<p><b>demirtas</b> 2007-01-23 15:00:38 -0700 (Tue, 23 Jan 2007)</p><p>Format errors are eliminated and<br>
the text is revised.<br>
<br>
MD<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/wrfvar/technote/suites.tex
===================================================================
--- trunk/wrfvar/technote/suites.tex 2007-01-22 03:53:28 UTC (rev 39)
+++ trunk/wrfvar/technote/suites.tex 2007-01-23 22:00:38 UTC (rev 40)
@@ -1,50 +1,23 @@
\chapter{WRF Suite Scripts}
\label{suites}
-Barker, Demirtas\\
+Barker, Demirtas
+\vspace{0.5cm}
An introduction to the WRF Suite Scripts System is given in this chapter.
-The overview section highlights the basis for this system.
-The following sections are organized to give details of the script suite.
+The overview section highlights the basis for this system.
+The following sections are organized to give details of the Suite Scripts System.
\section{Overview}
The suite scripting software allows data assimilation cycles to be run with minimal setup.
It is designed to use a specific type of directory structure for WRF system
-code and data.
+code and data. Organization of source code and data directories are given in Table 1.1.
-A sample code directory structure might look like:\\
-\$CODE\_DIR
-\begin{itemize}\setlength{\parskip}{-4pt}
-\item wrfvar
-\item wrf
-\item wrfplus
-\item wps
-\item update\_bc
-\item obsproc
-\item wps
-\end{itemize}
-With directory structure for a particular region composed of reference files for all runs,
-and directories for each individual experiment.
-
-A sample data directory structure might look like: \\
-\$DAT\_DIR
-
-\begin{itemize}\setlength{\parskip}{-4pt}
-\item model\_input\_data: ncep, gfs
-\item test\_domain: con200
-\item subdirs for experiment type: noda, nobs, coldstart, cycling, update, and etc.
-\item subdir for re\_occurring data: rc
-\item subdir for forecast results: fc
-\item subdir(s) for gen\_be results: be
-\item subdir(s) for WPS geo results: geo
-\end{itemize}
-
The script suite system have two categories of scripts: control scripts and components of main suite script. A wrapper script may be needed to set up some environment variables to specify the user's experiment. This script calls {\it da\_run\_job} which creates {\it job.ksh} script on the fly.
The {\it job.ksh} executes the main {\it da\_run\_suite} script. Depending on what kind of specifications
-defined in the user's wrapper script, the {\it da\_run\_suite} script calls its component scripts
+defined in the user's wrapper script, the {\it da\_run\_suite} script calls its component scripts
listed below:
-
\begin{itemize}\setlength{\parskip}{-4pt}
\item \it da\_restore\_data\_ncep.ksh
\item \it da\_restore\_data\_rtobs.ksh
@@ -54,14 +27,15 @@
\item \it da\_run\_wrfvar.ksh
\item \it da\_run\_wrf.ksh
\end{itemize}
-\\
-In a flow-daigram of the script suite can be shown as:\\
-\\
-{\it A wrapper script}--${>}{\it da\_run\_job} --${>}{\it job.ksh}--${>}{\it da\_run\_suite}--${>}{\it components\_of\_suite script} \\
-\\
+
+In a flow-daigram of the script suite can be shown as:\vspace{0.5cm}
+
+{\it A wrapper script}---$>${\it da\_run\_job}---$>${\it job.ksh}---$>${\it da\_run\_suite}---$>${\it components\_of\_suite script}
+\vspace{0.5cm}
+
The following section provides detailed information about these scripts.
-\section{Suite Scripts}
+\section{Suite Script System}
Suite scripts are organized in two categories; control scripts and a suite script which executes run scripts of various components of the WRF system.
@@ -70,97 +44,113 @@
There are two main control scripts:
\begin{itemize}\setlength{\parskip}{-4pt}
-\item {\bf {A Wrapper Script}}\\
+\item {\bf {A Wrapper Script}}
+\vspace{0.5cm}
-A wrapper script may be needed to set up some environment variables to specify the user's experiment. This script calls {\it da\_run\_job} script.\\
+A wrapper script may be needed to set up some environment variables to specify the user's experiment. This script calls {\it da\_run\_job} script.
+\vspace{0.5cm}
-\item {\bf {da\_run\_job.ksh}}\\
+\item {\bf {da\_run\_job.ksh}}
+\vspace{0.5cm}
This script contains the logic for submitting jobs to various queuing systems, and creates {\it job.ksh} script on the fly.
-The {\it job.ksh} script understands IBM's Loadleveller and LSF queuing systems. The {\it da\_run\_job.ksh} script may need tailoring
-for the user's local machine. The {\it job.ksh} executes the main {\it da\_run\_suite} script - which is explained in the following section.\\
+The {\it job.ksh} script understands {\it Loadleveller} and {\it Load Sharing Facility} (LSF) queuing systems. The {\it da\_run\_job.ksh} script may need tailoring
+for the user's local machine. The {\it job.ksh} executes the main {\it da\_run\_suite} script - which is explained in the following section.
+\vspace{0.5cm}
\end{itemize}
\subsection{Main Suite Script and Its Components}
-The control scripts set required environmental variables and the main suite script, {\bf da\_run\_suite.ksh},
-executes various run scripts of WRF system.
+The control scripts set required environmental variables and the main suite script, {\it da\_run\_suite.ksh},
+executes various other run scripts of WRF system.
-
\begin{itemize}\setlength{\parskip}{-4pt}
-\item {\bf {da\_run\_suite.ksh}}\\
+\item {\bf {da\_run\_suite.ksh}}
+\vspace{0.5cm}
This script runs data assimilation suites, with WPS, REAL, WRF, WRFVAR, OBSPROC and UPDATEBC components.
-These are given below:\\
+These are given below:
+\vspace{0.5cm}
-\item {\bf {da\_get\_date\_range.ksh}}\\
+\item {\bf {da\_get\_date\_range.ksh}}
+\vspace{0.5cm}
This script helps for setting some environment variables such as:
-\\
-START\_YEAR\\
-START\_MONTH\\
-START\_DAY\\
-START\_HOUR\\
-END\_YEAR\\
-END\_MONTH\\
-END\_DAY\\
-END\_HOUR\\
+\vspace{0.5cm}
-\item {\bf {da\_run\_wps.ksh}}\\
+START\_YEAR
+START\_MONTH
+
+START\_DAY
+
+START\_HOUR
+
+END\_YEAR
+
+END\_MONTH
+
+END\_DAY
+
+END\_HOUR
+
+\item {\bf {da\_run\_wps.ksh}}
+\vspace{0.5cm}
+
This script runs the WPS preprocessing software.
-(The WRF Preprocessing System (WPS) is a replacement for the WRF Standard Initialization (SI) software.)\\
+(The WRF Preprocessing System (WPS) is a replacement for the WRF Standard Initialization (SI) software.)
+\vspace{0.5cm}
-\item {\bf {da\_run\_real.ksh}}\\
+\item {\bf {da\_run\_real.ksh}}
+\vspace{0.5cm}
-This script runs the WRF REAL software.\\
+This script runs the WRF REAL software.
+\vspace{0.5cm}
-\item {\bf {da\_run\_wrf.ksh}}\\
+\item {\bf {da\_run\_wrf.ksh}}
+\vspace{0.5cm}
- This script runs the WRF Model.\\
+ This script runs the WRF Model.
+ \vspace{0.5cm}
-\item {\bf {da\_run\_obsproc.ksh}}\\
+\item {\bf {da\_run\_obsproc.ksh}}
+\vspace{0.5cm}
-This script runs OBSPROC observation preprocessing software.\\
+This script runs OBSPROC observation preprocessing software.
+\vspace{0.5cm}
-\item {\bf {da\_run\_wrfvar.ksh}}\\
+\item {\bf {da\_run\_wrfvar.ksh}}
+\vspace{0.5cm}
-This script runs the WRFVAR data assimilation software.\\
+This script runs the WRFVAR data assimilation software.
+\vspace{0.5cm}
-\item {\bf {da\_update\_bc.ksh}}\\
+\item {\bf {da\_update\_bc.ksh}}
+\vspace{0.5cm}
This script runs the WRF Boundary Conditions update mechanism, used after a regional
-WRFVAR run to combine the analysis with an external lateral boundary conditions file.\\
+WRFVAR run to combine the analysis with an external lateral boundary conditions file.
+\vspace{0.5cm}
-\item {\bf {da\_restore\_data\_ncep.ksh}}\\
+\item {\bf {da\_restore\_data\_ncep.ksh}}
+\vspace{0.5cm}
-This script restores NCEP data from NCAR's MSS.
-(It is suitable for NCAR users.)\\
+This script restores NCEP data from NCAR's Mass Storage System (MSS).
+(It is suitable for NCAR users.)
+\vspace{0.5cm}
-\item {\bf {da\_restore\_data\_rtobs.ksh}}\\
+\item {\bf {da\_restore\_data\_rtobs.ksh}}
+\vspace{0.5cm}
This script restores RTOBS (an archive of conventional data) from NCAR's MSS.
-(It is suitable for NCAR users.)\\
+(It is suitable for NCAR users.)
+\vspace{0.5cm}
+
\end{itemize}
-\subsection{Ways to Check Suite Runs}
+\section{Types of Runs}
-The {\it job.ksh} script produces {\it html} based log files. Utilities such as
-{\it lynx} and {\it mozilla} can be used to display {\it html} files produced
-by the user's run. When using {\it lynx}, some instructions appear on the screen.
-A user may simply look into anything that is bold.\\
-\\
-{\bf Examples for {\it lynx} and {\it mozilla}:}\\
-\\
-{\it lynx \$/data/con200/trunk\_rsl\_xlf\_bluesky\_noobs\_1\\
-\\
-mozilla \$/data/con200/trunk\_rsl\_xlf\_bluesky\_noobs\_1}\\
-\\
-where trunk\_rsl\_xlf\_bluesky\_noobs\_1 is the directory that contains the user's run.\\
-
-\section{Run Types}
-
The suite scripts may be used to run the following types of runs:
\begin{itemize}\setlength{\parskip}{-4pt}
@@ -169,334 +159,455 @@
\item Cycling runs
\end{itemize}
-\subsection{NO DA runs}
+\subsection{NO DA Runs}
-This type of run contains: WPS, REAL and WRF.\\
-\\
-A wrapper script may be set to contain following settings:\\
-RUN\_WPS=\$\{RUN\_WPS:-true\}\\
-RUN\_REAL=\$\{RUN\_REAL:-true\}\\
-RUN\_WRF=\$\{RUN\_WRF:-true\}\\
-\\
-{\bf WPS:}\\
-\\
-{\bf Input files required:}
+Since it does not involve any data assimilation run, it is called NO DA.
+This type of run contains: WPS, REAL and WRF runs.
+\vspace{0.5cm}
+
+A wrapper script may be set to contain following settings:
+\vspace{0.5cm}
+
+RUN\_WPS=true
+
+RUN\_REAL=true
+
+RUN\_WRF=true
+\vspace{0.5cm}
+
+{\bf WPS:}
+\vspace{0.5cm}
+
+
+{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item Terrain data: wps\_geog (see WPS)
-\item Model data: NCEP's various data sets
-\item namelist.wps
+\item Terrain data: Topography data set (should be in \$WPS\_GEOG\_DIR)
+\item Model data: NCEP's various data sets (should be in \$WPS\_INPUT\_DIR)
+\item namelist.wps: Created by {\it {da\_run\_wps.ksh}} on the fly.
\end{itemize}
+
{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item geogrid: /data/test\_domain/geo/geo\_em.d01.nc
-\item ungrib: /data/test\_domain/name\_of\_experiment/wps/working/FILE:datestamp
-\item metgrid: /data/test\_domain/rc/met\_em.d01\_datestamp}
+\item geogrid: \$RC\_DIR/geo\_em.d01.nc
+\item ungrib: \$EXP\_DIR/\$DATE/wps/working/FILE:datestamp
+\item metgrid: \$RC\_DIR/\$DATE/met\_em.d01\_datestamp
\end{itemize}
-{\bf WRF\_Real:}\\
-\\
+\vspace{0.5cm}
+
+{\bf WRF\_Real:}
+\vspace{0.5cm}
+
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
\item namelist.input
-\item /data/test\_domain/rc/met\_em.d01\_datestamp
+\item \$RC\_DIR/\$DATE/met\_em.d01\_datestamp
\end{itemize}
- {\bf Output files created:}
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item /data/test\_domain/rc/DATE/wrfinput (initial conditions for WRF )
-\item /data/test\_domain/rc/DATE/wrfbdy (lateral boundary conditions for WRF)
+\item \$RC\_DIR/\$DATE/wrfinput (initial conditions for WRF )
+\item \$RC\_DIR/\$DATE/wrfbdy (lateral boundary conditions for WRF)
\end{itemize}
-\\
-{\bf WRF:}\\
-\\
+\vspace{0.5cm}
+
+{\bf WRF:}
+\vspace{0.5cm}
+
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
\item namelist.input
\item Various physics tables/files
-\item /data/test\_domain/rc/DATE/wrfinput (initial conditions for WRF)
-\item /data/test\_domain/rc/DATE/wrfbdy (lateral boundary conditions for WRF)
+\item \$RC\_DIR/\$DATE/wrfinput (initial conditions for WRF )
+\item \$RC\_DIR/\$DATE/wrfbdy (lateral boundary conditions for WRF)
\end{itemize}
-\\
- {\bf Output files created:}
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item /data/test\_domain/name\_of\_experiment/fc/DATE/wrfout\_d01\_datestamp
+\item \$FC\_DIR/\$DATE/wrfout\_d01\_datestamp
\end{itemize}
-\\
-\subsection{COLD START runs}
-These runs involve: WPS, REAL, OBSPROC, WRF-VAR and UPDATE\_BC.\\
-\\
-A wrapper script may be set to contain following settings:\\
-RUN\_WPS=\$\{RUN\_WPS:-true\}\\
-RUN\_REAL=\$\{RUN\_REAL:-true\}\\
-RUN\_OBSPROC=\$\{RUN\_OBSPROC:-true\}\\
-RUN\_WRFVAR=\$\{RUN\_WRFVAR:-true\}\\
-RUN\_UPDATE\_BC=\$\{RUN\_UPDATE\_BC:-true\}\\
-\\
-WPS and REAL runs are as in no obs runs. \\
-\\
-{\bf OBSPROC:}\\
-\\
+
+\subsection{Cold Start Runs}
+
+These runs involve: WPS, REAL, OBSPROC, WRF-VAR and UPDATE\_BC runs.
+A wrapper script may be set to contain following settings:
+\vspace{0.5cm}
+
+RUN\_WPS=true
+
+RUN\_REAL=true
+
+RUN\_OBSPROC=true
+
+RUN\_WRFVAR=true
+
+RUN\_UPDATE\_BC=true
+\vspace{0.5cm}
+
+WPS and REAL runs are as in no obs runs.
+\vspace{0.5cm}
+
+{\bf OBSPROC:}
+\vspace{0.5cm}
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
\item namelist (namelist.3dvar\_obs)
-\item /data/test\_domain/ob/DATE/obs.2006080806
+\item \$OB\_DIR/\$DATE/obs.datestamp
\end{itemize}
-\\
+
+
{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item /data/test\_domain/ob/DATE/ob.ascii
+\item \$OB\_DIR/\$DATE/ob.ascii
\end{itemize}
-\\
-{\bf WRF-Var:}\\
-\\
+\vspace{0.5cm}
+
+{\bf WRF-Var:}
+\vspace{0.5cm}
+
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
\item namelist.input
-\item DA\_FIRST\_GUESS /rc/2006080806/wrfinput\_d01 (output from REAL)\\
- (wrfinput\_d01 linked as /rc/2003050100/wrfinput\_d01)\\
- (fg01 linked as /rc/2006080806/wrfinput\_d01)
-\item ob01.ascii linked as /ob/2003050100/ob.ascii (output from OBS\_PROC)
-\item DA\_BACK\_ERRORS /be/gen\_be.NMC.dat (output from "gen\_be")\\
+\item DA\_FIRST\_GUESS: \$RC\_DIR/\$DATE/wrfinput\_d01 (output from REAL)
+
+ (wrfinput\_d01 linked as \$RC\_DIR/\$DATE/wrfinput\_d01)
+
+ (fg01 linked as \$RC\_DIR/\$DATE/wrfinput\_d01)
+\item ob01.ascii linked as \$OB\_DIR/\$DATE/ob.ascii (output from OBS\_PROC)
+\item DA\_BACK\_ERRORS: \$BE\_DIR/\$DATE/gen\_be.NMC.dat (output from "gen\_be")
+
(fort.34 linked as /be/gen\_be.NMC.dat)
-\end{itemize}
-\\
+\end{itemize}
+
{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item DA\_ANALYSIS /fc/2006080806/analysis
+\item DA\_ANALYSIS: \$FC\_DIR/\$DATE/analysis
\item Text type of output files: cost\_fn, grad\_fn, statistics
\end{itemize}
-\\
-{\bf UPDATE\_BC:}\\
-\\
+\vspace{0.5cm}
+
+{\bf UPDATE\_BC:}
+\vspace{0.5cm}
+
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
\item parame.in
-\item DA\_ANALYSIS /fc/2006080806/analysis\\
- (wrfvar\_output linked as /fc/2003050100/analysis)
-\item DA\_FIRST\_GUESS /rc/2006080806/wrfinput\_d01
-\item BDYIN /rc/2006080806/wrfbdy\_d01
+\item DA\_ANALYSIS: \$FC\_DIR/\$DATE/analysis
+
+ (wrfvar\_output linked as \$FC\_DIR/\$DATE/analysis)
+\item DA\_FIRST\_GUESS: \$RC\_DIR/\$DATE/wrfinput\_d01
+\item BDYIN: \$RC\_DIR/\$DATE/wrfbdy\_d01
\end{itemize}
-\\
+
{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item BDYOUT /fc/2006080806/wrfbdy\_d01
+\item BDYOUT: \$FC\_DIR/\$DATE/wrfbdy\_d01
\end{itemize}
-\\
-\subsection{CYCLING runs}
-These runs involve: WPS, REAL, OBSPROC, WRF-VAR, UPDATE\_BC and WRF.\\
-\\
-A wrapper script may be set to contain following settings:\\
-RUN\_WPS=\$\{RUN\_WPS:-true\}\\
-RUN\_REAL=\$\{RUN\_REAL:-true\}\\
-RUN\_OBSPROC=\$\{RUN\_OBSPROC:-true\}\\
-RUN\_WRFVAR=\$\{RUN\_WRFVAR:-true\}\\
-RUN\_UPDATE\_BC=\$\{RUN\_UPDATE\_BC:-true\}\\
-RUN\_WRF=\$\{RUN\_WRF:-true\}\\
-CYCLING=\$\{CYCLING:-true\}\\
-\\
-{\bf \It First Step:}\\
-WPS, REAL and OBSPROC runs are as in cold start runs. \\
-{\bf WRF-VAR:}\\
-\\
+\subsection{Cycling Runs}
+
+These runs involve: WPS, REAL, OBSPROC, WRF-VAR, UPDATE\_BC and WRF runs.
+A wrapper script may be set to contain following settings:
+\vspace{0.5cm}
+
+RUN\_WPS=true
+
+RUN\_REAL=true
+
+RUN\_OBSPROC=true
+
+RUN\_WRFVAR=true
+
+RUN\_UPDATE\_BC=-true
+
+RUN\_WRF=true
+
+CYCLING=true
+\vspace{0.5cm}
+
+{\bf First Step:}
+
+WPS, REAL and OBSPROC runs are as in cold start runs.
+\vspace{0.5cm}
+
+{\bf WRF-VAR:}
+\vspace{0.5cm}
+
{\bf Input files required:}
+
\begin{itemize}\setlength{\parskip}{-4pt}
-\item DA\_FIRST\_GUESS /rc/2006080806/wrfinput\_d01 (output from REAL)\\
- (wrfinput\_d01 linked as /rc/2006080806/wrfinput\_d01)
-\item DA\_BACK\_ERRORS /be/gen\_be.NMC.dat (output from "gen\_be")
-\item OB\_DIR /ob/date\_stamp/ob.ascii (output from OBS\_PROC)
+\item DA\_FIRST\_GUESS: \$RC\_DIR/\$DATE/wrfinput\_d01 (output from REAL)
+
+ (wrfinput\_d01 linked as \$RC\_DIR/\$DATE/wrfinput\_d01)
+\item DA\_BACK\_ERRORS: \$BE\_DIR/\$DATE/gen\_be.NMC.dat (output from "gen\_be")
+\item OB\_DIR: \$OB\_DIR/\$DATE/ob.ascii (output from OBS\_PROC)
\end{itemize}
-\\
-{\bf Output data created:}
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item DA\_ANALYSIS /fc/2006080806/analysis
+\item DA\_ANALYSIS: \$FC\_DIR/\$DATE/analysis
\end{itemize}
-\\
-{\bf UPDATE\_BC:}\\
-\\
+\vspace{0.5cm}
+
+{\bf UPDATE\_BC:}
+\vspace{0.5cm}
+
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item DA\_ANALYSIS: /fc/2006080806/analysis (output from WRF-VAR)
-\item DA\_FIRST\_GUESS: /rc/2006080806/wrfinput\_d01 (output from REAL)
-\item BDYIN: /rc/2006080806/wrfbdy\_d01 (output from REAL)
+\item DA\_ANALYSIS: \$FC\_DIR/\$DATE/analysis (output from WRF-VAR)
+\item DA\_FIRST\_GUESS: \$RC\_DIR/\$DATE/wrfinput\_d01 (output from REAL)
+\item BDYIN: \$RC\_DIR/\$DATE/wrfbdy\_d01 (output from REAL)
\end{itemize}
-{\bf Output data created:}
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item BDYOUT: /fc/2006080806/wrfbdy\_d01 (output from UPDATE\_BC)
+\item BDYOUT: \$FC\_DIR/\$DATE/wrfbdy\_d01 (output from UPDATE\_BC)
\end{itemize}
-\\
-{\bf WRF:}\\
-It is important to note that in cycling runs {\It wrfinput} and {\It wrfinput} files are NOT obtained from REAL.\\
-\\
+\vspace{0.5cm}
+
+{\bf WRF:}
+\vspace{0.5cm}
+
+It is important to note that in cycling runs {\bf wrfinput} and {\bf wrfbdy} files are {\it not} obtained from REAL.
+\vspace{0.5cm}
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item WRF\_INPUT /fc/2006080806/analysis (output from WRF-VAR)
-\item WRF\_BDY /fc/2006080806/wrfbdy\_d01 (output from UPDATE\_BC)
+\item WRF\_INPUT: \$FC\_DIR/\$DATE/analysis (output from WRF-VAR)
+\item WRF\_BDY: \$FC\_DIR/\$DATE/wrfbdy\_d01 (output from UPDATE\_BC)
\end{itemize}
-\\
-{\bf Output data created:}
+
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item wrfout\_d01\_datestamp
+\item \$FC\_DIR/\$DATE/wrfout\_d01\_datestamp
\end{itemize}
-\\
-{\bf \It Other Steps:}\\
- \\
-{\bf WRF-VAR:}\\
-\\
+\vspace{0.5cm}
+
+{\bf Other Steps:}
+ \vspace{0.5cm}
+
+{\bf WRF-VAR:}
+\vspace{0.5cm}
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item DA\_FIRST\_GUESS /rc/2006080806/wrfout\_d01\_datestamp (output from WRF)\\
-\item DA\_BACK\_ERRORS /be/gen\_be.NMC.dat (output from "gen\_be")
-\item OB\_DIR /ob/date\_stamp/ob.ascii (output from OBS\_PROC)
+\item DA\_FIRST\_GUESS: \$RC\_DIR/\$DATE/wrfout\_d01\_datestamp (output from WRF)
+\item DA\_BACK\_ERRORS: \$BE\_DIR/\$DATE/gen\_be.NMC.dat (output from "gen\_be")
+\item OB\_DIR: \$OB\_DIR/\$DATE/ob.ascii (output from OBS\_PROC)
\end{itemize}
-\\
-{\bf Output data created:}
+
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item DA\_ANALYSIS /fc/2006080806/analysis
+\item DA\_ANALYSIS: \$FC\_DIR/\$DATE/analysis
\end{itemize}
-\\
-{\bf UPDATE\_BC:}\\
-\\
+\vspace{0.5cm}
+
+{\bf UPDATE\_BC:}
+\vspace{0.5cm}
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item DA\_ANALYSIS: /fc/2006080806/analysis (output from WRF-VAR)
-\item DA\_FIRST\_GUESS: /rc/2006080806/wrfout\_d01\_datestamp (output from WRF)
-\item BDYIN: /rc/2006080806/wrfbdy\_d01 (output from REAL)
+\item DA\_ANALYSIS: \$FC\_DIR/\$DATE/analysis (output from WRF-VAR)
+\item DA\_FIRST\_GUESS: \$RC\_DIR/\$DATE/wrfout\_d01\_datestamp (output from WRF)
+\item BDYIN: \$RC\_DIR/\$DATE/wrfbdy\_d01 (output from REAL)
\end{itemize}
-{\bf Output data created:}
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item BDYOUT: /fc/2006080806/wrfbdy\_d01 (output from UPDATE\_BC)
+\item BDYOUT: \$FC\_DIR/\$DATE/wrfbdy\_d01 (output from UPDATE\_BC)
\end{itemize}
-\\
-{\bf WRF:}\\
-It is importnant to note that in cycling runs {\It wrfinput} and {\It wrfinput} files are NOT obtained from REAL.\\
-\\
+\vspace{0.5cm}
+
+{\bf WRF:}
+\vspace{0.5cm}
+
+It is importnant to note that in cycling runs {\bf wrfinput} and {\bf wrfbdy} files are {\it not} obtained from REAL.
+\vspace{0.5cm}
+
{\bf Input files required:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item WRF\_INPUT /fc/2006080806/analysis (output from WRF-VAR)
-\item WRF\_BDY /fc/2006080806/wrfbdy\_d01 (output from UPDATE\_BC)
+\item WRF\_INPUT: \$FC\_DIR/\$DATE/analysis (output from WRF-VAR)
+\item WRF\_BDY: \$FC\_DIR/\$DATE/wrfbdy\_d01 (output from UPDATE\_BC)
\end{itemize}
-\\
-{\bf Output data created:}
+
+{\bf Output files created:}
\begin{itemize}\setlength{\parskip}{-4pt}
-\item wrfout\_d01\_datestamp
+\item \$FC\_DIR/\$DATE/wrfout\_d01\_datestamp
\end{itemize}
-\\
+
+
{\bf Final Results of Cycling Run:}
- /fc/2006080806
+
+\$FC\_DIR/\$DATE/
\begin{itemize}\setlength{\parskip}{-4pt}
\item analysis (output from WRF-VAR)
\item wrfbdy\_d01 (output from UP\_DATE)
-\item wrfout\_d01\_2006-08-08\_06:00:00 (output from WRF)
-\item wrfout\_d01\_2006-08-08\_12:00:00 (output from WRF)
+\item wrfout\_d01\_datestamp (output from WRF)
+\item wrfout\_d01\_datestamp (output from WRF)
\end{itemize}
-\section{Environment Variables}
+\section{Ways to Check Suite Runs}
-The suites are controlled by environment variables.
-\\
-% Requires the booktabs if the memoir class is not being used
-\begin{table}[htbp]
-% \centering
- %\topcaption{Table captions are better up top} % requires the topcapt package
- \begin{tabular}{@{} lll @{}} % Column formatting, @{} suppresses leading/trailing space
- \toprule
- \multicolumn{2}{c}{\bf Environment Variables} \\
- \\
- \cmidrule % Partial rule. (r) trims the line a little bit on the right; (l) & (lr) also possible
- {\bf Variable} & {\bf Default} & {\bf Description}\\
- \\
-\midrule
- REL\_DIR & \$HOME/trunk & Top level for\\
- & & a collection of code builds\\
- WRFVAR\_DIR & \$REL\_DIR/wrfvar & Top level for wrfvar build\\
- WRF\_DIR & \$REL\_DIR/wrf &Top level for WRF build\\
- WRF\_NL\_DIR & \$REL\_DIR/wrf\_nl & Top level for WRF NL build\\
- WPS\_DIR & \$REL\_DIR/wps &Top level for WPS reconfiguration tool\\
- DATE & 2003010112 & Current date\\
- INITIAL\_DATE & 2003010100 & Date a suite starts\\
- FINAL\_DATE & 2003020100 & Date a suite ends\\
- START\_DATE & 2003010109 & Start of a date range used locally. \\
- & & No user control\\
- END\_DATE & 2003010115 & End of a date range used locally.\\
- & & No user control\\
- PREV\_DATE & 2003010106 & Previous data in cycle. No user control\\
- NEXT\_DATE & 2003010118 & Next date in cycle. No user control\\
- DAT\_DIR & \$HOME/data & Top level for all test data\\
- REGION & con200 & Region of the globe\\
- REG\_DIR & \$DAT\_DIR/\$REGION& Top level for test data for a particular region\\
- OB\_DIR & \$REG\_DIR/ob & Observation directory\\
- BE\_DIR & \$REG\_DIR/be & Background error directory\\
- RC\_DIR & \$REG\_DIR/rc & Model data reconfigured with WPS, REAL,\\
- & & often static\\
- FC\_DIR & \$EXP\_DIR/fc & Model data from WRFVAR and WRF\\
- WPS\_INPUT\_DIR & \$RC\_DIR & Input for WPS\\
- WRF\_NAMELIST & \$WRF\_DIR & Force a particular namelist for WRF\\
- & /test/em\_real/namelist.input &\\
- NCEP\_DIR & \$DAT\_DIR/ncep & NCEP global forecasts\\
- DA\_FIRST\_GUESS & \$FC\_DIR & wrfvar "first guess" input\\
- & /$DATE/wrfinput\_d01 &\\
- DA\_ANALYSIS & \$FC\_DIR/$DATE/analysis & wrfvar analysis\\
- DA\_BOUNDARIES & \$FC\_DIR & wrfvar boundaries input\\
- & /$DATE/wrfbdy\_d01 &\\
- DA\_BACK\_ERRORS & \$BE\_DIR & wrfvar background errors\\
- & /gen\_be.NMC.dat &\\
- \bottomrule
- \end{tabular}
-% \caption{Environment variables.}
-% \label{tab:booktabs}
+The {\it job.ksh} script produces {\it html} based log files. Utilities such as
+{\it lynx} and {\it mozilla} can be used to display {\it html} files produced
+by the user's run. When using {\it lynx}, some instructions appear on the screen.
+A user may simply look into anything that is bold.
+
+\vspace{0.5cm}
+
+Examples for {\it lynx} and {\it mozilla}:
+\vspace{0.5cm}
+
+{\it lynx} \$EXP\_DIR/index.html
+\vspace{0.5cm}
+
+{\it mozilla} \$EXP\_DIR/index.html
+\vspace{0.5cm}
+
+(For expanded directory names see Table 1.1.)
+\vspace{0.5cm}
+
+\begin{table}
+\caption{Environment Variables - Directories}
+\label{Environment Variables - Directories}
+$$\vbox
+{\halign{#\hfil \quad & #\hfil \quad & #\hfil \quad & # \hfil \cr
+\multispan3\hrulefill \cr
+Variables & Default & Description \cr
+\multispan3\hrulefill \cr
+REL\_DIR & HOME/trunk & Top level for code builds \cr
+WRFVAR\_DIR & \$REL\_DIR/wrfvar & Top level for WRFVAR build \cr
+WRF\_DIR & \$REL\_DIR/wrf & Top level for WRF build \cr
+WRF\_NL\_DIR & \$REL\_DIR/wrf\_nl & Top level for WRF NL build\cr
+WRF\_NAMELIST & \$WRF\_DIR & A particular namelist\cr
+ & /test/em\_real/namelist.input & for WRF\cr
+WPS\_DIR & \$REL\_DIR/wps & Top level for WPS\cr
+DAT\_DIR & \$HOME/data & Top level for all test data\cr
+ & & a particular region\cr
+NCEP\_DIR & \$DAT\_DIR/ncep & NCEP global forecasts\cr
+WPS\_INPUT\_DIR & \$NCEP\_DIR & Global or regional model data\cr
+ & & to run WPS ungrib\cr
+WPS\_GEOG\_DIR & \$DAT\_DIR/wps\_geog & Input data for WPS geogrid\cr
+REGION & con200 & Region of the globe\cr
+REG\_DIR & \$DAT\_DIR/\$REGION & Top level for test data.\cr
+OB\_DIR & \$REG\_DIR/ob & Observation directory\cr
+BE\_DIR & \$REG\_DIR/be & Background error directory\cr
+RC\_DIR & \$REG\_DIR/rc & Directory for WPS and REAL\cr
+ & & run results\cr
+EXPT & test & Identifier of experiment for\cr
+ & & a particular region\cr
+EXP\_DIR & \$REG\_DIR/\$EXPT &Top level directory for \cr
+ & & a particular experiment. \cr
+FC\_DIR & \$EXP\_DIR/fc & Directory for WRFVAR and \cr
+ & & WRF experimental run results.\cr
+DA\_FIRST\_GUESS & \$FC\_DIR/\$DATE/wrfinput\_d01 & wrfvar "first guess" input\cr
+DA\_ANALYSIS & \$FC\_DIR/\$DATE/analysis & wrfvar analysis\cr
+DA\_BOUNDARIES & \$FC\_DIR\$DATE/wrfbdy\_d01 & wrfvar boundaries input\cr
+DA\_BACK\_ERRORS & \$BE\_DIR/gen\_be.NMC.dat & wrfvar background errors\cr
+RUN\_DIR & \$EXP\_DIR/\$DATE/run & Top level run directory for\cr
+ & & a particular experiment.\cr
+WORK\_DIR & \$RUN\_DIR/working & Working directory for run,\cr
+ & & by using CLEAN flag.\cr
+\multispan3\hrulefill \cr
+}}$$
\end{table}
-% Requires the booktabs if the memoir class is not being used
-\begin{table}[htbp]
-% \centering
- %\topcaption{Table captions are better up top} % requires the topcapt package
- \begin{tabular}{@{} lll @{}} % Column formatting, @{} suppresses leading/trailing space
- \toprule
- \multicolumn{2}{c}{\bf Environment Variables} \\
- \\
- \cmidrule % Partial rule. (r) trims the line a little bit on the right; (l) & (lr) also possible
- {\bf Variable} & {\bf Default} & {\bf Description}\\
- \\
-
- RTTOV & \$HOME & RTTOV\\
- & /rttov/rttov85\_{compiler} &\\
- CRTM & \$HOME & CRTM\\
- & /crtm/crtm\_{compiler} &\\
- DA\_RTTOV\_COEFFS & \$RTTOV/rtcoef\_rttov7 & \\
- NUM\_PROCS & 1 & Number of processors for parallel jobs\\
- EXPT & test & Identifier of experiment for this region\\
- EXP\_DIR & \$REG\_DIR/\$EXPT & Top level directory for experimental run.\\
- & & Does not change\\
- RUN\_DIR & \$EXP\_DIR/\$DATE/{wrfvar} & Top level for each component.
- & & Changes during a suite run.\\
- WORK\_DIR & \$RUN\_DIR/working & Working directory for run,\\
- & & can be removed after run using CLEAN\\
- CLEAN & false & Remove \$WORK\_DIR after run\\
- DUMMY & false & A bogus run test.\\
- RUN\_CMD & mpirun -np \$NUM\_PROCS & Command to run executable.\\
- & -nolocal -machinefile \$HOSTS} & Leave blank for non mpi.\\
- HOSTS & \$PWD/hosts & hosts file for MPI runs\\
- NL\_* & & Registry produced namelist variables\\
- CHECK\_SVNVERSION & true & Check subversion release,
- & & slows down job submission,\\
- & & but is useful to document runs\\
- LL\_* & & Loadleveller control\\
- LL\_NODE\_USAGE & shared & Whether to share nodes with other jobs\\
- & & (shared/non\_shared).\\
- LL\_PTILE & 8 & Number of processors per node.\\
- & & Set to 16 to take advantage\\
- & & of SMT on bluevista\\
- LSF\_* & & LSF control\\
- LSF\_MAX_RUNTIME & 01:30:00 & Maximum wallclock time.\\
- LSF\_EXCLUSIVE & -x & Whether to share nodes with other jobs\\
- & & (-x to use, blank to not)\\
- POE & false & Use the poe job submission system.\\
- MP\_SHARED\_MEMORY & YES & IBM MPI optimisation\\
- \bottomrule
- \end{tabular}
-% \caption{Environment variables.}
-% \label{tab:booktabs}
+\begin{table}
+\caption{Environment Variables - Run Flags}
+\label{Environment Variables - Run Flags}
+$$\vbox
+{\halign{#\hfil \quad & #\hfil \quad & #\hfil \quad & # \hfil \cr
+\multispan3\hrulefill \cr
+Variables & Default & Description \cr
+\multispan3\hrulefill \cr
+RUN\_RESTORE\_DATA\_NCEP & false & For NCAR users to get\cr
+ & & data from MSS.\cr
+RUN\_RESTORE\_DATA\_RTOBS & false & For NCAR users to get\cr
+ & & obs-data from MSS.\cr
+RUN\_WPS & false & If set "true" to run WPS\cr
+RUN\_GEOGRID & false & WPS-geogrid needs \cr
+ & & to be run only once.\cr
+RUN\_REAL & false & If set "true" to run WRF\_REAL\cr
+RUN\_WRF & false & If set "true" to run WRF\cr
+RUN\_OBSPROC & false & If set "true" to run OBSPROC\cr
+RUN\_WRFVAR & false & If set "true" to run WRFVAR\cr
+RUN\_UPDATE\_BC & false & If set "true" to run UPDATE\_BC\cr
+CYCLING & false & Cold start (false), cycle (true).\cr
+FIRST & true & Cold start (false), cycle (true).\cr
+CLEAN & false & Remove \$WORK\_DIR after run\cr
+DUMMY & false & A bogus run test.\cr
+\multispan3\hrulefill \cr
+}}$$
\end{table}
+\begin{table}
+\caption{Environment Variables - Time Information}
+\label{Environment Variables - Time Information}
+$$\vbox
+{\halign{#\hfil \quad & #\hfil \quad & #\hfil \quad & # \hfil \cr
+\multispan3\hrulefill \cr
+Variables & Default & Description \cr
+\multispan3\hrulefill \cr
+DATE & 2003010112 & Current date of the suite\cr
+PREV\_DATE & 2003010106 & Previous data in cycle. (No user control)\cr
+NEXT\_DATE & 2003010118 & Next date in cycle. (No user control)\cr
+INITIAL\_DATE & 2003010100 & Date a suite starts\cr
+FINAL\_DATE & 2003010300 & Date a suite ends\cr
+START\_DATE & 2003010100 & Start of a date range used locally.\cr
+ & & (No user control)\cr
+END\_DATE & 2003010200 & End of a date range used locally.\cr
+ & & (No user control)\cr
+LBC\_FREQ & 03 & Frequency of lateral boundary conditions.\cr
+CYCLE\_PERIOD & 6 & Data assimilation cycle period.\cr
+OBS\_FREQ & 12 & Frequency of obs data set\cr
+LONG\_FCST\_TIME\_1 & 00 & Starting time for long forecast.\cr
+LONG\_FCST\_RANGE\_1 & 72 & Range of the long forecast.\cr
+\multispan3\hrulefill \cr
+}}$$
+\end{table}
-
+\begin{table}
+\caption{Environment Variables - Job Submission}
+\label{Environment Variables - Job Submission}
+$$\vbox
+{\halign{#\hfil \quad & #\hfil \quad & #\hfil \quad & # \hfil \cr
+\multispan3\hrulefill \cr
+Variables & Default & Description \cr
+\multispan3\hrulefill \cr
+NUM\_PROCS & 1 & Number of processors for \cr
+ & & parallel jobs for WRF-Var/WRF.\cr
+RUN\_CMD & mpirun \-np \$NUM\_PROCS & Command to run executable.\cr
+ & \-nolocal \-machinefile \$HOSTS & Leave blank for non mpi.\cr
+HOSTS & \$PWD/hosts & hosts file for MPI runs\cr
+NL\_* & & Registry produced namelist \cr
+ & & variables\cr
+CHECK\_SVNVERSION & true & Check subversion release,\cr
+ & & slows down job submission,\cr
+ & & but is useful to document runs\cr
+LL\_* & & Loadleveller control\cr
+LL\_NODE\_USAGE & shared & Whether to share nodes \cr
+ & & with other jobs\cr
+ & & (shared/non\_shared).\cr
+LL\_PTILE & 8 & Number of processors per node.\cr
+ & & Set to 16 to take advantage\cr
+ & & of SMT (on NCAR's IBM bluevista)\cr
+LSF\_* & & LSF control\cr
+LSF\_MAX\_RUNTIME & 01:30:00 & Maximum wallclock time.\cr
+LSF\_EXCLUSIVE & x & Whether to share nodes\cr
+ & & with other jobs\cr
+ & & (-x to use, blank to not)\cr
+POE & false & Use the poe job submission\cr
+ & & system (e.g. on IBMs).\cr
+MP\_SHARED\_MEMORY & YES & IBM MPI optimisation\cr
+PROJECT\_ID & User's default project-id & Project identification number.\cr
+\multispan3\hrulefill \cr
+}}$$
+\end{table}
</font>
</pre>