GSI Setup, Run and Namelist

Transcription

1 GSI Setup, Run and Namelist Hui Shao GSI Community Tutorial, June 28-30, 2010, Boulder, CO

2 Observation Error Observation Observation processing and assimilation PrepBUFR and BUFR processing: 06/29, Tue Community Tools (1): PrebBUFR Converter: 06/29, Tue Satellite Radiance Assimilation: 06/29, Tue Radar Observation Assimilation: 06/30, Wed GPS RO Data Assimilation: 06/30, Wed Advanced GSI 4D-Var: 06/30, Wed GSI Background Background Error Output GSI Diagnostics: 06/29, Tue Analysis and diagnostics Overall Overview of GSI: 06/28, Mon GSI Code (SE Aspect): 06/28, Mon GSI Setup, Run and Namelist: 06/28, Mon Background Error and Observation Background and Observation Error Estimation and Tuning: 06/29, Tue Community Tools (2): GEN_BE: 06/29, Tue

3 Outline Installing GSI Running GSI Cycling, partly cycling, cold-start Basic runtime options (namelist) This talk is tailored based on GSI Community Release V2.0.

4 Installing GSI (Community Release only) For people who are using the NCEP version of GSI, please be aware the installation procedure and portability of the GSI code might be different from the community release.

5 Source Codes Download GSI source code (comgsi_v2.tar.gz) from o Unpack the tarball, you may use the command tar zxvf comgsi_v2.tar.gz or gunzip comgsi_v2.tar.gz and tar xvf comgsi_v2.tar

6 GSI Core and Extra Features makefile clean configure compile GSI Community Release until/ arch/ NCEP GSI Repository run/ fix/ src/ libs/ fix main/ src makefile scripts

7 Fortran Compiler Supported and Tested Platforms IBM: xlf LINUX: pgi 7.0,8.0,9.0 LINUX: Intel 10.0 and 11.0 MAC OSX: PGI 8.0 Supported and Tested by a 3rd party SGI Altix: Intel 10.0 o Use which (e.g., which xlf) command to find the compiler path. o To check version number, use xlf qversion, pgf90 V and ifort v for xlf, pgi and Intel Fortran compilers. Please share with us your experience on the various platforms and compilers.

8 External Libraries Required by GSI netcdf (network Common Data Form) v3.6+ (not v4.0 yet): WRF I/O API (WRF I/O and Model Coupling Application Program Interface) v3.2: WRF-ARW or NMM provided in the same tar file or ESSL (IBM) or LAPACK and BLAS (LINUX and MAC OSX) ESSL (Engineering and Scientific Subroutine Library): Usually, the IBM compiler automatically set up the ESSL. No manual set up required. LAPACK (Linear Algebra PACKage): BLAS (Basic Linear Algebra Subprograms): LINUX: usually, the PGI compiler automatically set up the lib. LINUX: Intel compiler, please set up the lib manually. MAC OSX: PGI compile, please set up the lib manually. To set up environment variable. o csh/tcsh users: use setenv (e.g., setenv NETCDF $netcdfpath) o bash/ksh users: use export (e.g., export NETCDF $netcdfpath)

9 Internal Libraries Required by GSI in the GSI tarball) Name (~/src/libs) (included Description crtm_gfsgis makefile NCEP BUFR Library JCSDA clean Commuity Radiative Transfer Model (CRTM) gfsio configure Unformatted Fortran record for GFS I/O sfcio NCEP GFS surface file I/O module compile sigio NCEP GFS atmospheric file I/O module until/ bufr sp w3 GSI Community Release NCEP spectral-grid transforms (global application only) arch/ NCEP GSI run/library (date/time manipulation,repository NCEP W3 GRIB) fix/ src/ libs/ fix main/ src makefile scripts No manual setup/compilation required if you use configure/compile utility provided by the GSI tarball.

10 Configure and Compile GSI makefile clean configure compile until/ GSI arch/ Functions: Community NCEP GSI run/ Release Checks the system hardware and software (netcdf, WRF, andrepository math libraries). Offers the user choices forfix/ configuring GSI. fix Creates configure.gsi, which containslibs/ compilation options, paths, rules, src/ etc. specific to your computer and compiler choice, and cansrc be edited to main/ change compilation options, if desired. scripts Compiles both internal libraries and GSImakefile source code and create gsi.exe.

11 Configure GSI > cd $your_sourcecode_dir/comgsi_v2 >./configure./configure.gsi will be created if succeed. Example 1: NETCDF path was set up but not WRF directory Will use NETCDF in dir: /usr/local/netcdf ** WARNING: No path to WRF_DIR and environment variable WRF_DIR not set. ** would you like to try to fix? [y] Example 2: Compilation options on IBM Will use NETCDF in dir: /usr/local/netcdf Will use WRF in dir: /ptmp/huishao/tutorial/comgsi_v2/../wrfv Please select from among the following supported platforms. 1. AIX 64-bit (dmpar) 2. AIX 32-bit (dmpar) dmpar: distributed-memory parallel Enter selection [1-2] : For unsupported platforms, you may start from ~/comgsi_v2/arch/configure.defaults. Change the settings for your platform then rerun configure.

12 Compile GSI > cd $your_sourcecode_dir/comgsi_v2 >./compile (or./compile >& $your_log_filename) ~/comgsi_v2/run/gsi.exe will be created if succeed. Get help on the compilation: >./compile h Clean the GSI directory before making your next compilation: >./clean -a

13 Running GSI The following is tailored for 3D-Var and regional applications.

14 Example: GSI in a WRF System xlbc Background Preprocessing (WPS, real) xb xf Cycled Background Cold-Start Background yo, Background Error (gen_be) R GSI B0 xa Update Lateral & Lower BCs (UPDATE_BC) Forecast (WRF) Blue --> Supported by GSI Team

15 GSI Input and Output Namelist Observation GSI Background Statistical and control files ( fixed ) Background Observation Error Error Analysis and diagnostics

16 Before You Run Check GSI executable has been created approximately ~/comgsi_v2/run/gsi.exe Obtain background files Depending in which mode (cycling or cold start) the GSI is run, the background files for the GSI can either come from the forecast from the previous cycle or from any other model simulations or forecasts. WRF NMM input field in binary format WRF NMM input field in netcdf format WRF ARW input field in binary format WRF ARW input field in netcdf format GFS input field in binary format GMAO global model input field in binary format

17 Before You Run Obtain observation files. The NCAR CISL Research Data Archive (RDA): NCEP public server: NCAR Mass Storage System (MSS): authorized access GSD Mass Storage System: authorized access Or any places you may obtain PREPBUFR formatted data: conventional (including satellite derived data) BUFR formatted data: satellite radiance, radar reflectivity, GPS radio occultation(ro) refractivity/bending angle GSI can run pseudo single observation test (PSOT) without real observations.

18 Before You Run Check statistic and control files under ~/comgsi_v2/fix Background errors (BE) nam_nmmstat_na (nam_glb_berror.f77_little_endian): computed from NCEP NAM statistics nam_glb_berror.f77 (nam_glb_berror.f77_little_endian): computed from NCEP GFS statistics Or you may produce your own BE using the community tool GEN_BE (talk on 06/29) Observation errors nam_errtable.r3dv Observation data control file (info files) Global_convinfo.txt: Conventional obs. Information file Global_pcpnfo.txt: Satellite channel information file global_satinfo.txt: precipitation rate observation information file Bias correction used by radiance analysis Global_satangbias.txt: Satellite scan angle dependent bais correction file ndas.t06z.satbias.tm03: satellite variational bias correction coefficient file Radiance coefficient used by CRTM (~/comgsi_v2/fix/crtm_gfsgsi) 18

19 Set up GSI We do provide a sample run script for you to start from ~/comgsi_v2/run/run_gsi.ksh The following slides will describe the basic steps for running GSI, assuming conventional data are assimilated. Create a working directory ($WORK_ROOT in run_gsi.ksh), for example, your_choice_of_ working_dir. > mkdir your_choice_of_working_dir Go into the working directory: > cd your_choice_of_working_dir

20 Working Directory - Input > cp ~/comgsi_v2/run/gsi.exe ($GSI_EXE)./gsi.exe > cp your_bk_dir// /arw_wrfinput_d01_ _00:00:00 ($BK_FILE)./wrf_inout > ln -s your_dat_dir/ /obs/le_nam.t00z.prepbufr.tm00.nr ($PREPBUFR)./prepbufr >cp ~/comgsi_v2/fix/nam_glb_berror.f77 ($BERROR)./berror_stats >cp ~/comgsi_v2/fix/global_convinfo.txt ($CONVINFO)./convinfo >cp ~/comgsi_v2/fix/nam_errtable.r3dv ($OBERROR)./errtable > Set up your own GSI namelist and name it as./gsiparm.anl The background file will be replaced after running GSI therefore please make sure it is copied to the working directory (instead of using link command).

21 Observation File Names Used in GSI (GSI Users Manual-Chapter 3)

22 Fixed File Names Used in GSI (GSI Users Manual-Chapter 3)

23 Running GSI > gsi.exe >&! stdout (or your own log file name) If running in distributed-memory mode, you need to set up the computer resources (e.g., processor numbers, memory, wallclock ) based on the platform you are using. GSI finished but not necessarily succeed!

24 Working Directory - Output Please refer to the talk GSI diagnostics for more information. In your_choice_of_working_dir, you may have the following files after running GSI successfully: stdout Standard text output file, which is the most often used file to check GSI analysis processes as well as basic and important information about the analyses. We will explain the content of stdout in Section 4.1 and users are encouraged to read this file in detail to get an idea about GSI process order. Fort.201(202,203, ) statistic results of observation innovations according to observation variables. Diag_conv(amsu_n1 5, )_ges_* (Depends on the etup of the namelist option write_diag): diagnostic files for conventional observations at initial analysis step (background) Diag_conv(amsu_n1 5, )_anl_* (Depends on the etup of the namelist option write_diag): diagnostic files for conventional observations at final analysis step Conv(sat )info Information about data usage Wrf_inout Analysis xa (only if using WRF background).

25 Working Directory - Output Some intermediate files:

26 Run_gsi.ksh: Structure Ask for computer resources to run GSI Set environment variables for the machine Set experiments variables (experiment name, analysis time, background and observation) Check the definition of required variables Generate a run directory for GSI (working or temp directory) Copy GSI executable to run directory Copy background file to run directory Copy or link observations to run directory Copy fixed files to run directory Generate namelist for GSI Run the GSI executable Save the GSI analysis results 26

27 Run_gsi.ksh: Setup (Example from Practical Sessions) # Machine dependent configuration GSIPROC=1 ARCH= LINUX_PGI # analysis time (YYYYMMDDHH) ANAL_TIME= # working direcotry, where GSI runs WORK_ROOT=/data1/class05/GSI/gps_arw_${ANAL_TIME} # path and name of background file BK_FILE=/wrfhelp/GSI/Datafiles/ /arw_wrfinput_d01_ _00:00:00 # path of observations OBS_ROOT=/wrfhelp/GSI/Datafiles/ /obs PREPBUFR=/wrfhelp/GSI/Datafiles/ /obs/le_nam.t00z.prepbufr.tm00.nr # path of fix files FIX_ROOT=/data1/class05/GSI/comGSI_v2/fix # path and name of the gsi executable GSI_EXE=/data1/class05/GSI/comGSI_v2/run/gsi.exe #which WRF core is used as background (NMM or ARW) bk_core=arw # which background error covariance and parameter will be used (GLOBAL or NAM) bkcv_option=nam 27

28 Running OptionsNamelist Run_gsi.ksh has the namelist inside the script.

29 What is a Namelist? The Fortran namelist (namelist.input) file helps the user to configure a GSI run without recompiling the code. Specific Fortran 90 namelist format &namelistname / - start - end Description of WRF-Var namelist variables are given in GSI User s Guide and gsimod.f90.

30 GSI Namelist &SETUP miter=2,niter(1)=5,niter(2)=5, write_diag(1)=.true.,write_diag(2)=.false.,write_diag(3)=.true., qoption=1, gencode=78,factqmin=0.005,factqmax=0.005,deltim=$deltim, ndat=59,npred=5,iguess=-1, oneobtest=.false.,retrieval=.false.,l_foto=.false., use_pbl=.false., $SETUP / &GRIDOPTS JCAP=$JCAP,NLAT=$NLAT,NLON=$LONA,nsig=$LEVS,hybrid=.true., wrf_nmm_regional=.false.,wrf_mass_regional=.true., diagnostic_reg=.false., filled_grid=.false.,half_grid=.true.,netcdf=.true., regional=.true.,nlayers(63)=3,nlayers(64)=6, $GRIDOPTS

31 GSI Namelist SETUP: General control variables. GRIDOPTS: Grid setup variab;e, including global regional specific namelist variables. BKGERR:Background error related variables. ANBKGERRAnisotropic background error related variables. JCOPTS: Constraint term in cost function (Jc) STRONGOPTS: Strong dynamic constraint. OBSQC: Observation quality control variables. OBS_INPUT: Input data control variables. SPEROB_RADAR: Level 2 BUFR file of radar wind superobs. LAG_DATA: Lagrangian data assimilation related variables. SINGLEOB_TEST: Pseudo single observation test setup.

32 GSI Namelist-SETUP Nhr_assimilation: Assimilation time interval (currently 6 hours for global, 3 hours for regional )

33 GSI Namelist-SETUP(cont.) miter=2: number of outer loops of analysis. niter(1)=50: maximum iteration number of 1st inner loop iterations. Inner loop will stop either reach this maximum number or reach convergence condition or broken. niter(2)=50: maximum iteration number of 2nd inner loop iterations Niter_no_qc: Inner loop iteration at which to turn on variational quality control

34 GSI Namelist-SETUP(cont.) qoption = 1 or 2: option of moisture analysis variable; 1:q/ qsatg 2:normalized RH When qoption=1, the moisture analysis variable is pseudo- relative humidity. The saturation specific humidity, qsatg, is computed from the guess and held constant during the inner loop. Thus, the RH control variable can only change via changes in specific humidity, q. When qoption=2, the moisture analysis variable is normalized RH. In this formulation we allow RH to change in the inner loop via changes to surface pressure (pressure), temperature, or specific humidity.

35 GSI Namelist-SETUP(cont.) Diag_rad, diag_pcp, : logical to turn off or on the diagnostic radiance file (true=on) Write_diag: Logical to write out diagnostic files for outer iteration

36 GSI Namelist-GRIDOPTS regional: if true, perform a regional GSI run using either ARW or NMM inputs as background. If false, perform a global GSI analysis. wrf_nmm_regional: if true, background comes from WRF NMM. When use WRF ARW or perform a global analysis, set it to false. wrf_mass_regional: if true, background comes from WRF ARW. When use WRF NMM or perform a global analysis, set it to false. netcdf: if true, wrf files are in NETCDF format, otherwise wrf files are in binary format. This option only works for performing a regional GSI analysis.

37 GSI Namelist-GRIDOPTS(cont.) Nlon_regional: Number of x grid point in whole regional domain Nlat_reginoal: Number of y grid point in whole regional domain Nsig: number of sigma levels

38 GSI Namelist-BKGERR Refer to the talk Background Errors Estimation and Tuning

39 GSI Namelist-ANBKGERR Currently used in the RTMA operational run (for surface data analysis) and some hurricane studies. Research topic?

40 GSI Namelist-SETUP ndat=43: number of observation variables (not observation types). This number should be consistent with the lines in OBS_INPUT. So if adding a new observation variable, ndat must be incremented by one and one new line is added in OBS_INPUT. Based on dimensions of the variables in OBS_INPUT (e.g., dfile), the maximum value of ndat is 100.

41 GSI Namelist-OBS_INPUT dfile(01)='prepbufr': observation file name. The observation file contains observations used for a GSI analysis. This file can include several observation variables from different observation types. The file name is default in GSI and cannot be changed. dtype(01)='ps': analysis variable name that GSI can read in and handle. As an example here, GSI will read all ps observations from the file prepbufr. Please note this name should be consistent with that used in the GSI code. Otherwise, GSI will give a warning message like: this is unknown observation variables and it will not be used in GSI analysis

42 More or less namelist variables? Need to check other talk