MODULE utilities_mod

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$Id: utilities_mod.html 6597 2013-11-11 15:55:33Z nancy $



Provides a number of tools used by most DART modules including tools for file IO, diagnostic tools for registering modules and recording namelist arguments, and an error handler.



This namelist is read from the file input.nml. Namelists start with an ampersand '&' and terminate with a slash '/'. Character strings that contain a '/' must be enclosed in quotes to prevent them from prematurely terminating the namelist.

   TERMLEVEL      = 1,
   logfilename    = 'dart_log.out',
   nmlfilename    = 'dart_log.nml',
   module_details = .true.,
   print_debug    = .false.,
   write_nml      = 'file'

The namelist controls how the logging, namelist, messages, and general utility routines behave.

Item Type Description
TERMLEVEL integer Level at which calls to error manager terminate program. The default setting is warnings and errors terminate the program. Setting this to 2 (E_ERR) means only errors terminate. Setting this to 3 means even errors do not cause an exit (which is not a good idea). /TD>
logfilename character(len=129) File to which the log messages are written.
nmlfilename character(len=129) File to which the namelist output is written. Can be the same name as the logfile.
module_details logical Each source code module can write out the repository version number and filename to the logfile. Verbose, but useful for knowing what version of the code was used during the run.
print_debug logical Setting this to .true. causes additional debug messages to print. These can be very verbose and by default are turned off.
write_nml character(len=32) String which controls where to write the namelist values that are being used for this execution. Valid values are: 'none', 'file', 'terminal', 'both'. 'none' turns off this write. 'file' writes a copy only to the nmlfilename. Writes are always in append mode, so the most recent information will be at the end of an existing file. 'terminal' will write to the job's standard output. 'both' will write both to the nml file and the standard output unit.





use utilities, only : file_exist

A note about documentation style. Optional arguments are enclosed in brackets [like this].

var = file_exist(file_name)
logical                      :: file_exist
character(len=*), intent(in) :: file_name

Returns true if file_name exists in the working directory, else false.

var   True if file_name exists in working directory.
file_name   Name of file to look for.

var = get_unit()
integer :: get_unit

Returns an unused unit number for IO.

var   An unused unit number.

var = open_file(fname [, form, action])
integer                                :: open_file
character(len=*), intent(in)           :: fname
character(len=*), optional, intent(in) :: form
character(len=*), optional, intent(in) :: action

Returns a unit number that is opened to the file fname. If form is not present or if form is "formatted" or "FORMATTED", file is opened for formatted IO. Otherwise, it is unformatted. The action string is the standard action string for Fortran IO (see F90 language description).

var   Unit number opened to file fname.
fname   Name of file to be opened.
form   Format: 'formatted' or 'FORMATTED' give formatted, anything else is unformatted. Default is formatted.
action   Standard fortran string description of requested file open action.

call timestamp([string1, string2, string3,]  pos)
character(len=*), optional, intent(in) :: string1
character(len=*), optional, intent(in) :: string2
character(len=*), optional, intent(in) :: string3
character(len=*), intent(in)           :: pos

Prints the message 'Time is YYYY MM DD HH MM SS' to the logfile along with three optional message strings. If the pos argument is 'end', the message printed is 'Finished... at YYYY MM DD HH MM SS' and the logfile is closed.

string1   An optional message to be printed.
string2   An optional message to be printed.
string3   An optional message to be printed.
pos   If 'end' terminates log_file output.

call close_file(iunit)
integer, intent(in) :: iunit

Closes the given unit number. If the unit is not open, nothing happens.

iunit   File unit to be closed.

call register_module(src, rev, rdate)
character(len=*), intent(in) :: src
character(len=*), intent(in) :: rev
character(len=*), intent(in) :: rdate

Writes the source name, revision number and revision date to both the logfileunit and to standard out. All dart modules are supposed to register when first called.

src   source file name.
rev   Revision number of source.
rdate   Date of revision.

call error_handler(level, routine, text, src, rev, rdate [, aut, text2, text3])
integer, intent(in)                    :: level
character(len=*), intent(in)           :: routine
character(len=*), intent(in)           :: text
character(len=*), intent(in)           :: src
character(len=*), intent(in)           :: rev
character(len=*), intent(in)           :: rdate
character(len=*), optional, intent(in) :: aut
character(len=*), optional, intent(in) :: text2
character(len=*), optional, intent(in) :: text3

Prints an error message to standard out and to the logfileunit. The message contains the routine name, an error message, the source file, revision and revision date, and optionally the author. The level of severity is message, debug, warning, or error. If the level is greater than or equal to the TERMLEVEL (set in the namelist), execution is terminated. The default TERMLEVEL only stops for ERRORS.

level   Error severity (message, debug, warning, error). See below for specific ations.
routine   Name of routine generating error.
text   Error message.
src   Source file containing routine generating message.
rev   Revision number of source file.
rdate   Revision date of source file.
aut   Author of routine.
text2   If specified, the second line of text for the error message.
text3   If specified, the third line of text for the error message.

call find_namelist_in_file(namelist_file_name, nml_name, iunit, [,write_to_logfile_in])
character(len=*),  intent(in)          :: namelist_file_name
character(len=*),  intent(in)          :: nml_name
integer,           intent(out)         :: iunit
logical, optional, intent(in)          :: write_to_logfile_in

Opens the file namelist_file_name if it exists on unit iunit. A fatal error occurs if the file does not exist (DART requires an input.nml to be available, even if it contains no values). Searches through the file for a line containing ONLY the string &nml_name (for instance &filter_nml if nml_name is "filter_nml"). If this line is found, the file is rewound and the routine returns. Otherwise, a fatal error message is issued.

namelist   Name of file assumed to hold the namelist.
nml_name   Name of the namelist to be searched for in the file, for instance, filter_nml.
iunit   Channel number on which file is opened.
write_to_logfile_in   When the namelist for the utilities module is read, the logfile has not yet been open because its name is in the namelist. If errors are found, have to write to standard out. So, when utilities module calls this internally, this optional argument is set to false. For all other applications, it is normally not used (default is false).

call check_namelist_read(iunit, iostat_in, nml_name, [, write_to_logfile_in])
integer, intent(in)                    :: iunit
integer, intent(in)                    :: iostat_in
character(len=*), intent(in)           :: nml_name
logical, optional, intent(in)          :: write_to_logfile_in

Once a namelist has been read from an opened namelist file, this routine checks for possible errors in the read. If the namelist read was successful, the file opened on iunit is closed and the routine returns. If iostat is not zero, an attempt is made to rewind the file on iunit and read the last line that was successfully read. If this can be done, this last line is printed with the preamble "INVALID NAMELIST ENTRY". If the attempt to read the line after rewinding fails, it is assumed that the original read (before the call to this subroutine) failed by reaching the end of the file. An error message stating that the namelist started but was never terminated is issued.

iunit   Channel number on which file is opened.
iostat_in   Error status return from an attempted read of a namelist from this file.
nml_name   The name of the namelist that is being read (for instance filter_nml).
write_to_logfile_in   When the namelist for the utilities module is read, the logfile has not yet been open because its name is in the namelist. If errors are found, have to write to standard out. So, when utilities module calls this internally, this optional argument is set to false. For all other applications, it is normally not used (default is false).

call find_textfile_dims (fname, nlines, linelen)
character(len=*), intent (IN)  :: fname
integer,          intent (OUT) :: nlines
integer,          intent (OUT) :: linelen

Determines the number of lines and maximum line length of an ASCII text file.

fname input, character string file name
nlines output, number of lines in the file
linelen output, length of longest line in the file

call file_to_text (fname, textblock)
character(len=*),               intent (IN)  :: fname
character(len=*), dimension(:), intent (OUT) :: textblock

Opens the given filename and reads ASCII text lines into a character array.

fname input, character string file name
textblock output, character array of text in the file

var = is_longitude_between(lon, minlon, maxlon [, doradians])
real(r8), intent(in)           :: lon
real(r8), intent(in)           :: minlon
real(r8), intent(in)           :: maxlon
logical,  intent(in), optional :: doradians
logical                        :: is_longitude_between

Uniform way to test longitude ranges, in degrees, on a globe. Returns true if lon is between min and max, starting at min and going EAST until reaching max. Wraps across 0 longitude. If min equals max, all points are inside. Includes endpoints. If optional arg doradians is true, do computation in radians between 0 and 2*PI instead of default 360. There is no rejection of input values based on range; they are all converted to a known range by calling modulo() first.

var   True if lon is between min and max.
lon Location to test.
minlon Minimum longitude. Region will start here and go east.
maxlon Maximum longitude. Region will end here.
doradians Optional argument. Default computations are in degrees. If this argument is specified and is .true., do the computation in radians, and wrap across the globe at 2 * PI. All inputs must then be specified in radians.

var = get_next_filename( listname, index )
character(len=*),  intent(in) :: listname
integer,           intent(in) :: index
character(len=128)            :: get_next_filename

Returns the specified line of a text file, given a filename and a line number. It returns an empty string when the line number is larger than the number of lines in a file.

Intended as an easy way to process a list of files. Use a command like 'ls > out' to create a file containing the list, in order, of files to be processed. Then call this function with an increasing index number until the return value is empty.

var An ascii string, up to 128 characters long, containing the contents of line index of the input file.
listname The filename to open and read lines from.
index Integer line number, starting at 1. If larger than the number of lines in the file, the empty string '' will be returned.

call to_upper(string)
character(len=*), intent (INOUT) :: string

Converts the character string to UPPERCASE - in place. The input string is modified.

string any character string

call nc_check(istatus, subr_name [, context])
integer, intent(in)                    :: istatus
character(len=*), intent(in)           :: subr_name
character(len=*), optional, intent(in) :: context

Check the return code from a netcdf call. If no error, return without taking any action. If an error is indicated (in the istatus argument) then call the error handler with the subroutine name and any additional context information (e.g. which file or which variable was being processed at the time of the error). All errors are currently hardcoded to be FATAL and this routine will not return.

This routine calls a netCDF library routine to construct the text error message corresponding to the error code in the first argument. An example use of this routine is:
call nc_check(nf90_create(path = trim(ncFileID%fname), cmode = nf90_share, ncid = ncFileID%ncid), &
             'init_diag_output', 'create '//trim(ncFileID%fname))

istatus   The return value from any netCDF call.
subr_name   String name of the current subroutine, used in case of error.
context   Additional text to be used in the error message, for example to indicate which file or which variable is being processed.

call set_tasknum(tasknum)
integer, intent(in)               :: tasknum

Intended to be used in the MPI multi-task case. Sets the local task number, which is then prepended to subsequent messages.

tasknum   Task number returned from MPI_Comm_Rank(). MPI task numbers are 0 based, so for a 4-task job these numbers are 0-3.

call set_output(doflag)
logical, intent(in)               :: doflag

Set the status of output. Can be set on a per-task basis if you are running with multiple tasks. If set to false only warnings and fatal errors will write to the log. The default in the multi-task case is controlled by the MPI module initialization code, which sets task 0 to .TRUE. and all other tasks to .FALSE.

doflag   Sets, on a per-task basis, whether messages are to be written to the logfile or standard output. Warnings and errors are always output.

var = do_output()
logical                      :: do_output

Returns true if this task should write to the log, false otherwise. Set by the set_output() routine. Defaults to true for the single task case. Can be used in code like so:

if (do_output()) then
 write(*,*) 'At this point in the code'
var   True if this task should write output.

call initialize_utilities( [progname] [, alternatename] )
character(len=*), intent(in), optional :: progname
character(len=*), intent(in), optional :: alternatename

Reads the namelist and opens the logfile. Records the values of the namelist and registers this module.

progname   If given, use in the timestamp message in the log file to say which program is being started.
alternatename   If given, log filename to use instead of the value in the namelist. This permits, for example, different programs sharing the same input.nml file to have different logs. If not given here and no value is specified in the namelist, this defaults to dart_log.out

call finalize_utilities()

Closes the logfile; using utilities after this call is a bad idea.

call dump_unit_attributes(iunit)
integer, intent(in) :: iunit

Writes all information about the status of the IO unit to the error handler with error level message.

iunit   Unit about which information is requested.

integer :: E_DBG, DEBUG
integer :: E_MSG, MESSAGE
integer :: E_WARN, WARNING
integer :: E_ERR, FATAL
   Severity levels to be passed to error handler. Levels are debug, message, warning and fatal. The namelist parameter TERMLEVEL can be used to control at which level program termination should occur.

integer :: logfileunit
logfileunit Unit opened to file for diagnostic output.

integer :: nmlfileunit
nmlfileunit Unit opened to file for diagnostic output of namelist files. Defaults to same as logfileunit. Provides the flexibility to log namelists to a separate file, reducing the clutter in the log files and perhaps increasing readability.







get_unit No available units Unable to open enough IO channels
check_nml_error while reading namelist _____ Fatal error reading namelist. This could be caused by having an entry in the namelist input file that is not in the namelist, by having illegal values for namelist variables, or by a variety of other compiler dependent problems.
find_namelist_in_file Namelist entry &____ must exist in namelist_nml. There must be an entry for the required namelist, for instance &filter_nml, in the input.nml namelist file. Even if no values are to be changed from the default, an entry like &filter_nml followed by a line containing only / is required.
find_namelist_in_file Namelist input file: input.nml must exist The namelist input file (usually input.nml) must exist.
check_namelist_read INVALID NAMELIST ENTRY: ___ in namelist ____ While reading the namelist, either a bad entry was found or an end of file was encountered. The most confusing case is when a namelist is being read successfully but is not appropriately terminated with a /. The line printed out by the error message will be the start of the next namelist in the input.nml file in this case.


none at this time








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Contact: DART core group
Revision: $Revision: 6597 $
Source: $URL: $
Change Date: $Date: 2013-11-11 08:55:33 -0700 (Mon, 11 Nov 2013) $
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