- 2Compiling input files on Abel
- 6Real.exe
Geo WPS allows to track your geographic position using macOS wi-fi geo-tracking and other available hardware inside and connected to your Mac to detect your coordinate in the best precise way via Apple core location. Geo WPS is an alternative to Apple map, it uses the well know OpenLayers map databases. The GeoServer WPS extension includes a request builder for testing out WPS processes through the Web administration interface. This tool can also be used to demonstrate processes, and construct your own examples. Accessing the request builder¶ To access the WPS Request Builder.
About WRF
The WRF ARW model is a fully compressible, nonhydrostatic model (with a hydrostatic option). Its vertical coordinate is a terrain-following hydrostatic pressure coordinate. The grid staggering is the Arakawa C-grid. The model uses higher-order numerics. This includes the Runge-Kutta 2nd- and 3rd-order time integration schemes, and 2nd- to 6th-order advection schemes in both horizontal and vertical directions. It uses a time-split small step for acoustic and gravity-wave modes. The dynamics conserves scalar variables.
[ARW Online Tutorial]
This work flow may need some modifications, especially after updates on Abel, but this general overview should work (given that the model has been set up for your user). See also the WRF user guide, from page 5-7 (pdf version in the bottom left corner of that web page).
Compiling input files on Abel
Compile WPS
Log on to Abel.uio.no.
- ssh -YC irenebn@abel.uio.no
- cd WRF
In case of new updates on Abel, several overlapping modules may exist, which in turn leads to conflict. The following commands loads the correct modules.
- module list
- module --version
- module unload <modulenames>
- module load netcdf.intel
For each logon, wps.intel_setup.sh must be run. Alternatively, this can be done automatically in the script .bash_login . The file wpsintel_setup.sh should look like this before sourcing it.
- emacs wpsintel_setup.sh &
Then, source it:
- source ../wpsintel_setup.sh
If the input data is in a different folder than @abel:~/WRF/WPS, link the gribfiles of your input to /WPS, and copy the namelist file into /WPS:
- cd WPS
- cp <file path to the namelist.wps> .
- ./link_grib.csh <file path to gribfiles>
Update the domain resolutions and dates in namelist.wps
- emacs namelist.wps &
Run intel_setup.sh from the folder @abel:~/WRF
- cd ..
- source intel_setup.sh
- ./clean -a
Configure and compile WPS. Use compiler number 20, (linux NO_GRIB)
- cd WPS
- ./configure
- 20
- ./compile >& comp.log
The output will be written to the file comp.log. You may log on to abel from a different terminal and access this file while it is compiling, using:
- tail -f comp.log
Geogrid.exe
To produce NC files called geo_em..., run geogrid.exe. First, a namelist.wps must be created for the correct domain and time step. WRF Domain wizard or WRFPortal may be used to visualise the wanted domain. Please note that the data ordered must cover a greater region than the wanted domain.
To look at the ordered gribfiles, (for instance to check which variables are ordered at which times and atmospheric levels), install g1print or grib_ls.
- g1print.exe ../gribfiler/ma20080808.mars
- grib_ls ../gribfiler/ma20080808.mars
Then run geogrid.exe.
- ./geogrid.exe >& geogrid.log
Check if the run was sucessful:
- tail geogrid.log
and see if the geo_em.d*.nc files were produced
- ls -l
To view a summary of the .nc file, type
- ncdump -h geo_em.d01.nc
Ungrib.exe
If the Vtable files are in a different folder, they must be linked to @abel/WRF/WPS:
- ln -sf <file path to Vtable files>Vtable.ECSURF Vtable
If the input data is in a different folder than @abel:~/WRF/WPS, link the gribfiles of your input to /WPS using link_grib.csh:
- ./link_grib.csh <file path to gribfiles (.mars)>
Check that the links are produced (using ll or ls -l) and check that the namelist file refers to the following under &Ungrib: prefix=SURF
- more namelist.wps
Now, run Ungrib to produce SURF files for each date.
- ./ungrib.exe >& ungrib.log
- tail ungrib.log
Also, check that files on the form SURF:1992-01-31_00 have been made.
To produce ATM files, linked the Vtable to @abel/WRF/WPS using:
- ln -sf <file path to Vtable files>Vtable.ECATM Vtable
Check that the links are produced (using ll or ls -l) and check that the namelist file refers to the following under &Ungrib: prefix=ATM
- more namelist.wps
Now, run Ungrib to produce ATM files for each date.
- ./ungrib.exe >& ungrib.log
- tail ungrib.log
Similarly, check that files on the form ATM:1992-01-31_00 have been made.
If you get the error message ERROR: Grib2 file or date problem, stopping in edition_num., try the following (and the first time you open emacs, ensure that prefix=ATM and the second time, change it to prefix=SURF):
(Inspiration from the WRF forum)
Metgrid.exe
First, link up the correct METGRID.TBL
- ln -sf <file path to METGRID.TBL files>METGRID.TBL METGRID
- ln -sf WPS/metgrid/METGRID.TBL.ARW METGRID
To produce met_em ... .nc files, run
- ./metgrid.exe >& metgrid.log
- tail metgrid.log
Visualise the input files on Rossby or Sverdrup
To check the input files, log on to rossby (which has NCview installed), and copy all nc files produced at Abel.
- ssh -YC irenebn@rossby.uio.no
- scp irenebn@abel.uio.no:~/WRF/WPS/met_em* .
- ncview met_em_d01...
In NCview, click the 3Dvar and choose any parameter.
Summary of calls to run WPS
tail geogrid.log
Compiling WRF on Abel
Open namelist.wps before navigating to @abel~/WRF/WRFV3/run, where namelist.input is opened and corrected. Make sure that the date, time resolution, and e_we and e_sn are correct. Check the WRF user guide, p 5-25 (pdf version in the bottom left corner).
- emacs namelist.wps &
- cd ../WRFV3/run
- emacs namelist.input &
Link the met_em files to the folder @abel~/WRF/WRFV3/run
- ln -sf ../../WPS/met_em*
Real.exe
To produce wrfinput and wrfbdy, prepare a namelist.input and run real.exe via SBATCH or qlogin. First, link to the met_em* files:
- ln -sf ../../WPS/met_em* .
For large jobs, it must be run in parallel. One possibility is to use qlogin:
- qlogin --account=geofag --ntasks-per-node=8 --nodes=1 --mem-per-cpu=4000M
- source /cluster/bin/jobsetup
- ulimited -s unlimited
- mpirun real.exe
- squeue -U geofag
This can also be specified in a batch file wrfintel_setup.sh. In that case, run source wrfintel_setup.sh before mpirun real.exe.
The job is finished when your username disappears from the queue. Check that the run was successful (the files rsl.out and rsl.error.0000 should be produced):
- squeue -U geofag
- tail rsl.out
- tail rsl.error.0000
- grep -i error rsl.*
- grep cfl rsl.error.*
- grep -i warning rsl.*
- exit
Then quit qlogin using exit.
To delete a job, run
- scancel JOBID <number>
WRF.exe
To run WRF, all of the steps above are required, that is, producing geogrid, metgrid and ungrib, and running real.exe. WRF.exe is also run in parallel on Abel, from the folder @abel~/WRF/WRFV3/run. Check the following in the file wrf_job_intel.sh, depending on your job:
- Constraint...
- emacs wrf_job_intel.sh &
- sbatch wrf_job_intel.sh
- squeue -U geofag
Depending on the size and the number of nodes, the job may take a while. The job is finished when your username disappears from the queue. Check that the run was successful (the files rsl.out and rsl.error.0000 should be produced):
- cd WrfJob_<date>
- squeue -U geofag
- tail rsl.out
- tail rsl.error.0000
- grep -i error rsl.*
- grep -i warning rsl.*
- grep cfl rsl.error.*
- grep cfl wrf.out
- exit
Geo Wostenholm & Sons
Visualise the output files on Rossby or Sverdrup
To check the output files, log on to rossby (which has NCview installed), and copy all nc files produced at Abel.
- ssh -Y irenebn@rossby.uio.no
- scp irenebn@abel.uio.no:~/WRF/WRFV3/run/WrfJob<date>/wrfout* .
- ncview wrfout...
In NCview, click the 3Dvar and choose any parameter. The parameter VEGFRA should give an impression of the map.
Geo Wostenholm Ixl