1 RCE Setup

1.1 Access

You can access the RCE using the NoMachine remote desktop software, or via the command line using ssh. If you are a command line wizard and only need to run batch jobs ssh is the way to go; for most of us however nomachine is a much more useful way to access the RCE. It allows you to interact with the applications on the cluster much as you interact with applications on your local computer.

To get started, download the NoMachine client for your operating system:

After downloading, Windows users should right-click on the nomachine-client-windows-latest.zip file and choose Extract to here. Open the NoMachine Client folder and double-click on the .exe files to start the installation (the Windows zipfile contains the NX client, plus optional font packages. HMDC recommends installing all font packages, though this is not required). Mac users should double-click on the nomachine-client-osx-latest.dmg and double-click on the installer package to begin the installation.

Once you have installed the NoMachine software you should launch the NoMachine application and set up your login credentials.

Once the application launches:

  • Click Continue.
  • Click Click here to create a new connection.
  • Keep clicking Continue until you get to the Hosts screen.
  • Fill in the Host field with rce.hmdc.harvard.edu.
  • Keep clicking Continue until you get to the Name screen.
  • Fill in the Name field with RCE6 and click Done.

Once you have configured NoMachine you should test it out to make sure you can connect to the RCE:

  • Click on the RCE6 entry and then click Connect.
  • Fill in the user name and password fields with your RCE user name and password.
  • On the following screen click on New virtual desktop or custom session.
  • Click on Create a new virtual desktop and click Continue.

After completing these steps you should see an instruction screen; click OK and you should see your RCE desktop, which will look something like this:

If you have any difficulties installing NoMachine, detailed documentation is available at http://projects.iq.harvard.edu/rce/nx4; if you do not find a solution there send and email to help@iq.harvard.edu and someone will assist you.

1.2 Compute nodes

You can run applications on the RCE interactively or using the batch system. If you simply want a more powerful version of your PC (e.g., more memory, more CPUs) then the interactive nodes are what you want. If you want to split your task up into hundreds of pieces and run each piece simultaneously, then you want the batch modes.

More specifically, the RCE provides three levels of service:

Login nodes
Provides access to a desktop environment (similar to Remote Desktop) from which you can launch applications. The login nodes should not be used for computationally intensive jobs; the main function of the login nodes is to provide access to the interactive and batch nodes. You access the login nodes using the NoMachine client, as described in Accessing the RCE.
Interactive nodes
Interactive nodes allow you to run applications on very powerful computers. You can launch applications on the interactive nodes from the login node desktop using the Applications --> RCE Powered Applications menu. Applications launched from this menu will run on more powerful machines with large memory resources (up to 256GB) and up to 24 CPU cores.
Batch nodes
Where interactive nodes give you access to a single very powerful computer, batch nodes provide a swarm of hundreds of small computers. You can run your computation in parallel on each of them, which can provide dramatically reduced compute time for many applications. You access the batch nodes using the command line which you can access by starting a terminal application from the Applications --> Accessories --> terminal menu.

1.3 Project folders & shared space

When your RCE account was created a home folder was set up for you, with Documents, Downloads, Desktop and other common sub-directories. However you can only store a maximum of 5Gb in your home folder. For larger projects you should use a project folder; one was probably set up for you when your account was activated. There is a shortcut in your home directory named shared space, which will contain any project folders you have access to. You should store large data sets and other large or numerous files in these project folders.

Project space can be used privately, or shared with collaborators (hence the name, ‘shared space’). For more details on project folders refer to http://projects.iq.harvard.edu/rce/book/projects-and-shared-space and http://projects.iq.harvard.edu/rce/book/project-space-collaboration.

1.4 Moving your data on and off

People often use the RCE for memory or CPU intensive data analysis projects. If this is your intention as well, chances are that you have one or more (potentially large) data files that you will need to copy to the RCE. Remember that disk space in your home directory is limited, so if you have a large amount of data make sure to transfer data directly to your project space folder.

The simplest approach is to use the NoMachine client to transfer data from your local machine to the RCE (and from the RCE to your local machine). Click on the red !M icon in the upper right-hand corner and select the Send a file from the client menu, as shown below.

If you prefer to transfer files using another file transfer client, anything that uses ssh (e.g., FileZilla) should work. Just point your favorite client to rce.hmdc.harvard.edu.