Login to ECMWF Cray High Performance Computing Facility (HPCF)

Each group or participant will have a training user account on the ECMWF system, beginning with 'troifs'. This is different from the user account on the classroom computers.

...

ssh troifsXX@ecgb06troifsXX@ecaccess.ecmwf.int		               # substitute your user id for XX
troifsXX@ecgb06troifsXX@ecaccess.ecmwf.int's password:              # give your password when prompted using the securID hardware token (one time password)

Next login to the Cray login nodesWhen prompted select 'cca' :

ssh cca
troifs@cca-login2:~> 

troifs1@140.105.20.128's password: 
Select hostname (ecgate, cca, ccb) [ecgate]: cca

'cca' is the "front-end" computer to the ECMWF Cray high performance computer facility.

The contents of the account should look like:

...

Creating the experiment initial files

This section will explain how to copy and change the experiment id.

...

You do not need to run these experiments, the forecasts from a 10 member ensemble are made available on the classroom computers.

Copy previous experiment initial files

Before creating the experiment, first create the initial data. If you plan to rerun the ob00 or clim experiments and use the initial data 'as-is' you can skip this step.

...

cd inidir/ob01
cp -rL /perm/rd/openifs/oifs_workshop_2017/expts-inidata/ob00/2015110[1-5]* .     # this will take some time

Please Please only copy the initial dates you intend to use. Each date uses 0.5 Gbyte of file storage.

cd inidir/ob01
cp -rL /perm/rd/openifs/oifs_workshop_2017/expts-inidata/ob00/2015110[1-3]* .      # this will take some time.

Change experiment id

OpenIFS forecasts are identified by an 'experiment id', a four letter string.

Change experiment id

OpenIFS forecasts are identified by an 'experiment id', a four letter string.

An experiment could consist of a single forecast date or multiple starting dates. It can be of any length and could also include a restarted forecast. However, An experiment could consist of a single forecast date or multiple starting dates. It can be of any length and could also include a restarted forecast. However, an experiment only has one horizontal and vertical resolution.

...

If you are using multiple dates, remember to change the experiment id for each date.

Initial files

The initial files containing 2D and 3D fields to start the forecast are contained in file that begin with ICM* : ICMGG* are the initial gridpoint files, ICMSH* are the initial spectral fields. ICMCL* is the file containing the climatological forcing fields.

...

grib_ls ICMGGob00INIT
grib_ls ICMSHob00INIT

OpenIFS namelist

The file: fort.4 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 wave model, WAM, also has a separate namelist. For this workshop, none of the switches in this file needs to be changed.

Listing the experiment id

The command 'exptid' can be used to check and change the experiment id in the GRIB files.

...

Note that the ICMCL and ICMGG*INIT files both have a experimentVersionNumber key of '0001'. This is used for climatological fields.

Set new experiment id

Use the exptid command to set the new experiment id to 'ob01':

...

troifs0@cca-login3:> rm ICM*ob00*
rm: remove regular file `ICMCLob00INIT'? y
rm: remove regular file `ICMGGob00INIT'? y
rm: remove regular file `ICMGGob00INIUA'? y
rm: remove regular file `ICMSHob00INIT'? y

Further modification to initial files

Now the initial files with the correct experiment ID have been prepared, further modifications to the input files can be made.

To modify the SST for example, see the tutorial on 'Modifying the SST'.

Creating the forecast experiment

Once the initial data directory is prepared, the next step is to create the experiment directory structure where the model will run. This is not the same location as the initial files just created.

...

This would create the ob01 forecast directories for a single date. The default is to create the experiment directory in your 'scratch' directory with the same name as the experiment id. e.g $HOME/scratch/ob01.

New experiment: ob01 - single data, 10 members

Following the creation of the initial files for the experiment id 'ob01' given above, let's create a forecast experiment with 5 ensemble members for a single forecast date:

troifs0@cca-login3:~> createEX -d 2015110100 -e ob01 -i scratch/inidir -m 910

We tell this command it can find our new initial files in scratch/inidir. By default, this command will create the experiment directory also in scratch. Be careful not to confuse the initial data directory with the experiment directory. These should be kept separate.

...

Creating directory structure for experiment ob01 in directory /scratch/ectrain/troifs0/ob01/...
Date :  2015110100
Copying files from directory (inidir):  scratch/inidir
Date:  2015110100
.........
Created forecast experiment directory : /scratch/ectrain/troifs0/ob01/2015110100/05/
Linking files and copying namelist.
Using IFS data directory: /fwsm/lb/project/openifs/ifsdata/
Created forecast experiment directory : /scratch/ectrain/troifs0/ob01/2015110100/06/
Linking files and copying namelist.
Using IFS data directory: /fwsm/lb/project/openifs/ifsdata/
Created forecast experiment directory : /scratch/ectrain/troifs0/ob01/2015110100/07/
Linking files and copying namelist.
Using IFS data directory: /fwsm/lb/project/openifs/ifsdata/
Created forecast experiment directory : /scratch/ectrain/troifs0/ob01/2015110100/08/
Linking files and copying namelist.
Using IFS data directory: /fwsm/lb/project/openifs/ifsdata/
Created forecast experiment directory : /scratch/ectrain/troifs0/ob01/2015110100/09/
Linking files and copying namelist.
Using IFS data directory: /fwsm/lb/project/openifs/ifsdata/
All done: /scratch/ectrain/troifs0/ob01/ ready.

Directory structure

If we look at in the directory: /scratch/ectrain/troifs0/ob01/2015110100, we see:

...

Only the model namelists, fort.4 for the atmosphere, wam_namelist for the wave model, are individual to a forecast ensemble member directory.

Running the forecast experiment

The command 'oifs_run' is normally used to create and submit the batch job to run the model. This command has a large number of options. For this workshop, this command has been configured with the correct defaults for the T255 resolution seasonal length forecasts.

...

.........
Ensemble member: 05
60c60
<       NENSFNB=5,
---
>       NENSFNB=0,                 ! Ensemble forecast number
Running command: oifs_run -e ob01 -x 1 -q
Copied /home/ectrain/troifs0/bin/cce-opt/master.exe to current directory
Using existing namelist in : fort.4
OpenIFS job created: job1
Submitted job: 8430146.ccapar
......

Setting the ensemble member

The command 'run_all_ens' does this step, no action is needed. This section explains the use of the ensemble member number by IFS.

...

CTYPE="pf",        ! the type of forecast: 'pf=perturbed', 'cf=control'. The control (unperturbed) forecast is only used in medium-range forecasts, not in seasonal forecasts.
NENSFNB=2,         ! the ensemble member number. 
LSTOPH_SPBS=true,  ! enables the stochastic backscatter scheme in the model dynamics. This is only used in medium-range forecasts and will be 'false' for seasonal forecasts.
LSPSDT=true,       ! enables the stochastic scheme for the physics tendencies.

...

tendencies.

The only namelist variable that needs changing in these experiments is NENSFNB, which the run_all_ens command does for you.

Create and submit Cray batch job

This step is done by the run_all_ens command. No user action is needed. This section provide more information on the oifs_run command.

...

Checking the model output

During the course of the model run, files with names like ICMGGob01+00000, ICMGGob01+00012 etc will appear in the ensemble member directory.

...

Rerun the model job

A small file 'job1' (or jobN where N is the run number you used), is created in each of the ensemble member directories; 00, 01, 02, etc.

If for any reason the model fails, once you have determined the problem and corrected it, then the run can be submitted by:

qsub job1

There is no need to rerun the run_all_ens command as this will resubmit ALL the ensemble members again.

Anchor
postprocessing postprocessing

Postprocessing: preparing monthly means for plotting with Metview

The next step is to process the output of the successful run and create the monthly mean fields that can be transferred to ICTP for plotting using Metview.

...

This command only processes one date at a time. It needs to be run run separately for multiple dates in the same experiment id.

Monthly mean files

After the oifs_to_mv command finishes, the monthly mean files can be found in the directory 'mmeans' inside the top level date directory. For example, for experiment id ob01, date 2015110100, the directory is: ob01/2015110100/mmeans.

Inside this directory, there is one file per parameter with 5 monthly averages: Dec, Jan, Feb, March and April, with filenames for example as: oif_ob01_u_20151101_00.grib.

Transfer to ICTP classroom PCs

The monthly mean files can be transferred to ICTP with the ftp sftp command, to be used on the classroom PC with metview.

Useful Unix commands

qsub job

...

Quota for $HOME and $PERM:
Disk quotas for user troifs0 (uid 16144): 
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
cnasa1:/vol/home
                   226M    480M    500M             132   20000   22000        
Disk quotas for user troifs0 (uid 16144): 
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
cnasa2:/vol/perm
                      0  26624M  27648M               1    200k    210k        

Quota for $SCRATCH ($TEMP) including $SCRATCHDIR ($TMPDIR):
Disk quotas for user troifs0 (uid 16144):
     Filesystem  kbytes   quota   limit   grace   files   quota   limit   grace
  /lus/snx11062 767099824  32212254720 32212254720       -  116570  5000000 5000000       -
Disk quotas for group ectrain (gid 1400):
     Filesystem  kbytes   quota   limit   grace   files   quota   limit   grace
  /lus/snx11062 767105640       0       0       -  118078       0       0       -

...