running 3D-Var

Running 3D-Var

To run 3D-Var one needs configuration file, a set of scripts as well as the executable.

Content

1-4 Set up the system environment (these steps are needed to be done just once)
   5 The executable
   6 The scripts
   7 The configuration
   8 Set up the directory for output
   9 Launching the model

if you are very new user, let us say, there is empty in your HOME, you need to do:

1.    Create two links in your HOME:

cd
ln -fs ~winger/ssm-domains/setup/v_001 ECssm
ln -fs ECssm/dot-profile-setup_1.0_multi/bin/.profile
Change the name of two files (or remove them):
mv .bash_profile .bash_profile-
mv .bashrc .bashrc-
Log out and back in.

2.    There is no .profile_usr anymore. It got replaced by several .something_profile files which all have to reside in your HOME in a directory
         called '.profile.d'.
      Have a look at Katja's .profile.d:
      ls -al ~winger/.profile.d

       I suggest you link to the same group profiles Katja links to:

cd ~/.profile.d
ln -s ~winger/.published_profile.d/.group_profile
ln -s ~winger/.published_profile.d/.group0_profile

      This will give you some basic aliases Katja finds quite useful. Have a look at them if you like.

      Your own personal aliases, exports, s.ssmuse.dot etc. for interactive use will go into the file
        .interactive_profile

      which you will have to create. In the .interactive_profile, you need these lines:

. s.ssmuse.dot ovbin diagtools difftools runtools vistools fulldev
export PATH=/home/${USER}/scripts:${PATH}
export SOUMET_EXTRAS="-q hb"

Then you either log out and back in again or source the new .profiles.

3. Allow 'ssh $TRUE_HOST' without typing password:

cd ~/.ssh
Only if there is no(!) file 'id_rsa.pub' create it with:
ssh-keygen (press just 'Enter' whenever asked a question, 3 times)
then
cat id_rsa.pub >> authorized_keys2

4. Add the running account, at HOME

cp /home/pingduuqam/. CLUMEQ_accnt .

The reference is: new environment set up

5.     The executable

      The 3D-Var executable on guillimin is var3d_{BASE_ARCH}.Abs

        To create the executable, refer to the different version.

6.      The scripts

         Basically, for running 3D-Var the script is felix and its package for each version. Take the version V_11.02.0 for example,
         simply you can do as follows:

1) cd ~/scripts;

cp /home/pingduuqam/scripts/felix11.02.0 .

cp /home/pingduuqam/scripts/gsfn .

mkdir env; cd env

cp -r /home/pingduuqam/scripts/env/felix11.02.0 .

2) cd ~/bin

ln –s /home/${USER}/scripts/felix11.02.0 felix

7.     The configuration files

        3D-Var needs two configuration files: 'Bcmk1102.cfg', and 'flnml'

        Bcmk1102.cfg: file to control where to run the model, where to prepare the input, and the model output, etc.
    It must stay in the directory of
    ~/.fmain_rc
     so you need

mkdir ~/.fmain_rc
cp /home/pingduuqam/.fmain_rc/Bcmk1120.cfg.ALL Bcmk1120.cfg

in this Bcmk1102.cfg, you need to modify:

gest='localhost:/sb/project/xgk-345-ab/pingduuqam/bcmk';
retour='localhost:/sb/project/xgk-345-ab/pingduuqam/bcmk';
abs='localhost:/home/pingduuqam/var3d/v11.2.0/bcmk/var3d_Linux_x86-64.Abs';
Just change pingduuqam to your user name in Guillimin

        Click on the following links to get more information: experiment configuration

        flnml: the namelist for defining the model grid, the different schemes for model procedures, etc.
        Click flnml for more information.

8.     set up your directory for the output

mkdir /sb/project/xgk-345-ab/${USER}/bcmk (refer to the retour in the Bcmk1120.cfg)

9. Launching the model

Suppose you have Bcmk1102.cfg, the experiment configuration, just type:

felix Bcmk1102

       then the model starts running.