Login to ECMWF Cray
Each participant will have a training user account on the ECMWF Cray system. This is different from the user account on the classroom computers.
Begin by logging onto the Cray login nodes:
ssh troifsXX@ccb <<< use your Cray user id Password: xxxxxxxx troifs@ccb-login2:~>
The contents of the account should look like:
troifs1@ccb-login2:~> ls bin oifs38r1 scratch
If any are missing please let us know.
Directory: oifs38r1
This directory contains the OpenIFS source code and OpenIFS executable.
For the purpose of this workshop, the model has already been compiled to avoid delay and adding unnecessary load to the login nodes.
Exercise
Examine the files in the oifs38r1 directory if you are unfamiliar with the OpenIFS model.
Directory: scratch
This is the directory in which we will run OpenIFS.
Creating the OpenIFS ensemble experiment
An ensemble experiment consists of a 'control' and multiple 'perturbed' forecasts, or 'ensemble members'. For the operational ECMWF ensemble forecast, 50 members are used.
For this exercise, to save computer time, each participant will run a single, different 'ensemble member' and we will create the complete forecast ensemble from the individual ensembles run by the class as a whole.
The exercises show how to create the experiment directories, prepare the jobs and submit them to the ECMWF Cray.
createENS command
Use the command createENS
to create the ensemble experiment:
Please only use the 2013102400 start date to ensure we can create the full ensemble from everyone's runs.
Use the createENS command to create an ensemble with just a single member
createENS -d 2013102400 -m 1
createENS --help usage: createENS [-h] -d <startdate/enddate/hr_inc> [-m <members>] Set up ensemble forecast for the OpenIFS 2015 workshop optional arguments: -h, --help show this help message and exit -d <startdate/enddate/hr_inc>, --date <startdate/enddate/hr_inc> List of date(s) to retrieve, format: YYYYMMDDHH. The only dates available are: 2013102400/2013102700/24 -m <members>, --members <members> Number of ensemble members to create e.g. 3 (default 1)
Exercise
Change to the experiment directory labelled by the date chosen:
cd scratch/ENFO/2013102400/
There are two experiment directories: cf000 and pf001. cf000 is for the control forecast which is not used here. pf001 is the single perturbation forecast.
cd pf001 ls
Understand what the different files in the experiment directory are for.
Initial files
ICM* : these are the initial starting files. ICMGG* are the initial gridpoint files, ICMSH* are the initial spectral fields.
Note that part of the file name is 'oifs'. This is known as the 'experiment id' (exptid). It is also encoded into the Grib file itself.
Use the 'grib_ls' command to examine the initial files:
grib_ls ICMGGoifsINIT grib_ls ICMSHoifsINIT
Fortran namelist
The file: namelistfc is the model 'NAMELIST'. It contains a list of variable settings or 'switches' that control what the model does. These variables are grouped into separate fortran namelists.
The model will read this file when it starts up. There are many options to control the model. For more information, it is best and recommended to check the comments in the code. Please ask if you are interested.
Creating the OpenIFS namelist
Set the ensemble member
In IFS, each ensemble member uses the stochastic physics schemes to generate uncertainty. A random number 'seed' is used by the stochastic scheme to generate a different forecast. This random number seed is changed by altering the ensemble member value in the model's namelist. Each ensemble member must have a unique number and therefore random number seed, in order to produce a different forecast.
Exercise
Make sure you are in the 'pf001' directory.
Make a copy of the namelist file and edit it to set the ensemble member value to the one you are given.
cp namelistfc mynamelist gedit mynamelist # or use your favourite text editor; vi, emacs etc.
and make the following changes to the namelist variables:
CTYPE="pf", ! change the type of forecast to 'perturbed' from 'control' NENSFNB=2, ! change the ensemble member number to your assigned value.
LSTOPH_SPBS=true, ! this enables the stochastic backscatter scheme in the model dynamics LSPSDT=true, ! this enables the stochastic scheme for the physics tendencies
The variable NENSFNB is important as this determines the random number seed used by the stochastic schemes, by altering the ensemble member value.
diff mynamelist namelistfc
This is different from how the ensemble would be run in practice. Ensemble member '2' would be run in directory pf002, member number '3' in pf003 and so on. But to keep this exercise simple, everyone will use the same experiment directory name but with a different ensemble member number.
Create and submit Cray batch job
The next steps are to create and submit a batch job to run on the ECMWF Cray XC30 system.
To create the batch job, use the oifs_run command. This creates a small batch job file ready to submit.
oifs_run -e exptid [-l namelist] [-f fcast len]
For this exercise the only arguments to use are: -e, -l, -f. Other options are available which can be left to their default values.
Note! the -f argument, the length of the forecast, is specified as: dNN, for example d10 means '10 days'.
Exercise
Use the oifs_run
command to create the job.
The exptid to use with the '-e' options passed to oifs_run
must be "oifs". It is part of the filename of the initial files for the model (the files starting with "ICM").
The '-l' option is the name of the fortran namelist file you edited above.
oifs_run -e oifs -l mynamelist
This will create a file 'job1
'.
Submit this job:
qsub job1
Check the job status:
qstatu
These forecasts complete in about 15mins.
During the course of the model run, files with names like ICMGGoifs+00000, ICMGGoifs+00012 etc will appear in the experiment directory.
These are the model output files. There is 1 per output interval. In these experiments the output interval is every 3 hours.
Checking the model output
After the qstatu command shows that the job has completed, there will be a 'batch log file' in the pf001 directory:
oifs_troifs1.o1481792
Exercise
Using your favourite text editor, check this file to make sure the model has run correctly. It's usually best to start from the bottom of the file and scroll up.
If you see:
!!!!!!!!!!!!!!!!!!!!!!!!!!!!! OPENIFS JOB FAILED !!!!!!!!!!!!!!!!!!!!!!!!!!!!!
the model run has failed.
The output from each model run goes into a directory named 'output1'.
If the model fails, there are 2 files to look at in the 'output' directory:
NODE.001_01 : this is the output from the model as it is running (i.e. all the print/write fortran statements). This is a large file, so in case of errors, start from the bottom up!
oifs.log : this is where the model writes any error messages.
When the model completes the forecast successfully, the following files will be found in the output directory. Files with '+' in the name are the model output files. ICMSH are the spectral fields, ICMGG are the gridpoint fields.
ICMGGoifs+000000 ICMGGoifs+000048 ICMGGoifs+000096 ICMGGoifs+000144 ICMSHoifs+000016 ICMSHoifs+000064 ICMSHoifs+000112 ICMSHoifs+000160 oifs.log
ICMGGoifs+000016 ICMGGoifs+000064 ICMGGoifs+000112 ICMGGoifs+000160 ICMSHoifs+000032 ICMSHoifs+000080 ICMSHoifs+000128 NODE.001_01
ICMGGoifs+000032 ICMGGoifs+000080 ICMGGoifs+000128 ICMSHoifs+000000 ICMSHoifs+000048 ICMSHoifs+000096 ICMSHoifs+000144 ifs.stat
Preparing files for Metview
The next step is to take the output of the successful run and prepare it for the Metview based exercises.
As the data files and Metview scripts have been optimized by selecting specific areas, we have made a script available to do the work.
oifs_to_mv -e pf001
This will generate files in scratch/metview.
This task is only to prepare the output fields for Metview. The tutor will then use these files and combine them with the other ensemble members to create the final files that will be used in the plotting exercises.
If errors are encountered please let us know. If the command completes successfully (it will take a while), this task is complete. There is no need to inspect the files.
This script may take a few minutes to run.