This page describes how to extract forcing data to run the Single Column Model from the ECMWF data archive.

Initial setup

There are a number of required steps before the extraction can be done. These are steps that only need to be done once.

Access to 'ifs' group

You need to be in the 'ifs' unix group in order to run the scripts to generate the SCM forcing.

To check you have access, login to ecgate, and type:

groups

If you do not see 'ifs' listed in the output, please contact ECMWF Service Desk (servicedesk@ecmwf.int) and ask to be added, explaining why.

ssh keys

Make sure you have set up your ssh_keys so that you don't need to use password to go from ecgate to cca and from cca to ecgate:

ssh-keygen (no passphrase)
ssh-copy-id -i ~/.ssh/id_rsa.pub name_of_remote_host

Install workflow suite

The forcing data is created using a 'workflow' developed at ECMWF.

A workflow is a defined order in which a number of separate scripts are run. The workflow software used at ECMWF is called 'sms'. SMS is a 'workflow manager' that a user interacts with to control the executation of scripts (or 'tasks') in the workflow.

The workflow 'suite', the sequence of the scripts that will be run, is defined in a .def file.

The following steps explain how to install and customize this workflow and it's scripts for your use.

1. Download the workflow suite: sms.tar.gz (last updated Jan/2018)   and unpack it to your ecgate user home directory:

   cd $HOME mkdir sms tar zxvf sms.tar.gz

   
   

2. Choose either ECMWF operational analysis (OPER-cray.def) or the ERA-Interim analyses (ERAI-cray.def) and copy to 'cray.def'.

   cp OPER-cray.def cray.def

   
   

3. Edit cray.def to correct it for your user details:
   
   i)  replace all '/home/ms/se/usr' by your actual home directory path where 'usr' is your username (e.g. /home/ms/se/batman)
   ii) replace 'acnt' by your billing units account.
       To find your account, type the command:

   account -l your_user_name

        where your_user_name is replaced by your username (e.g. batman).
   iii) replace 'usr' in OWNER and USER to your username.
   iv) set LOGDIR to a directory on the HPC (where this job runs) where you want to store the log files.

4. In the directory, 'sms/cray', edit the files:  sms/cray/getdata_scm.sms  and  sms/cray/getmars_scm.sms  to set the unix directory paths to your user account:

   export SCRATCH=/ws/scratch/rd/rdx # only useful for $SCMDATA definition export SCMDATA=$SCRATCH/pafv/data # will define the place your resulting profiles are stored TMPDIR=/scratch/rd/pafv/scm_cray # working directory on cca

   It is important that these directories are set the same in both getdata_scm.sms and getmars_scm.sms.

5. In the directory sms/include_cray, you need copy the script files from either 'OPER' if you want to use operational analyses, or 'ERAI-0_12' if you want to use ERA-Interim.
   Copy the files into the sms/include_cray directory:

   cd sms/include_cray cd OPER # we will use the ECMWF operational analysis to create the forcing files cp getini1c* .. # copy the files to sms/include_cray

   
   

6. Edit the files: sms/include_cray/getini1c_setup_cycle_validation_SCM_FC_cray*,  and replace the text 'usr' in "EXPVER=usr" to your real username.

7. Invoke the sms server to find your 'sms identifier', which is the number in the command output after the PROGNUM parameter, needed to log in to ecgate and set up server.

   /usr/local/apps/sms/current/bin/sms_start

   This command starts up your personal workflow manager on ecgate.

8. Set up server in the xcdp viewer. This is a visual view of the workflow and the tasks as they execute.

   xcdp & # run the workflow viewer 'xcdp' in the background

   
   

9. Once the xcdp window appears, add your server to the list of servers known to xcdp by the menus: Edit → Preferences → Servers

   Add entry to 'Name' (e.g. myserver), add entry to 'Host' (e.g. ecgate) and set PROGNUM value (step 7) for the 'Number' field.
   After configuring the server, select it's name from the Servers menu. You may need to click the red circle arrow top right, to load the suite.

Set up the job to retrieve forcing

1. Define the starting day(s) of your experiment(s) by adapting the YMD variable in sms/cray.def. The current setting uses the starting date of 1st of April 2016:

   define rcmd { repeat string YMD 20160401 }

   If you want to do multiple experiments simply add other dates in the following way:

   define rcmd { repeat string YMD 20160401 20160402 20160403 }

   
   

2. Edit following two files:

   sms/include_cray/getini1c_setup_cycle_validation_SCM_FC_cray sms/include_cray/getini1c_setup_cycle_validation_SCM_FC_cray.dataonly

   between the lines labelled as "definition area" to reflect your desired points.

3. If using only one time step keep the forward slash '/' afterwards for correct use of sed command.

   If you request fields at 1 hour frequency, some fields won't be available from the MARS archive. It is better to use a 3 hour interval for the operational forecast. Note  the start time has to be either 00 or 12 for the operational forecast archive. While multiple dates can be specified, there is no way to have multiple starting time in the similar way. getini1c_mars_run_validation_SCM_FC has information on which variables are read from MARS archive

   
   

Run the job to retrieve forcing

1. Make sure the sms server is already running by using the following command. If it is, this command will do nothing:

   /usr/local/apps/sms/current/bin/sms_start

   
   

2. Load your suite into the SMS server and start running it:

   cd ~/sms # change to the directory with the SMS scripts cdp # start the workflow manager 'cdp' CDP> set SMS_PROG your_sms_identifier # the command prompt will change to 'CDF'; set the SMS_PROG value

   where your_sms_identifier is given in the the output after invoking the sms server, look for variable called PROGNUM.

   login -t 60 ecgate your_user_name 314159 # password 314159, can also be 1 instead of 314159

   
   

   If errors occur, likely need to invoke sms server

   
   

3. Run (or 'play') the workflow suite:

   CDP> play -r /cray<cray.def # load the workflow suite into the workflow manager CDP> begin /cray<cray.def # start running the suite CDP> ctrl-D # CTRL-D to quit the CDP workflow manager

   
   

4. To cancel a running application:

   CDP> cancel -y -f /cray

   before entering the play command.

5. Start the xcdp viewer, a graphical display of the running tasks:

   xcdp & # run the viewer in the background

   
   

6. In the viewer, xcdp window, expand the branch of jobs on the host by middle mouse click on the symbol to right. Get further information on the job by right mouse button.

Color coding for xcdp tasks

More information on errors can be found in either getmars_scm.* or getmars_scm.* in folder LOGDIR on cca (cray) depending on which process crashes.

Restart failed tasks

Before restarting a failed job ('task') check the job is not still running by the command:

qstat -u your_user_name

which will list all batch jobs for your user name.

If the job is still running, kill it by:

qdel process_id

where the process_id should be replaced by from the list returned by qstat.

To restart a failed task, select the task, right click and select 'Restart'. All scripts in tree below will also be restarted and executables again copied to the Cray (cca) (changes included on ecgate will be activated). However, there is no restart of cray.def file needed. If a date change is required, login to cdp to change the date.

Retrieving data

After all the tasks are completed (shown as yellow in the xcdp window),  your forcing data is retrieved successfully and you should find your results in the directory specified in $SCMDATA.

Download the data from the web interface to ecgate, http://ecaccess.ecmwf.int. For instructions see: ECMWF User Docs: File Transfer.

The data can be download from: Browsing → ECscratch files → data → click on symbol to left (page with red arrow) to download.

Adapting extraction to other operational systems

The scripts in this workflow are configured for the most recent operational IFS operational since March 2016 (IFS cycle 43r1).

Changes to the following scripts are required for dates prior to this:

sms/include_cray/getini1c_setup_cycle_validation_SCM_FC_cray
sms/include_cray/getini1c_setup_cycle_validation_SCM_FC_cray.dataonly

For example, retrieving forcing data from the period June 2013 – March 2016, the operational model was IFS cycle 40r3. Modify the scripts by setting:

CYCLE=40r3
dataid2="t1279_2010"
CLIMVERSION=climate.v011
GTYPE=l_2

and substitute the script:

$TMPDIR/run_parallel /home/rd/nag/bin/getini1c_TCo1279_geostr

by the script (as used for ERA-I):

$TMPDIR/run_parallel /home/rd/nag/bin/getini1c_lowres_geostr

IFS operational updates

Changing horizontal resolution:

• change ZDELTA with a coarser grid so that the point is found in circle around desired location.
• choose large enough but not to large so that point further away is detected.
• TSTEP is not used in getini1c script, not important to set.

Changing vertical resolution:

• change the value of the variable LEVELS.
• change option -l 137 in getini1c_mars_run_validation_SCM_FC call in include_cray/getini1c_setup_cycle_validation_SCM_FC_cray.dataonly according to new number of levels (default 137).

Extracting forcing from ERA-Interim

Use the scripts in directory include_cray/ERA-I instead and also ERAI-cray.def.

Acknowledgements

The following people contributed to the development and documentation: Filip Váña (ECMWF), Nils Wedi (ECMWF), Paul Dando (ECMWF), Kerstin Hartung (University of Stockholm) and Glenn Carver (ECMWF).