User Documentation

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Frequently Asked Questions

How to generate ssh keys?

In order to access the LinkSCEEM/Cy-Tera computer systems you need to generate an ssh key pair. This pair consists of a public and a private part. Here we briefly describe how to generate such a pair.

On Linux/UNIX/Mac

In order to create a new ssh key pair login to your local machine from where you want to connect to the LinkSCEEM/Cy-Tera computer systems:

1. Open a shell and use the following command

You are asked for a file name and location where the key should be saved. Unless you really know what you are doing, please simply take the default by hitting the enter key. This will generate the ssh key in the .ssh directory of your home directory ($HOME/.ssh).
Next, you are asked for a passphrase. Please, choose a secure passphrase, don't leave the passphrase empty.

2. Send your public key ( to the user support team, for your account to be created. You must keep the private part ($HOME/.ssh/id_rsa) confidential.

Important: Do NOT remove it from this location and do NOT rename it!

On Windows

You can generate the key pair using for example the PuTTYgen tool, which is provided by the PuTTy project. Start PuTTYgen and choose SSH-2 RSA at the bottom of the window and set the 'number of bits in the generated key' to 1024 and press the 'Generate' button.

PuTTYgen will prompt you to generate some randomness by moving the mouse over the blank area. Once this is done, a new public key will be displayed at the top of the window. Please, choose a secure passphrase, don't leave the passphrase empty.

Save the public and the private key. Send your public key to the user support team, for your account to be created. You must keep the private part (.ppk) confidential.

Note: The private key can be copied on other computers from where you would like to login to the LinkSCEEM/Cy-Tera systems. Hence, having your private key allows you to login from any system you want.

For what do I need the module tool?

On LinkSCEEM/Cy-Tera systems, open source software and libraries are made available to users through the use of the module command. The user's environment in the current shell will be updated so that the software under consideration can be used. To get an overview of the modules available on LinkSCEEM/Cy-Tera systems type module avail on the command line. Further useful commands are:

Command Description
module load <module> Enables the use of the corresponding software package
module list Prints out a list of loaded modules
module help <module> Gives some information about the package under consideration
module unload <module> Opposite of module load <module>. Some software packages provoke conflicts if several versions are installed at the same time, so it might make sense to unload versions that are not needed for the moment
module show <module> Shows information about the location of the software and variables that will be set by invoking this <module>

I have deleted some critical files by mistake, is it possible to recover them?

On Cy-Tera system only the $HOME directory is backed up and on the BA system only the $WORK directory is backed up for a retention period of two weeks. Back up starts at 18:00 every day. Please contact the site administrators for such issues (

Please be advised that the $HOME directory is relatively small and you have a quota of 20 GB of space on Cy-Tera and 100 MB on the BA cluster. It is intended for storing binaries, source and modest amounts of data. $WORK is a larger area (according to your project disk allocation) which is intended for storing files between jobs and for long term data storage.

Can I access the BA cluster from another IP address?

Yes, it is possible. Please contact the site administrator ( to guide you through this.

Can I login to the LinkSCEEM/Cy-Tera resources from another system apart from my local host?

Yes, as long as you are using the same public/private key pair to login to both systems. Please follow the steps below to enable agent forwarding in ssh:

Can I run jobs that require more that 24 hours to be completed?

Yes, by using checkpointing and restart mechanisms. The job checkpoint and restart feature enables you to stop jobs and then restart them from the point at which they stopped, which optimizes resource usage. Please contact the site administrators for help.

How do I pass environment variables to the processes of my parallel program?

The specific method depends on the process manager and version of mpi process spawner of a given system.
You should also consult policy LS2_11-98 for certain variables available before and during run-time.
Kindly pick the habit of using such variables, so that your code is more easily portable across sites.

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