Computer Science | Mathematics | Statistics and Actuarial Science | Applied Mathematical and Computational Sciences | Informatics

Running Jobs on the Statistics Cluster

Pre-requisites for using LAM/MVAPICH2/PVM/OpenMPI

You must be able to ssh to any node machines w/o being prompted for a password. This can be accomplished a couple different ways.

• From a CSG-managed linux workstation

These instructions will only be useful if you are working from a CSG-managed linux workstation (which includes the NoMachine servers). They will not work from a home machine.
Initial Set-up
1. Create an ssh key: ssh-keygen -b 2048 -C "First LastName" -t rsa -f /space/username/.ssh/id_rsa
2. Using a text editor (e.g. vi, emacs, nano, pico, gedit), create the file ~/.ssh/config with the following contents:

   Host *
    ForwardAgent yes
    ForwardX11 yes
   
           

3. Create an ssh directory on cluster: ssh beowulf.stat.uiowa.edu "mkdir ~/.ssh/;chmod 700 ~/.ssh"
4. Copy the public key to the cluster head node: scp ~/.ssh/id_rsa.pub beowulf.stat.uiowa.edu:.ssh/authorized_keys2
5. Copy the ~/.ssh/config file to the cluster: scp ~/.ssh/config beowulf.stat.uiowa.edu:.ssh/config
6. Add the ssh key to your ssh key agent: ssh-add ~/.ssh/id_rsa
7. Connect to the cluster head node: ssh beowulf.stat.uiowa.edu (you should NOT be asked for a password or a passphrase)
8. From the head node, connect to a client node: ssh node01 (you should NOT be asked for a passphrase)
9. Ongoing requirement: Each time you log in to your linux workstation, you must run: ssh-add ~/.ssh/id_rsa

• From a terminal on beowulf.stat.uiowa.edu/node00

These instructions involve more effort for the day-to-day usage
Initial Set-up
1. Login to the head node: ssh beowulf.stat.uiowa.edu
2. Create an ssh key: ssh-keygen -b 2048 -C "First LastName" -t rsa -f /space/username/.ssh/id_rsa
3. Using a text editor (e.g. vi, emacs, nano, pico, gedit), create the file ~/.ssh/config with the following contents:

   Host *
    ForwardAgent yes
    ForwardX11 yes
   
           

4. Copy your public key to your authorized_keys2 file: cp ~/.ssh/id_rsa.pub ~/.ssh/authorized_keys2
5. Set appropriate permissions on your .ssh directory: chmod 700 ~/.ssh
6. Start the ssh key agent: eval `ssh-agent`
7. Add your key to the ssh key agent: ssh-add ~/.ssh/id_rsa
8. Connect to a client node: ssh node02 (you should NOT be asked for a password)
9. Before logging out, you'll need to disable the ssh-agent. You can do this manually by running "ssh-agent -k" or you can add it to your shell logout file:
   For (t)csh users, put this in your ~/.logout file, for bash users put it in ~/.bash_logout:
   ssh-agent -k >& /dev/null
   
10. Ongoing requirement: each time you log in to the head node, you will need to run: eval `ssh-agent`;ssh-add ~/.ssh/id_rsa

Using LAM/MPI

• This the default MPI environment on the cluster. If you change it to someting else, you'll need to run "mpi-selector --set lam-x86_64" to change it back.
• Please see the documentation listed on the Software Tools page.
• Be sure to do a "lamhalt" after you are done.

Using MVAPICH2/MPI

• Run "mpi-selector --set mvapich2-1.4-gcc-x86_64" to have MVAPICH2 as the default MPI environment. You will have to log out and then log back in for this to take effect.
• Read the documentation listed on the Software Tools page. Be sure to follow the link listed for MVAPICH2.

Using OpenMPI/MPI

• Run "mpi-selector --set openmpi-1.4-gcc-x86_64" to have OpenMPI as the default MPI environment. You will have to log out and then log back in for this to take effect.
• Read the documentation listed on the Software Tools page. Be sure to follow the link listed for OpenMPI.

Using PVM