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README.md

PSU WRF Ensemble-Variational Data Assimilation System

Codes and Authors:

Control Scripts: Michael Ying (yxy159@psu.edu), Jonathan Poterjoy, Yonghui Weng. Last updated 2015/01/20

EnKF component code: Fuqing Zhang, Yonghui Weng, Michael Ying, Jonathan Poterjoy. Last updated 2014/08/01

4DVar compoent: WRFDA package from NCAR.

WRF model: from NCAR

WRFDA_4denvar: WRFDA code modified for 4DEnVar: Jonathan Poterjoy.

MULTI_INC: utility programs for running multi-incremental 4DVar

WRF_BC_v2.1_alltime: WRF_BC_v2.1 modified by Zhiyong Meng to update/perturb lateral boundary condition at a given time.


List of components

Top level files:

config/katrina_enkf configuration file(s), see README.config for details

run_cycle.sh runs cycling DA from DATE_START (initialization step) to DATE_CYCLE_END

run_forecast.sh runs forecast from analyses at each cycle to DATE_END

run_gen_be.sh runs the model and calculate be.dat from outputs using gen_be package

gen_be/ WRFDA gen_be package modified to allow parallelization

Namelists generators:

namelist_wps.sh creates namelist.wps for WPS input

namelist_wrf.sh creates namelist.input for WRF input. usage: namelist_wrf.sh use_for domain_id use_for=wrf - for WRF runs (all domains) use_for=wrfvar - for da_wrfvar.exe (1 domain) use_for=ndown - for ndown.exe (2 domains, parent and child)

namelist_wrfvar.sh creates namelist.input for da_wrfvar.exe (the &wrfvar parts)

namelist_obsproc.sh creates namelist.obsproc for obsproc.exe

Modules:

module_icbc.sh runs geogrid.exe ungrib.exe and metgrid.exe from WPS and real.exe from WRF to prepare initial and boundary conditions. input: first guess ($FG_DIR) geog ($GEOG_DIR) output: $WORK_DIR/rc/$DATE/wrfbdy_d01|wrfinput_d0?

module_obsproc.sh runs obsproc.exe to create LITTLE_R formatted inputs for EnKF and WRFDA input: raw observations data (NCAR_LITTLE_R, MADIS, BUFR, ...) output: $WORK_DIR/obs/$DATE/obs_gts_.3DVAR|4DVAR Note: if data is preprocessed, this module can be omitted.

module_perturb_ic.sh for generating ensemble perturbations. input: be.dat, $WORK_DIR/rc/$DATE/wrfinput_d01 output: 100 random perturbations (rc/random_samples) and the first NUM_ENS becomes the initial ensemble. If having nested domains, the perturbations are nested down to create wrfinput files for the nested domains.

module_enkf.sh runs the EnKF component. input: observations, $WORK_DIR/fc/$PREVDATE/wrfinput_<domain_id><member_id> output: $WORK_DIR/fc/$DATE/wrfinput_<domain_id>_<member_id> If coupled with 4DVar, the ensemble mean is replaced with 4DVar analysis If REPLACE_MEAN=true, the ensemble mean is also replaced with specified file.

module_4dvar.sh runs the 4DVar component. input: observations, fg fg02, ep (if coupled with EnKF) output: $WORK_DIR/fc/$DATE/wrfinput_<domain_id>_<DATE+OBS_WIN_MIN>

module_wrf_ens.sh runs ensemble forecast to next EnKF analysis time. The boundary condition is perturbed using random_samples. input: $WORK_DIR/fc/$DATE/wrfinput_<domain_id><member_id> $WORK_DIR/fc/wrfbdy_d01<member_id> output: $WORK_DIR/fc/$DATE/wrfinput_<domain_id><member_id>

module_wrf_window.sh runs wrf forecast from 4DVar analysis input: $WORK_DIR/fc/$DATE/wrfinput_<domain_id><DATE+OBS_WIN_MIN> $WORK_DIR/fc/wrfbdy_d01 output: $WORK_DIR/fc/$DATE/wrfinput<domain_id> (coupled with EnKF) or $WORK_DIR/fc/$DATE/wrfinput<domain_id>_<NEXTDATE+OBS_WIN_MIN> (4DVar only)

module_wrf_window1.sh runs wrf forecast across observation window input: $WORK_DIR/fc/$PREVDATE/wrfinput_<domain_id><DATE+OBS_WIN_MIN> $WORK_DIR/fc/wrfbdy_d01_window output: $WORK_DIR/fc/$PREVDATE/wrfinput<domain_id>_<DATE+OBS_WIN_MAX>

module_wrf_ens_window1.sh runs ensemble forecast across observation window (preparing for ep*) input: $WORK_DIR/fc/$PREVDATE/wrfinput_<domain_id><DATE+OBS_WIN_MIN><member_id> $WORK_DIR/fc/wrfbdy_d01_window_<member_id> output: $WORK_DIR/fc/$PREVDATE/wrfinput_<domain_id>_<bin_date>window1<member_id> bin_date=DATE+[OBS_WIN_MIN:MINUTES_PER_SLOT:OBS_WIN_MAX]

Note: A schematic work flow diagram can be found at http://hfip.psu.edu/yxy159/PSU_DA_system_work_flow.jpg

Utilities:

jstat provides a real-time summary of job status usage: jstat $WORK_DIR

job_submit.sh submit and run jobs (currently supported clusters: stampede and jet) Two possible job submit modes: If $JOB_SUBMIT_MODE=1: run_cycle.sh is submitted into queue, it requestes resources and job_submit.sh executes program. The scheduling (choreograph) of jobs are taken care of in each module. If $JOB_SUBMIT_MODE=2: run_cycle.sh is executed directly, and job_submit.sh creates separate run scripts and submit them. The scheduling is done by the queue.

util.sh utility functions including math, time calculation, work flow control, etc.

util_change_nc_att.ncl ncl script that changes ncfile global attribute values

util_linint_nc_time.ncl ncl script that interpolates a ncfile in time

calc_domain_moves.sh calculates the preset move steps for nested inner domains that follows storm, move is defined by input tcvitals data ($TCVITALS_DIR)

calc_ij_parent_start.sh calculates initial nested domain locations in the parent domain according to tcvitals data

multi_physics_draw.sh if multi-physics ensemble is used, this randomly assign physics options in module_perturb_ic.sh. The following namelist_wrf.sh will read wrfinput files to get options instead of from configuration file.

multi_physics_reset.sh for deterministic runs, this resets the physics options to that defined in the configuration file for wrfinput files.


Notes on some specific functionalities:

Boundary condition file

At DATE_START, a wrfbdy_d01 file contains time steps form DATE_START to DATE_END is created. The update/ perturbation of boundary condition all happen to the same file, but at different time steps (n_1 option in WRF_BC_v2.1_alltime). A different copy is made for each member wrfbdy_d01_<member_id> and for different purpose: wrfbdy_d01 is for module_wrf_window.sh, wrfbdy_d01_window is for module_wrf_window1.sh.

Analysis time is different for EnKF/4DVar

In run_cycle.sh DATE starts from DATE_START and loops over all assimilation cycles (DATE_CYCLE_START to DATE_CYCLE_END). The analysis time for EnKF is $DATE and for 4DVar is $DATE+$OBS_WIN_MIN. [OBS_WIN_MIN OBS_WIN_MAX] defines the window in which observations are assimilated for the current cycle. For example, if the window is [-3 3] and DATE=6, the EnKF component will assimilate data from 3 to 9 and assume they are all valid at 6, while 4DVar will assimilate observations 3, 4, ..., 9 (7 bins) so that observations are assimilated at the correct time. The bin size can be adjusted by MINUTES_PER_SLOT(1). All numbers in hour units in this paragraph, but in minutes in configuration files.

For hybrid method, extra wrf runs are necessary to match the different analysis times:

  1. previous module_wrf_ens.sh will save ensemble at DATE+OBS_WIN_MIN and calculate mean -> fg
  2. module_wrf_window1.sh integrates fg to DATE+OBS_WIN_MAX -> fg02
  3. module_wrf_window.sh integrates 4DVar analysis at DATE+OBS_WIN_MIN to DATE -> replace ensemble mean

E4DVar vs 4DEnVar

The difference between 4DEnVar and E4DVar is that 4DEnVar uses a set of ensemble perturbations to approximate U(t)=M(t)U, therefore not using tangent linear and adjoint models. To generate ensemble perturbations, an extra ensemble forecast is run through the observation window (module_wrf_ens_window1.sh). E4DVar only need ep at the beginning of observation window, while 4DEnVar needs ep for all observation bins.

Nested domains

Currently the nested domains performs data assimilation separately, there could be discontinuity created by assimilation different amount of observations. We hope that the model will damp out the discontinuity just like the assimilation-induced imbalances. But there are still on-going development for solving this problem.

Moving (storm-following) nested domains

Data assimilation is performed for each domain separately, for 4DVar the domains should not be moving, thus fg and fg02 (and possible ep files) should come from fixed domain runs. For 4DEnVar, the eps should also come from fixed domain runs. On the other hand, the ensemble forecast and deterministic runs from analysis should still be moving domain runs. In the schematic diagram (in 1), pink denotes moving domain runs and yellow denote fixed domain runs.

CPU choreography

Ensemble forecast requires NUM_ENS*wrf_ntasks, all cpus on a node are utilized: wrf_ppn=HOSTPPN. If run_cycle.sh header specifies total_ntasks=NUM_ENS*wrf_ntasks, all runs will complete at the same time. If total_ntasks is smaller, the runs will complete in more than one batchs.

For EnKF/4DVar, due to larger memory demand we need to use smaller ppn, say enkf_ppn=4 (HOSTPPN=16). enkf_ntasks=NMCPU*NICPU*NJCPU and is usually set to (NUM_ENS+1)*1*1 (no domain decomposition). If total_ntasks is set to NUM_ENS*HOSTPPN (NUM_ENS nodes), 3 EnKFs can be run simultaneously with each EnKF occupying (NUM_ENS+1) CPUs or (NUM_ENS+1)/(HOSTPPN/enkf_ppn) nodes.

So far, no choreography designed for hybrid runs, since 4DVar and EnKF can be run simultaneously, it's hard to avoid conflicts over resources. So recommend using JOB_SUBMIT_MODE=2 for hybrid runs.


Installation tips and test case:

  1. Unpackage and compile all necessary code packages

  2. Modify run_cycle.sh header to assign CPU resources. The header should conform to your system's requirements. Modify the total_ntasks part (the name of system variable may be different). If necessary, modify job_submit.sh or even add your own execution lines.

  3. Modify configuration files to setup your experiment, change paths to the code packages, data files. Some model/DA options are given in the configuration file, if you want to personalize an option that's not in the configuration file, go modify the corresponding namelist generator/ module. The lowest part assigns CPU usage to different components (WRF runs, EnKF, 4DVar, etc)

  4. Submit/execute run_cycle.sh

  5. Check job status either by looking at standard error/output from run_cycle.sh, or use jstat to get a more dynamic look of each component's status

  6. Once completed, you will have analysis for each assimilation cycle, then run_forecast.sh to run forecast from these analyses.

Test case - Hurricane Katrina (2005)

A sample configuration file has been setup for the Katrina case: config/katrina_enkf

Test case data set can be found here: http://hfip.psu.edu/yxy159/katrinaTestData.tar

Once you completed steps 1 and 2, set DATA_DIR to the test data directory, then just submit/execute run_cycle.sh.

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