOc_set_log_level
     end interface
     ierr = PIOc_set_log_level(log_level)
   end function set_log_level
+
+  !>
+  !! @defgroup PIO_strerror
+  !<
+  !> 
+  !! @ingroup PIO_strerror
+  !! Returns a descriptive string for an error code.
+  !! 
+  !! @param errcode the error code
+  !! @retval a description of the error
+  !<
+  integer function strerror(errcode, errmsg) result(ierr)
+    integer, intent(in) :: errcode
+    character(len=*), intent(out) :: errmsg
+    interface
+       integer(C_INT) function PIOc_strerror(errcode, errmsg) &
+            bind(C, name="PIOc_strerror")
+         use iso_c_binding
+         integer(C_INT), value :: errcode
+         character(C_CHAR) :: errmsg(*)
+       end function PIOc_strerror
+    end interface
+    errmsg = C_NULL_CHAR
+    ierr = PIOc_strerror(errcode, errmsg)
+    call replace_c_null(errmsg)
+
+  end function strerror
+
 !> 
 !! @public
 !! @ingroup PIO_redef

diff --git a/tests/unit/driver.F90 b/tests/unit/driver.F90
@@ -27,6 +27,9 @@ Program pio_unit_test_driver
   integer, external :: nc_set_log_level2
 #endif
   integer ret_val
+  character(len=80) :: errmsg
+  character(len=80) :: expected
+
   ! Set up MPI
   call MPI_Init(ierr)
   call MPI_Comm_rank(MPI_COMM_WORLD, my_rank, ierr)
@@ -122,6 +125,16 @@ Program pio_unit_test_driver
   fail_cnt = 0
   test_cnt = 0
 
+  ! Test pio_strerror.
+  ret_val = PIO_strerror(-33, errmsg);
+  print *, 'errcode =', -33, ' strerror = ', errmsg
+  expected = 'NetCDF: Not a valid ID'
+  if (trim(errmsg) .ne. expected) then
+     err_msg = 'expected ' // trim(expected) // ' and got ' // trim(errmsg)
+     print *, err_msg
+     call parse(err_msg, fail_cnt)
+  end if
+
   do test_id=1,ntest
      if (ltest(test_id)) then
         ! Make sure i is a valid test number
@@ -146,6 +159,7 @@ Program pio_unit_test_driver
 #if defined( _NETCDF4) && defined(LOGGING)
         if(master_task) ierr = nc_set_log_level2(3)
 #endif
+
         ! test_create()
         if (master_task) write(*,"(3x,A,1x)") "testing PIO_createfile..."
         call test_create(test_id, err_msg)

diff --git a/tests/unit/test_names.c b/tests/unit/test_names.c
@@ -1,6 +1,6 @@
 /**
- * @file 
- * Tests for names of vars, atts, and dims.
+ * @file Tests for names of vars, atts, and dims. Also test the
+ * PIOc_strerror() function.
  *
  */
 #include <pio.h>
@@ -148,6 +148,52 @@ check_att_name(int my_rank, int ncid, int verbose)
     return 0;
 }
 
+/** Check the PIOc_strerror() function. 
+ *
+ * @param my_rank the rank of this process.
+ * @param verbose true to get printfs on stdout.
+ *
+ * @return 0 for success, error code otherwise.
+ */
+int
+check_strerror(int my_rank, int verbose) {
+
+#define NUM_TRIES 6
+    char errstr[PIO_MAX_NAME + 1];
+    int errcode[NUM_TRIES] = {PIO_EBADID,
+			      NC_ENOTNC3, NC4_LAST_ERROR - 1, 0, 1,
+			      PIO_EBADIOTYPE};
+    const char *expected[NUM_TRIES] = {"NetCDF: Not a valid ID",
+				       "NetCDF: Attempting netcdf-3 operation on netcdf-4 file",
+				       "unknown PIO error", "No error",
+				       nc_strerror(1), "Bad IO type"};
+    int ret = PIO_NOERR;
+
+    for (int try = 0; try < NUM_TRIES; try++)
+    {
+	char result[PIO_MAX_NAME];
+
+	/* Get the error string for this errcode. */
+	PIOc_strerror(errcode[try], errstr);	
+
+	/* Check that it was as expected. */
+	if (strcmp(errstr, expected[try]))
+	    ret = ERR_AWFUL;
+
+	/* Print some output to stdout if required. */
+	if (verbose)
+	{
+	    printf("%d: PIO strerror(%d) = %s\n", my_rank, errcode[try],
+		   errstr);
+	    strcpy(errstr, nc_strerror(errcode[try]));
+	    printf("%d: netCDF strerror(%d) = %s\n", my_rank, errcode[try],
+		   errstr);
+	}
+    }
+
+    return ret;
+}
+
 /** Run Tests for NetCDF-4 Functions.
  *
  * @param argc argument count
@@ -289,6 +335,10 @@ main(int argc, char **argv)
 	printf("%d: ParallelIO Library example1 running on %d processors.\n",
 	       my_rank, ntasks);
 
+    /* Check the error string function. */
+    if ((ret = check_strerror(my_rank, verbose)))
+	ERR(ret);
+
     /* keep things simple - 1 iotask per MPI process */    
     niotasks = ntasks;