RCE FAQs

Firefox or Thunderbird won't start!

The error Firefox is already running usually indicates that you must remove lock files before you can launch Firefox. To resolve this problem:

  • If you are working inside the HMDC RCE navigate to ApplicationsRCE UtilitiesClear Firefox Locks or Clear Thunderbird Locks. Then, try launching Firefox or Thunderbird again.

  • If you are not working inside the HMDC RCE, type the following command via a terminal to delete the Firefox lockfiles: rm -f ~/.mozilla/firefox/*.default/{lock,.parentlock}

What are the technical specifications of the RCE?

The RCE is divided into three parts:

  1. Login nodes: These servers provide a graphical or command line interface to the meat and potatoes of the RCE, the Interactive and Batch cluster. It operates like a personal desktop environment, but is not meant for running jobs.
  2. Interactive cluster: Run memory intensive jobs on these COD (compute-on-demand) nodes that require user interaction.
    • Size: 8 homogenous servers
    • CPU: Intel Xeon E5_2630 with 12 cores (24 counting hyper-threading) @ 2.3 Ghz
    • Memory: 250 GB each (2 TB total)
  3. Batch cluster: For jobs that do not require babysitting, and speed is king.
    • Size: 5 homogenous servers
    • CPU: Intel Xeon E5_2690 with 16 cores (32 counting hyper-threading) @ 2.9 Ghz
    • Memory: 125 GB each (1 TB total)
    • Each batch job process is allocated 1 CPU core and 4GB of RAM

Also see running multi-threaded jobs for more information.

Disk space options are as follows:

  • Home directories are allocated 500 MB. We do not increase this space, but you may request a project directory.
  • Project directories are available in storage sizes suited to each particular researcher. Please contact us to request storage space. Fees may be applicable to sizes over a certain amount. To read about using your storage space, please see:
  • 1 TB of shared scratch space is available to all users on our interactive cluster. Top level scratch space is world-writeable and -readable (Unix 1777 permissions). User created directories are only owner writeable/readable (1700) or owner/group (2770) if you are a member of a research group. Do not use the scratch space for permanent storage.

Why can't I connect to login.hmdc.harvard.edu?

We have retired the login.hmdc.harvard.edu name in favor of the other name for the Kennedy RCE login nodes, kennedy.fas.harvard.edu. If you are a KSG user you can login to kennedy.fas.harvard.edu. These nodes are exclusively for KSG students, staff and faculty.

Why does my screen lock frequently? Can I disable screen lock?

The RCE is a service that is remotely accessible, and many users work with sensitive data. Since we cannot guarantee the security of the physical environment around the user's computer, we are required to follow the Harvard information security policy for application availability which indicates that the screen lock timeout should "only be a few minutes."

The Harvard policy mandating screen lock is HEISP 2.6: http://security.harvard.edu/book/26-limit-application-availability-time

How do I copy/paste from a RCE terminal?

If you are running a RCE desktop session from a Windows client, you are probably used to using ctrl+c for copying and ctrl+v for pasting. Terminals remap these functions to shift+ctrl+c and shift+ctrl+v, respectively. The ctrl key is used for specific operations, such as terminating command-line operations (ctrl+c). You can also right-click in the terminal to copy and paste.

How do I stop windows from jumping to the foreground?

The default window behavior in the RCE uses the focus-follows-mouse model, in which the user selects windows by merely pointing at them, and the selected window jumps to the foreground.  To change this behavior go to:

Applications → RCE Utilities → Change Windows Focus Behavior

The focus policy change is immediate.

How do I share files with my collaborators?

Set up a project space

The simplest way to share files with collaborators in the RCE is to use a project space, which is a folder you all have access to. Send us a support request asking for a shared project space and we will create one for you. (Storage sizes over a certain amount are subject to a nominal fee.) Be sure to include the names of your collaborators.

Once you have a project space it will be linked from your RCE home directory under ~/shared_space/ by the name of the project. You may request more than one project space, but limitations on storage allocation apply.

Grant your collaborators access to the files you create in the project space

There are two ways to allow your collaborators access to the files you create in a project space. First and simplest -- do nothing. We run an automatic process each night that will change the permissions on your project files so that any permissions you have will also be granted to your project group.

If, however, you want to grant your collaborators immediate access to project files you have created, run the fixGroupPerm.sh command, as described in Projects & Shared Space.

Change your default file creation mode (optional)

If most or all of your work in the RCE is done in collaborative project spaces, you may want to change the default file creation mode (i.e. the file access permissions) for your RCE account so that all files you create can be modified by members of the group which owns them. For instructions see Projects & Shared Space

Copy/Paste to the RCE desktop isn't working!

When you copy and paste text between environments, you use the clipboard function.

If you have problems copying and pasting between environments, please try using ApplicationsRCE UtilitiesRestart Clipboard Sync.

Can I install my own software packages?

Many common statistical applications are already available, pre-installed in the RCE. If you need additional software for your work in the RCE, you are free to download, build, and install software within the space that has been allocated for your RCE home directory and project space.

When you run your configure script, give it an argument of --prefix=$HOME.

If the software you need is available from a trusted repository, we may also be able to add your software to the list of default applications in the RCE. Please contact us with your request.

I'm unable to log in -- what can I do?

There are several troubleshooting steps to take if you cannot log in to the RCE desktop:

  1. Verify that your credentials are correct by logging into the HMDC Account Self Service page. If you cannot log in, then the problem lies with your RCE credentials, and you will not be able to progress any further.  Please reset your password by visiting the Account Self Service page and clicking the "Forgot your password?" link, then try again.  If, after resetting your password, you are still unable to log into the Account Self Service page, please stop troubleshooting and contact us.
  2. Verify that you are logging into the correct RCE host.  Once you have logged into the Account Self Service page, make sure that you see a column labeled "HMDC RCE (Server) Account Information".  Check the "Account Access" section to find out the name of the RCE host to which you have access.  If you cannot determine the name of the RCE host to which you have access, check the email you received when your RCE account was originally created.  If you cannot find that email, please stop troubleshooting and contact us.
  3. Verify that you can connect to the RCE via SSH.  See Secure Shell under Accessing the RCE for instructions.  If you cannot connect to the RCE via SSH, then you will be unable to establish a NX connection.  Please stop troubleshooting and contact us. In your response, please include the name of the RCE host to which you tried to connect, the username that you used (but not the password!), and your IP address (visit http://www.whatismyip.com for this ); also, please include the full text of any error messages you saw.
  4. Verify that you have not exceeded your home directory's quota.  Once you have connected to the RCE via SSH, please check your disk quota usage.  Instructions for doing so are here: "How do I check RCE disk quota?".  If you have exceeded your home directory's disk quota, you will need to resolve this issue before you'll be able to continue.  Your options are as follows:
    1. Make sure that your Trash is empty.    When connecting via SSH, you can use the 'emptytrash' command to empty your Trash.  You should not see any output from this command; if you do, please stop troubleshooting and contact us
    2. Move large files to a project share or delete them.  If you have access to one or more project shares, they will appear in the output of the 'quotareport' command.  The "How do I check my RCE disk quota?" page contains some examples of using the command line to identify large files and move them to a project share; if you'd like assistance with this task, please let us know.  You can move and delete files using the command-line tools, or you can connect to the RCE via SFTP to organize your files graphically. After you have moved or deleted large files, run the 'quotareport' command again to recheck your disk usage.  Once you have resolved any quota issues affecting your home directory, you'll still need to terminate any existing NX session and reestablish it; please see the next troubleshooting step for further instructions.  If you cannot resolve your quota issues, please stop troubleshooting and contact us.
  5. Verify that you can establish a brand new NX session.  Once you have connected to the RCE via SSH, please terminate any existing NX sessions.  Instructions for doing so are here:  "How do I terminate my NX session?" . If you have multiple NX sessions, you'll need to terminate all of them before starting a new one.  Keep running the 'nxcleanup' command until it tells you that you have no NX sessions, then establish a new session. If you are unable to establish a new NX session after successfully completing all of these troubleshooting steps, please contact us.
  6. verify that you're nx4 client is using the NX protocol. Open the nxclient, highlight your connection, and instead of selecting "Connect", instead click "Edit" and verify the following: For the Protocol, it should be NX using port 4000