FAQ

B. How can I tell if the cluster is busy?

Sometimes you want to know the status of the cluster and scheduling -- this can help you determine why your jobs might be pending, or know that you need to reshape your jobs to ask for smaller resources to ensure you can get your jobs in and scheduled sooner than others.

Several commands, all in the terminal, will help give you a good picture:

  • bqueues will show you the different queues, how many jobs are running, and how many are pending
  • bjobs -u all will show you the list of jobs running and pending, and the order in...
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B. I launched an application in NoMachine or the terminal. Why isn't it running?

There are several reasons why an application may not appear to be running:

  • All of the licenses for the application may be in use by others.
  • More commonly, you may have reached the resource limit on your account (# of CPUs, memory limit, or # of interactive sessions).
  • If the compute grid is busy, there many not be enough RAM or CPUs on any of the compute nodes to run your application. See...
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B. I need an interactive session with more RAM. How do I do this?

NoMachine provides convenient access to interactive sessions via the drop-down menus. Choosing one item runs a 'wrapper' script with default parameters to start your sessions (for that reason, we call them default submission scripts). But if you need a larger RAM footprint than provided, you must write a custom submission script (see this document), which provides at least the queue name, the program to run, and your requested RAM amount. For example, to...

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C. How can I run an older version of a software title?

For simplicity and ease of use, only the latest versions are offered the in NoMachine drop-down menus and via the wrapper scripts. But there are ways that you can still run older versions.

Although we may not make wrapper scripts (and hence drop-down menus on which these are based) for all software titles, the older versions of the software are still installed on the cluster. 

In order to run jobs with these older versions, you will need to know the path to the program and use that in a custom LSF job submission that you must write. Please see our...

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C. How can I run Jupyter Notebooks on the HBSGrid

Jupyter Notebooks are a common form of scientific analysis and communication using a web-browser front-end and a language/analysis engine on the back-end (usually Python).

Unfortunately, running Jupyter Notebooks on the HBSGrid is not allowed at this time. This is due to their client-server architecuture, our secure-data environment, and the inability to provide a simple, turnkey, secure setup for any user.

RCS is currently working with HBS IT and IT Security to review options in order to provide similar services or secure setups given the constraints of our...

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C. How can I use the latest version of R or RStudio?

The current installation on the HBS compute grid for RStudio is v0.99.99 and its companion R version is v3.1.2, the latest that this version of RStudio can fully support. We are aware that these are not recent versions: this is an unfortunate result due to limitations of the operating system (OS) and how software installations are managed on the compute grid. We are currently working with HBS IT find a solution to overcome this limation, which we hope to have remedied by late fall 2018.

In the meantime, if you require a more current version of R within this version of...

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D. I'm getting 'permission denied' when trying to view files. What does this mean?

This occurs when either you or a collaborator have not correctly set permissions. Subsequently, the owner of the file will need to change the file's permissions. You can identify the owner (and other permissions details) via the command ls -l MyFile.txt. Please see our HOWTO document on Changing File Permissions. If you need assistance from RCS, please include the output from ls -l...

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D. Why do file permissions change when files are copied to research storage home folders and/or project spaces?

File transfer programs, including the Mac Finder and Windows Explorer, try to do  the best job possible matching permission when files are copies over. But since the operating systems typically are different between the source (your computer) and the destination (the storage on the compute grid), the programs attempt to match as best as possible. Of course, they often don't get it right. Please see our HOWTO document on Changing File...

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