PROGRAM `prepbufr`

General Overview

Converting NCEP PREPBUFR files into DART obs_seq.out files is a 2 step process. The first step uses NCEP software to convert the PREPBUFR file into an intermediate text file. This is described in this document. The second step converts the intermediate files into obs_seq.out files, which is done by create_real_obs, as described in PROGRAM create_real_obs . For details of the conversion process we refer users to the the sections starting with Prepbufr Overview (on this page below) and the create_real_obs documentation page. For those with access to Derecho looking for a quick overview of all steps in the conversion process see the Quickstart Instructions below.

Quickstart Instructions

This section provides a complete list of steps within the conversion process (prepbufr file to obs_seq.out) performed on Derecho. It is only recommended if you have a Derecho account, or prefer a comprehensive list of the required steps/commands. Otherwise please proceed to the Prepbufr Overview section for more details.

The following Derecho modules were loaded during the compiling process. This exact setup is not mandatory, but given for reference.

Currently Loaded Modules:
   1) ncarenv/23.09 (S)   3) intel/2023.2.1        5) cray-mpich/8.1.27  7) netcdf/4.9.2   9) ncl/6.6.2
   2) craype/2.7.23       4) ncarcompilers/1.0.0   6) hdf5/1.12.2        8) nco/5.2.4

Go to the DART prep_bufr observation converter directory and build the PREPBUFR utilities as follows:
```
cd $DART_DIR/observations/obs_converters/NCEP/prep_bufr
./install.sh
```
The install.sh script can be edited to use different compilers by setting the CCOMP and FCOMP sections at the start of the script.

Confirm the exe directory contains the executables prepbufr.x, prepbufr_03Z.x, grabbufr.x and cword.x.
Go to the $DART_DIR/build_templates/ directory and use the intel build template for compiling DART
```
cd $DART_DIR/build_templates
cp mkmf.template.intel.linux mkmf.template
```
Go to the $DART_DIR/observations/obs_converters/NCEP/prep_bufr/work/ directory and run quickbuild.sh to build the advance_time executable:
```
cd $DART_DIR/observations/obs_converters/NCEP/prep_bufr/work
./quickbuild.sh
```

Make a prepqm subdirectory in the data directory:

cd $DART_DIR/observations/obs_converters/NCEP/prep_bufr/data
mkdir prepqm

Obtain the PREPBUFR observations for your desired time. In the following examples observations from April 27, 2017 will be used. On Derecho you can go to the the campaign collections directory at:
```
cd /glade/campaign/collections/rda/data/d090000/2017/
cp A25328-201704prepqmB.tar $DART_DIR/observations/obs_converters/NCEP/prep_bufr/data/prepqm/
```
Alternatively, download the files directly from the NSF NCAR Research Data Archive page for the NCEP/NSF NCAR Global Reanalysis Products. Register on the site, click on the “Data Access” tab, and locate the “prepqm: BUFR observations files”. Use a similar approach to obtain the RDA ds337 prepbufr files. Locate and download the GDAS PREPBUFR files of your choice.

You may not be able to untar the downloaded files. In that case cosblocking command will unblock the file in place as:

cd $DART_DIR/observations/obs_converters/NCEP/prep_bufr/data/prepqm/
/glade/campaign/cisl/dares/Observations/cosconvert -b A25328-201704prepqmB.tar

Untar the data (organized into half months), then unzip the days of interest (6 hour chunks): To process a full day of observations you will need both the day of interest, and the following day.
```
tar -xvf A25328-201704prepqmB.tar
cd 201704
gzip -d prepqm17042*nr.gz
```
Some tar files create a subdirectory when the archive is unpacked. It may be easier to move all the files from the subdirectory to the main prepqm directory:
```
cd $DART_DIR/observations/obs_converters/NCEP/prep_bufr/data/prepqm/201704
mv prepqm* ..
```
Now all the individual 6-hour prepqm* files are in the data/prepqm directory. (If you decide to leave the files in the 201704 subdirectory, edit the BUFR_in variable in the prepbufr.csh script to include the subdirectory name.)
Confirm these files exist: prepqm17042706.nr, prepqm17042712.nr, prepqm17042718.nr, and prepqm17042800.nr and prepqm17042806.nr.
In the $DART_DIR/observations/obs_converters/NCEP/prep_bufr/work directory, edit the input.nml file. This file will control what observations will be used for your experiment, so the namelist options are worth investigating a bit here.

For example, for weather applications where you want only atmospheric observations close to your assimilation time, you could use the following:
```
&prep_bufr_nml
   obs_window    = 1.0
   obs_window_cw = 1.5
   otype_use     = 120.0, 130.0, 131.0, 132.0, 133.0, 180.0
                   181.0, 182.0, 220.0, 221.0, 230.0, 231.0
                   232.0, 233.0, 242.0, 243.0, 245.0, 246.0
                   252.0, 253.0, 255.0, 280.0, 281.0, 282.0
   qctype_use    = 0,1,2,3,15
   /
```
This defines an observation time window (obs_window) of +/- 1.0 hours, while cloud motion vectors (obs_window_cw) will be used over a window of +/- 1.5 hours. Observations outside of this time window are excluded from the analysis.

This will use observation types:
- sounding temps (120),
- aircraft temps (130,131),
- dropsonde temps (132),
- mdcars aircraft temps (133),
- marine temp (180),
- land humidity (181),
- ship humidity (182),
- rawinsonde U,V (220),
- pibal U,V (221),
- aircraft U,V (230,231,232),
- cloudsat winds (242,243,245),
- GOES water vapor (246),
- sat winds (252,253,255), and
- ship obs (280, 281,282)
Additionally, it will include observations with specified qc types only. Skip to the prepfbufr Namelist section at the bottom of this page for more available namelist controls.

For applications where you want to use all available observations in the 6-hour assimilation window, you would set obs_window to 3.0 or larger to avoid excluding any observations.
Within the $DART_DIR/observations/obs_converters/NCEP/prep_bufr/work directory, edit the prepbufr.csh file and change the following variables to match the locations and format of the data you downloaded as shown below:
```
set BUFR_dir  = ../data
set BUFR_idir = ${BUFR_dir}/prepqm
set BUFR_odir = ${BUFR_dir}/prepout
set DART_exec_dir = ../exe
..
set BUFR_in = ${BUFR_idir}/prepqm${sdtg}.nr
```
The daily variable in prepbufr.csh controls whether the output of the script is a single 24 hour file or 4, 6-hour files. Depending on what other observations you intend to merge later on, one option may be easier to use. For this example, we are leaving daily = no, and the script will make 4, 6-hour files.

Run the prepbufr.csh script for a single day:

cd $DART_DIR/observations/obs_converters/NCEP/prep_bufr/work
./prepbufr.csh 2017 04 27

Your PREPBUFR files have now been converted to an intermediate ASCII format. Confirm that temp_obs.20170427* files within ~/data/prepout exist. Please note that the script can function with only the 06 prepqm input file, but will also need the 12, 18, and following day 00 files to run to completion.
There is a separate executable to convert the observations from this intermediate text format into the native DART format. Edit the input.nml namelist file in the DART_DIR/observations/obs_converters/NCEP/ascii_to_obs/work. For this example:
```
&ncepobs_nml
   year       = 2017,
   month      = 4,
   day        = 27,
   tot_days   = 1,
   max_num    = 800000,
   select_obs = 0,
   ObsBase = '../../prepbufr/data/prepout/temp_obs.',
   daily_file = .false.,
   lat1       = 15.0,
   lat2       = 60.0,
   lon1       = 200.0,
   lon2       = 330.0
   /
```
Setting select_obs = 0 will select all the observations in the ASCII file. Set ObsBase to the directory you output the intermediate files from during the last step. If you wish to choose specific observations from the ASCII intermediate file or control other program behavior, there are many namelist options documented on the create_real_obs page.

It is now time to build ascii_to_obs. Run the following:

cd $DART_DIR/observations/obs_converters/NCEP/ascii_to_obs/work
./quickbuild.sh

Run create_real_obs to create the DART observation sequence files:

cd $DART_DIR/observations/obs_converters/NCEP/ascii_to_obs/work
./create_real_obs

The executable create_real_obs will create observation sequence files with one file for each six hour window. Confirm that the obs_seq20170427* files have been generated. For a cycled experiment, there are several options for naming the output observation files. Each month could be in a separate directory, or each 6-hour file could be in its own directory.

For a single obs file per directory, you can rename each as obs_seq.out, or you can include the timestamp in the filename, e.g. obs_seq.2017042706.out.

The observation types within the file should look like:

 obs_sequence
 obs_type_definitions
     19
RADIOSONDE_U_WIND_COMPONENT
RADIOSONDE_V_WIND_COMPONENT
RADIOSONDE_TEMPERATURE
RADIOSONDE_SPECIFIC_HUMIDITY
AIRCRAFT_U_WIND_COMPONENT
AIRCRAFT_V_WIND_COMPONENT
AIRCRAFT_TEMPERATURE
ACARS_U_WIND_COMPONENT
ACARS_V_WIND_COMPONENT
ACARS_TEMPERATURE
MARINE_SFC_U_WIND_COMPONENT
MARINE_SFC_V_WIND_COMPONENT
MARINE_SFC_TEMPERATURE
MARINE_SFC_SPECIFIC_HUMIDITY
SAT_U_WIND_COMPONENT
SAT_V_WIND_COMPONENT
RADIOSONDE_SURFACE_ALTIMETER
MARINE_SFC_ALTIMETER
LAND_SFC_ALTIMETER
num_copies:            1  num_qc:            1
num_obs:        68107  max_num_obs:        68107

Some models include a preprocessing program to do additional processing of the observations, for example, limiting obs to a sub-domain, superobbing spatially dense obs, and increasing the error for near boundary observations.

For example, the WRF weather model includes the wrf_dart_obs_preprocess program. There may be no further processing needed for some models, and the observation sequence file is ready to be used.

You have completed the Quickstart Instructions. See the following sections for more details of the prepbufr conversion package.

Prepbufr Overview

The prep_bufr package is external NCEP code and has not been completely incorporated into the DART architecture. It requires adaptation of the source codes and scripts to the computing environment where it will be run. It is not so robust that it can be controlled just with input parameters. It may not have the same levels of error detection and warning that the rest of DART has, so the user should very careful about checking the end product for correctness.

Install Prepbufr package

Running the install.sh script located within the $DART_DIR$/observations/obs_converters/NCEP/prep_bufr directory will build the library and main executable. You will probably have to edit this script to set the fortran compiler on your system.

If you have raw unblocked PREPBUFR files you will need to convert them to blocked format (what prepbufr expects as input). The blk/ublk section of the build script compiles the cword.x converter program.

If you are running on an Intel (little-endian) based machine you will need the grabbufr byte swapping program that is also built by this script.

One-shot mode

If you are converting a single obs file, or are walking through the process by hand for the first time, you can follow the more detailed build instructions below, and then run the prep_bufr.x program by hand. This involves the following steps:

Build the executables.
Run the blocker if needed (generally not if you have downloaded the blocked format PREPBUFR files).
Run the binary format converter if you are on an Intel (little-endian) machine.
Link the input file to a fixed input filename
Run prepbufr.x to convert the file
Copy the fixed output filename to the desired output filename

Production mode

If you have multiple days (or months) of observations to convert, there is a script in the work subdirectory which is set up to run the converter on a sequence of raw data files, and concatenate the output files together into one output file per day. Edit the work/prepbufr.csh script (as described in the Quickstart section) and set the necessary values in the ‘USER SET PARAMETERS’ section near the top. This script can either be run from the command line, or it can be submitted to a batch queue for a long series of conversion runs.

Overview of Prepbufr package

This package is currently organized into files under the DART/observations/NCEP/prep_bufr directory:

src           Source code of the NCEP PREPBUFR decoder
lib           NCEP BUFR library source
install.sh    A script to install the NCEP PREPBUFR decoder and the NCEP BUFR library.
exe           Executables of the decoder and converter.
data          Where the NCEP PREPBUFR files (prepqm****) could be loaded into
              from the NSF NCAR Mass Store (the script assumes this is the default location).
work          Where we run the script to do the decoding.
convert_bufr  Source code (grabbufr) to convert the binary big-endian PREPBUFR files to
              little-endian files, and a script to compile the program.
blk_ublk      Source code (cwordsh) to convert between blocked and unblocked format.
docs          Some background information about NCEP PREPBUFR observations.

Decoding program: src/prepbufr.f

The program prepbufr.f is used to decode the NCEP reanalysis PREPBUFR data into intermediate text files. This program was originally developed by NCEP. It has been modified to output surface pressure, dry temperature, specific humidity, and wind components (U/V) of conventional radiosonde, aircraft reports, and satellite cloud motion derived wind. There are additional observation types on the PREPBUFR files, but using them they would require significant modifications of prepbufr and require detailed knowledge of the NCEP PREPBUFR files. The NCEP quality control indexes for these observations based on NCEP forecasts are also output and used in DART observation sequence files. The NCEP PREPBUFR decoding program is written in Fortran 77 and has been successfully compiled on Linux computers using pgi90, SGI® computers with f77, IBM® SP® systems with xlf, and Intel® based Mac® with gfortran.

If your operating system uses modules you may need to remove the default compiler and add the one desired for this package. For example

which pgf90 (to see if pgf90 is available.)
module rm intel64 netcdf64 mpich64
module add pgi32

To compile the BUFR libraries and the decoding program, set the CCOMP and FCOMP variables in the install.sh script to match the compilers available on your system. Execute the install.sh script to complete the compilations for the main decoding program, the NCEP BUFR library, and the conversion utilities.

The executables (i.e., prepbufr.x, prepbufr_03Z.x) are placed in the ../exe directory.

Platforms tested:

Linux clusters with Intel, PGI, Pathscale, GNU Fortran,
Mac OS X with Intel, GNU Fortran,
SGI Altix with Intel
Cray with Intel, Cray Fortran.

Byte-swapping program: convert_bufr/grabbufr.f

For platforms with little-endian binary file format (e.g. Intel, AMD®, and non-MIPS SGI processors) the program grabbufr.f is used to convert the big-endian format NCEP PREPBUFR data into little-endian format. The grabbufr.f code is written in Fortran 90, and has been compiled can be compiled with the pgf90 compiler on a Linux system, with gfortran on an Intel based Mac, and the ifort compiler on other Linux machines. The install.sh script should build this by default, however instructions are in convert_bufr/README. In case of problems, go to the convert_bufr subdirectory, edit convert_bufr.csh to set your compiler, and run it to compile the converter code (grabbufr).

This program reads the PREPBUFR file into memory, and needs to know the size of the file (in bytes). Unfortunately, the system call STAT() returns this size as one number in an array, and the index into that array differs depending on the system and sometimes the word size (32 vs 64) of the compiler. To test that the program is using the right offset into this array, you can compile and run the stat_test.f program. It takes a single filename argument and prints out information about that file. One of the numbers will be the file size in bytes. Compare this to the size you see with the ‘ls -l’ command for that same file. If the numbers do not agree, find the right index and edit the grabbufr.f source file. Look for the INDEXVAL line near the first section of executable code.

If grabbufr.f does not compile because the getarg() or iargc() subroutines are not found or not available, then either use the arg_test.f program to debug how to get command line arguments into a fortran program on your system, or simply go into the grabbufr.f source and comment out the section which tries to parse command line arguments and comment in the hardcoded input and output filenames. Now to run this program you must either rename the data files to these predetermined filenames, or you can use links to temporarily give the files the names needed.

Blocking program blk_ublk/cword.x

The prepbufr.x program expects to read a blocked input file, which is generally what is available for download. However, if you have an unblocked file that you need to convert, there is a conversion program. The install.sh script will try to build this by default, but in case of problems you can build it separately. Change directories into the blk_ublk subdirectory and read the README_cwordsh file for more help. The cwordsh shell-script wrapper shows how to run the executable cwordsh.x executable.

This program is not required for blocked file formats.

Downloading Prepbufr raw data

The NCEP PREPBUFR files (prepqmYYMMDDHH) can be found within the NCEP/NCAR Global Reanalysis Products dataset, d090000, on NSF NCAR Research Data Archive (RDA). Operational observations can be found in the NCEP ADP Global Upper Air and Surface Weather Observations dataset, d337000.

To find the files:

go to the NSF NCAR/NCEP reanalysis archive.
Click on the “Data Access” tab.
Locate the preqm: BUFR observation files
Click on Complete File List link and Select the year you are interested in.
Depending on the year the format of the filenames change, but they should contain the year, usually as 2 digits, the month, and then either the start/stop day for weekly files, or the letters A and B for semi-monthly files.

Depending on the year you select, the prepqm files can be weekly, monthly, or semi-monthly. Each tar file has a unique dataset number of the form “A#####”. For example, for January of 2003, the 4 HPSS TAR files are: A21899, A21900, A21901, A21902. After September 2003, these files include AIRCRAFT data (airplane readings taken at cruising elevation) but not ACARS data (airplane readings taken during takeoff and landing). There are different datasets which include ACARS data but their use is restricted and you must contact the RDA group to get access.

If you are running on a machine with direct access to the NSF NCAR HPSS, then change directories into the prep_bufr/data
subdirectory and obtain the prepqm rawfile from:
> cd /glade/campaign/collections/rda/data/d#####
where ##### is the data set number you want.

These files may be readable tar files, or they may require running the cosconvert program first. See if the
tar command can read them:
> tar -tvf rawfile
If you get a good table of contents then simply rename the file and untar it:
> mv rawfile data.tar
> tar -xvf data.tar
However, if you get an error from the tar command, on the NSF NCAR machine Derecho run:
> /glade/campaign/cisl/dares/Observations/cosconvert -b data.tar

The output of tar should yield individual 6-hourly NCEP PREPBUFR data files for the observations in the +/- 3-hour time windows of 00Z, 06Z, 12Z, and 18Z of each day. Note that DART obs_seq files are organized such that a 24 hour file with 4 6-hour observation windows would contain observations from 3:01Z to 3:00Z of the next day, centered on 6Z, 12Z, 18Z and “24Z”. In addition, there are some observations at 3:00Z on the PREPBUFR file labelled with 06Z. Then, in order to make a full day intermediate file incorporating all the required obs from the “next” day, you’ll need the PREPBUFR files through 6Z of the day after the last day of interest. For example, to generate the observation sequence for Jan 1, 2003, the decoded NCEP PREPBUFR text files for Jan 1 and 2, 2003 are needed, and hence the following PREPBUFR files are needed:

prepqm03010106
prepqm03010112
prepqm03010118
prepqm03010200
prepqm03010206

Execution of Prepbufr

In prep_bufr/work/prepbufr.csh set the appropriate values of the year, month, first day, and last day of the period you desire, and the variable “convert” to control conversion from big- to little-endian. Confirm that the raw PREPBUFR files are in ../data, or that prepbufr.csh has been changed to find them. Execute prepbufr.csh in the work directory.

Currently, this script generates decoded PREPBUFR text data each 24 hours which contains the observations within the time window of -3:01 hours to +3:00Z within each six-hour synoptic time. These daily output text files are named as temp_obs.yyyymmdd. These text PREPBUFR data files can then be read by DART/observations/NCEP/ascii_to_obs/work/PROGRAM create_real_obs to generate the DART daily observation sequence files.

There is an alternate section in the script which creates a decoded PREPBUFR text data file each 6 hours (so they are 1-for-1 with the original PREPBUFR files). Edit the script prepbufr.csh and look for the commented out code which outputs 4 individual files per day. Note that if you chose this option, you will have to make corresponding changes in the create_obs_seq.csh script in step 2.

Other modules used

This is a piece of code that is intended to be ‘close’ to the original, as such, we have not modified it to use the DART build mechanism. This code does not use any DART modules.

Namelist

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.

&prep_bufr_nml
   obs_window       = 3.0,
   obs_window_upa   = 1.5,
   obs_window_air   = 1.5,
   obs_window_sfc   = 0.8,
   obs_window_cw    = 1.5,
   land_temp_error  = 2.5,
   land_wind_error  = 3.5,
   land_moist_error = 0.2,
   otype_use        = missing,
   qctype_use       = missing,
/

Item	Type	Description
obs_window	real	Window of time to include observations. If > 0, overrides all the other more specific window sizes. Set to -1.0 to use different time windows for different obs types. The window is +/- this number of hours, so the total window size is twice this value.
obs_window_upa	real	Window of time to include sonde observations (+/- hours) if obs_window is < 0, otherwise ignored.
obs_window_air	real	Window of time to include aircraft observations (+/- hours) if obs_window is < 0, otherwise ignored.
obs_window_sfc	real	Window of time to include surface observations (+/- hours) if obs_window is < 0, otherwise ignored.
obs_window_cw	real	Window of time to include cloud wind observations (+/- hours) if obs_window is < 0, otherwise ignored.
otype_use	real(300)	Report Types to extract from bufr file. If unspecified, all types will be converted.
qctype_use	integer(300)	QC types to include from the bufr file. If unspecified, all QC values will be accepted.
land_temp_error	real	observation error for land surface temperature observations when none is in the input file.
land_wind_error	real	observation error for land surface wind observations when none is in the input file.
land_moisture_error	real	observation error for land surface moisture observations when none is in the input file.

Files

input file(s); NCEP PREPBUFR observation files named using ObsBase with the “yymmddhh” date tag on the end. Input to grabbufr if big- to little-endian is to be done. Input to prepbufr if not.
intermediate (binary) prepqm.little; output from grabbufr, input to prepbufr.
intermediate (text) file(s) “temp_obs.yyyymmddhh”; output from prepbufr, input to create_real_obs

References

DART/observations/NCEP/prep_bufr/docs/* (NCEP text files describing the PREPBUFR files)

PROGRAM prepbufr