The CHPC hosts a supercomputer comprising:

• 1008 regular compute nodes with 24 cores and 128 GiB of RAM each;
• 360 regular computes nodes with 24 cores and 64 GiB of RAM each;
• 5 large memory nodes with 56 cores and 1TiB of RAM each;
• 9 GPU nodes.

All these systems are accessed via a single login node: lengau.chpc.ac.za.

Connection to the login node of the CHPC cluster is via the ssh protocol. To connect to the system use

  ssh username@lengau.chpc.ac.za

where username is replaced by the user name assigned to your account at the CHPC.

A dedicated node, scp.chpc.ac.za is available for scp file transfers:

  scp src.tar.gz username@scp.chpc.ac.za:~/lustre/

Large data sets should be transferred by means of Globus. Globus is faster and more reliable than scp.

You can also use scp or sftp to transfer files to or from your home directory on the CHPC systems. For example

  scp src.tar.gz username@scp.chpc.ac.za:~/lustre/

to copy the file src.tar.gz to your lustre directory on the CHPC cluster. Please do not transfer files directly to lengau.chpc.ac.za. It is a shared login node, and in order not to overload it, file transfer should be done to the dedicated scp server. Please note that storage space in your home directory is very limited. Large amounts of data should rather be transferred to your storage space on the lustre file system. For a typical user, there will be a symbolic link to the user's directory on lustre, hence the ~/lustre/ target. Alternatively, you may wish to copy directly to your lustre storage, in which case you could do the following:

  scp src.tar.gz username@scp.chpc.ac.za:/mnt/lustre/users/username/

If you would like a more user-friendly method, consider FileZilla

Note: use scp.chpc.ac.za as the server when transferring files.

The best way to connect via ssh is to create ssh keys which authenticate you instead of your password.

First create your private and public keys on your main work computer. These steps assume that is a desktop or laptop computer running Linux:

  ssh-keygen -t dsa

This creates two new files in your .ssh directory

It is the latter file that you need to add to the .ssh/authorized_keys file in your home directory on the CHPC login node.

From a recent Linux distribution you can simply do this :-

  ssh-copy-id username@lengau.chpc.ac.za

From older Unix setups you might have to do this :-

  cat ~/.ssh/id_dsa.pub | ssh username@lengau.chpc.ac.za "cat >> .ssh/authorized_keys; chmod 0700 .ssh; chmod 0600 .ssh/authorized_keys"

And the next time you ssh or scp to the CHPC login node you won't have to use your password!

Notice that you need to change the permissions of the .ssh directory and the authorized_keys file on the login nodes to make them private and readable by you only before ssh will use the new public key.

chmod -R g-rwx,o-rwx ~/.ssh

You also need to make sure your home directory does not have write w enabled for group and other fields.

ls -ld ~
drwxr-xr-x 19 user user 4096 Aug 15 12:01 /home/user

which is done with

chmod 0750 ~

to make your entire home directory private; or

chmod 0755 ~

to allow other users to view your files.

This error occurs if the keys used by the host are different from that used last time you connected to it.

You can use

ssh-keygen -R badhost

to remove all keys associated with the host badhost from your known_hosts file.

This is safe to do because the new host key entry will be added back in next time you ssh in.

If you want to look at or edit the .ssh/known_hosts file, it is located in the .ssh sub-directory within your home directory on the Lengau cluster.

For example, after logging in:

cd .ssh/
ls
authorized_keys  id_ecdsa  id_ecdsa.pub  known_hosts

Once you have changed into the .ssh sub-directory you can then use an editor (e.g. nano known_hosts) to edit the file and delete the bad line.

Cygwin provides all the above Linux commands for the Windows command line (and replaces the limited CMD.EXE command line).

For first-timers there is a nice introduction at lifehacker.

Should you prefer a MS Windows application with a GUI to connect to the CHPC we suggest you download and install the open source PuTTY and WinSCP clients, or alternatively MobaXterm, which has a free “home” edition.

It is strongly recommended that you use ssh keys to connect to the CHPC. To generate and configure putty-ssh to use keys please see:

• HowToForge tutorial
• Putty-ssh documentation

To generate and configure Git to use ssh keys please see:

• http://inchoo.net/dev-talk/how-to-generate-ssh-keys-for-git-authorization

It may be that your account is blocked because of multiple failed logins. Check if that is so via https://users.chpc.ac.za/reports/ip_check/

It is important to note that if you had more than 6 failed login attempts, your account will be blocked and either you will have to log a call on https://users.chpc.ac.za/helpdesk or wait for 30 minutes before trying to login again. However if you wait for 30 minutes and try once again with an incorrect password, you will be locked for another 30 minutes until you login with a correct password where your username will be removed from the blocked list. Only then you will regain your 6 grace failed login attempts.