IP Addresses and Hosts

The "internal" IP addresses listed in the table below are accessible only from inside the Ouranos network (this building). For communication outside the building (including communication with Marvin, which physically resides in the UQAM computer facility), or from outside into this building, you will need to use the "external" IP addresses given here. Note that the firewall only allows selected machines to connect to network systems (Zaphod), so you will only be able to contact Zaphod at its external IP from Marvin.

Machine Description	IP Address	Address Type	Host Name	Unnecessary Image
Cluster	132.208.132.89	external	marvin
Diagnostics/Storage	192.168.0.30	local	zaphod
	207.162.87.210	external	zaphod

The username and password information on Marvin (the cluster) uses a Network Information System to distribute information across nodes. This means that running passwd to change your password will not produce the desired result. To change your password run the command: yppasswd

Customizing the Environment

NOTE: Skip this section and go directly to the tutorial instructions if your account has already been created for the UQAM tutorial. In this section, we run through an example of creating a user account on Marvin, the UQAM cluster. The user name will be foo, and the user ID will be 9999. Both of these values should be replaced when creating an account on the cluster.

1. [root] Check user ID on rhea.ouranos.ca using (replace the user name foo with the requested user name): ssh rhea.ouranos.ca grep foo /etc/passwd | awk 'BEGIN {FS=":"}{print $3}'
2. [root] Add user account (replace the user name foo and id 9999 with the real user name and the result of the previous command, repectively): adduser -u 9999 -g 100 foo
3. [root] Remove the default password from the account (replacing foo): perl -pi -e 's/^(foo:)x(:)/$1$2/o' /etc/passwd
4. [root] Log in as the user (replacing foo): su -l foo
5. [user] Have the user change his/her password: passwd
6. [user] Log off user account: exit
7. [root] Update NIS account and password information: cd /var/yp; make; cd -
8. [root] Log in as the user (replacing foo): su -l foo
9. [user] Set up password-free secure login for nodes (see the local SSH Page for more information): mkdir ~/.ssh; cd ~/.ssh; ssh-keygen -t rsa; cat id_rsa.pub >>authorized_keys; cd -
10. [user] Check online at the SSM Installation Guide and follow the instructions under the User Accounts section.
11. [user] Copy standard user setup into the user's home: cp /etc/.profile_usr .
12. [user] (Optional) Open up user home to group: cd /home; chmod g+rx ${USER}; cd -
13. [user] Log out of the user account: exit
14. [user] Have the user log in an check his/her account on another window.
15. [root] From your root window, create a space for the user on a free disk (for example, /local/sata1 for user foo): cd /local/sata1; mkdir foo; chown foo.users foo; cd -
16. [user] Instruct the user to follow the COMM Model Running Instructions, with the $GEMSSM environment variable in step 1 set to (or replaced with) ~armnlib/ssm_gemclim_3.2.2, ignoring the permission error that will occur during step 1, and skipping the path modification in step 4 that has already been done. A detailed example of running the GEMCLIM benchmark is described below, but at least steps 1-4 of the COMM Model Running Instructions should be followed before continuing.

In this section, we will help you to set up and run a benchmark simulation with the GEM climate (GEMCLIM) model. If you need additional support for running the model, see the RPN COMM community modelling website or the SSM installation guide. This example assumes that you have already completed the basic account setup steps described above.

Data from this benchmark simulation will be stored in /local/sata1/${USER}/model_storage/final/bcmk. This data should be transferred to Zaphod for viewing, since only a rudimentray set of tools are available on the cluster.

1. Make and enter a benchmark experiment directory: mkdir -p /local/sata1/${USER}/gemclim/v3.2.2/bcmk; cd /local/sata1/${USER}/gemclim/v3.2.2/bcmk
2. Set up an active experiment: ouv_exp base -RCSPATH "/home/armnlib/ssm_gemclim_3.2.2/all/share/modeles/GEMCLIM/v_3.2.2/RCS_DYN /home/armnlib/ssm_gemclim_3.2.2/all/share/modeles/GEMCLIM/v_3.2.2/RCS_PHY /home/armnlib/ssm_gemclim_3.2.2/all/share/modeles/PHY/CLASS/v_3.0/RCS"
3. Build a makefile: r.make_exp
4. Create a build directory: mkdir malib${EC_ARCH}
5. Build GEMCLIM: make gemclim
6. If you wish to make modifications to the GEMCLIM source code, see the expanded description below.
7. Build and enter a configuration directory: mkdir -p configs/lam; cd configs/lam
8. Copy the benchmark configuration scripts into the current directory: cp /local/sata1/data/configs/gemclim_3.2.2-lam/* .
9. [First time only]Create a model listing directory for runtime text output: mkdir -p $HOME/listings/headnode
10. [First time only]Create a model runtime directory
mkdir -p /local/fiber1/${USER}/runtime; cd ~; ln -s /local/fiber1/${USER}/runtime ./gemclim; cd -
11. Replace the model configuration user name with your own user name: perl -pi -e 's/FOO/$ENV{USER}/g' configexp.dot.cfg
12. Launch the model run: Um_launch

This section describes how to make a basic modification to the model by modifying the source code. It is assumed that you have completed both the account setup and benchmark run described above and that you are comfortable with both Linux and FORTRAN.

1. Return to your experiment directory: cd /local/sata1/${USER}/gemclim/v3.2.2/bcmk
2. Get an RCS repository listing for the dynamics segment of the model: ls $MODEL_PATH/RCS_DYN
3. Get an RCS repository listing for the physics segment of the model: ls $MODEL_PATH/RCS_PHY
4. Extract the radiation scheme souce from the physics RCS repository: omd_exp newrad4.ftn
5. Use your favourite text editor to have a look at (and modify if you'd like) the source for newrad4.ftn.
6. Compile the modified (or unmodified) subprogram: make newrad4.o
7. (Optional) Directory cleanup: make clean
8. Recompile the model to use your newly-compiled subprogram: make gemclim
9. Return to your benchmark configuration directory: cd configs/lam
10. Continue as described in the sample description above.

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