General Usage

How do I gain access to Rivanna?

A faculty or research staff member must first request an allocation on Rivanna. Full details can be found here.

How do I log on to Rivanna?

Use an SSH client from a campus-connected machine and connect to Instructions for using ssh and other login tools, as well as recommended clients for different operating systems, are here. You can also access Rivanna through our Web-based interface Open OnDemand or FastX.

Off Campus?

Connecting to Rivanna from off Grounds via Secure Shell Access (SSH) or FastX requires a VPN connection. We recommend using the UVA More Secure Network if available. The UVA Anywhere VPN can be used if the UVA More Secure Network is not available. Only Windows and Mac OSX operating systems are supported by the Cisco client provided by ITS. Linux users should refer to these unsupported instructions to install and configure a VPN. The More Secure Network requires authentication through Duo; users should follow the instructions on the dialog box to enter "push" as the password.

Open OnDemand users do not need a VPN to access Rivanna.

How do I reset my current password / obtain a new password?

Access to the HPC cluster requires a valid Eservices password. Your Netbadge password is not necessarily the same thing, so if you are unable to log in, you should first try resetting your ITS password here. Resetting the Netbadge password should sync it with your Eservices password, which is no longer directly accessible to you. If the problem persists, contact ITS through their online Helpdesk. Keep in mind that ITS requires annual resetting of your password. If you see a “password expired” message, you will need to change it through ITS.

What happens to my account when I leave UVA?

ITS controls access to the University’s computing resources, so when you or your students leave, you/they may lose access to many of these resources. Sponsored accounts allow people who work or volunteer at UVA, but who are not paid by UVA, to access the University’s computing resources. Researchers with sponsored accounts cannot request RC services but they are allowed to use the systems we manage as members of a MyGroups (requires VPN connection) group controlled by a UVA Principal Investigator (PI). Details on sponsored accounts are posted on the ITS sponsored accounts page.


Some users logging in through ssh may encounter this error message. If you receive this message, please see our instructions on how to clear this error.

When I try to log in with ssh, nothing happens when I type my password!

When you type your passaword, the ssh program does not echo your typing or move your cursor. This is normal behavior.

When running Firefox on Rivanna, I get : “Firefox is already running, but is not responding. To open a new window, you must first close the existing Firefox process, or restart your system.” What can I do?

From your home directory on Rivanna, run the commands:

rm -rf ~/.mozilla/firefox/*.default/.parentlock

rm -rf ~/.mozilla/firefox/*.default/lock

How can I view .pdf or .csv files on Rivanna?

For .pdf files, run the command:

 atril filename.pdf

The atril command can also be used to display image files, e.g. .png and .jpg files.

For .csv files, run the command:

 oocalc filename.csv

where filename is a placeholder for the specific filename.

When should I use FastX Web, when should I use an Open OnDemand Desktop session?

Both allow you to run applications with graphical user interfaces in a Linux Desktop environment.

Open OnDemand Desktop:

  • Runs your session on allocated resources on a compute node.
  • Ideal for running compute-intensive single-node applications with graphical user interface.
  • Does not require a VPN connection from off-Grounds locations.
  • Recommended practice for running interactive jobs (particularly for coursework with a reservation).

FastX Web:

  • Runs all users' sessions on a single frontend node.
  • Good for light-weight file management, script editing.
  • Requires a VPN connection from off-Grounds locations.


What is an allocation?

Time on Rivanna is allocated as Service Units (SUs). One SU corresponds to one core-hour. Multiple SUs make up what is called an allocation (e.g., a new allocation = 100K SUs). Allocations are managed through MyGroups (requires VPN connection) groups that are automatically created for Principal Investigators (PIs) when they submit an allocation request. Full details can be found here.

How can I request an allocation?

The different Service Unit (SU) allocation types are explained in this article. It includes links to our allocation request webforms.

How do I check my allocation status on Rivanna?

Run the allocations command. The output may look like this:

Name           Balance  Reserved Effective Available
-------------- -------- -------- --------- ---------
rivanna_alloc  9885.811 1000.000  8885.811  8885.811

 for more information about a specific allocation,
 run: 'allocations -a <allocation group>'

The Balance column shows the total of unused service units (SUs); the Reserved column shows the number of SUs held for current active jobs (pending or running). The Effective and Available columns show the difference of Balance and Reserved, i.e. the amount of SUs available for future jobs. After a job completes, the SUs actually consumed will be deducted from the allocation Balance and any SUs unused by that job will be released from the Reserved pool.

In all cases you can only submit additional jobs if the available SU amount is sufficient to cover the full SU request for the jobs.

You do not need any allocation service units to access the frontend or files in your directories as long as your account is active.

If you don’t see your allocation, it may mean that you’ve been removed from the allocation group or that your allocation has expired.

How do I check an allocation’s expiration date?

To check an allocation’s expiration date run allocations -a <allocation group> command. Alternatively, run mam-list-allocations.

Only Standard Allocations, Dean’s Allocations and Instructional Allocations have an expiration date. PIs may request renewal of their expired allocation. Purchased Allocations never expire.

How are Service Units Reserved?

When a job is submitted the account manager calculates the required maximum amount of Service Units (SUs) using the assumption that the job will run the full amount of time requested. These SUs are held in reserve as a “lien” against the allocation charged for the job. When the job completes the lien is released and the actual SUs consumed are deducted from the allocation balance. See How do I check my allocation status on Rivanna? for specifics.

How are Service Units charged for specialty hardware, e.g. GPU and large memory nodes?

Service Units (SUs) serve as a general single currency on Rivanna. SUs in a given allocation account can be used freely to run jobs on nodes in the standard, parallel, gpu and largemem queues. Please note that the SU charge rate is different for some of the specialty hardware, e.g. the GPU nodes, as listed here.

How do I add or remove people from my allocations?

You must use the MyGroups (requires VPN connection) interface to do this, and you must have administrative access to the group.

How do I check allocation usage of individual group members?

Please visit here to see how to generate an allocation usage report.

I submitted a job and receive an error “Insufficient balance. Applying funds failure for JobId=”. What should I do?

The error indicates that your allocation group does not have enough service units to execute the job. Check your allocation status as described here. Also verify that your allocation has not expired, see here.

Only Standard Allocations, Dean’s Allocations and Instructional Allocations have an expiration date. PIs may request renewal of their expired allocation. Purchased Allocations never expire.

Research Software

How do I use research software that’s already installed?

We use the lmod system for managing software environments. Learn more about how to use lmod.

Does RC install research software?

Our staff will install software onto Rivanna if it is of wide applicability to the user community. Software used by one group should be installed by the group members, ideally onto leased storage for the group. We can provide assistance for individual installations.

For help installing research software on your PC, please contact Research Software Support at

Is there any other way to install research software that I need?

Some groups and departments have installed a bundle of software they need into shared space. Please see your departmental IT support personnel if your department has its own bundle.

Can I run this Docker container on Rivanna?

We do not run Docker on Rivanna. Instead we use Singularity. Singularity can run Docker images directly, or you can convert a Docker image to a Singularity image. To import existing Docker images, use the singularity pull command.

module load singularity
singularity pull docker://account/image

Software images built by Research Computing are hosted on Docker Hub. For example, to pull our PyTorch 1.5.1 image, run:

singularity pull docker://uvarc/pytorch:1.5.1

Please visit this page for more details.

Can I run application/container X on a GPU?

Please check the user manual for your application/container before running on a GPU. For instance, scikit-learn does not have GPU support; hence using GPUs for scikit-learn will not help with your job performance but will only cost you more service units (see SU charge rate here) and prevent other users from using the GPUs.

How can I make my Jupyter notebook from JupyterLab to run as a batch job on Rivanna?

  1. Capture the information that you use to start up a JupyterLab session. It helps to take a screenshot of the web form where you enter the partition, number of cores, amount of memory, etc. You will need that information for requesting resources on a compute node.

  2. Note which kernel is used to run your notebook. This information will be needed later.

  3. Convert the notebook to a regular script. To do this, go into the notebook that you want to convert. In the upper left corner, click on File > Export Notebook As > Export Notebook to Executable Script . This will download the script onto your laptop. On my computer, this leaves a blank window on my screen. But, if I close that tab on my browser, the tab with the notebook returns. I’m now down with the notebook and can terminate the session.

  4. Upload the “executable script” to Rivanna. In Open onDemand dashboard view, on the black ribbon across the top, click on Files > Home Directory. This will open a page that shows the files that you have in your home directory on Rivanna. At the top of the page, toward the right, is a button labelled “Upload”. Click on that button. In the dialog box that appears, click on “Choose File”. This will allow you to go to the downloaded file and select it.

  5. Create a Slurm script to run your code. The Slurm script list the resources and instructions that are needed to run your “executable script”. See the following link:

  6. Open a terminal window on Rivanna, and move to the location where your scripts are. We recommend using the web-based FastX application (see below). Once in a terminal window, type sbatch followed my the name of your Slurm script.

Job Management

How do I submit jobs?

You submit jobs by writing a Slurm script and submitting it with the sbatch command. Please see our Slurm documentation page.

How do I submit an interactive job?

If you wish to run a program that requires a graphical user interface or generates other graphics for display, such as a plot or chemical model, use one of the Open OnDemand interactive apps. Several are available, but if you one you wish to use isn’t in the list, submit an interactvie Desktop request.

If you will be using the command line for your interactive job you may use the locally-written ijob command. The minimum required options are -A and -c for allocation and number of cores. Run ijob -h for a list of all options.

For more information see the documentation.

What queues can I use?

After logging in, run the command qlist to see a list of queues and their availability. Run qlimits for the restrictions on submitting to each queue.

How do I choose which queue to use?

Queues (partitions to Slurm) are set up to emphasize one-core (serial or threaded), multi-node parallel, and specialty hardware including large-memory nodes and GPUs. More information about queue policy is at the Rivanna homepage.

How do I check the status of my jobs?

Run the command jobq

If reporting a problem to us about a particular job, please let us know the JobID for the job that you are having a problem with. You can also run jobq -l to relate particular jobs to specific submission scripts.

Why is my job not starting?

Several things can cause jobs to wait in the queue. If you request a resource combination we do not have, such as 28 cores on a parallel node, the queueing system will not recognize that this condition will not be met and will leave the job pending (PD). You may also have run a large number of jobs in the recent past and the “fair share” algorithm is allowing other users higher priority. Finally, the queue you requested may simply be very busy. If your job is pending there will be another field with the reason; if it is Resources that means that the resource you requested isn’t available, either because it is busy or because you requested a nonexistent resource. If the reason is “Priority” it means that a job with higher priority than yours is running. Your job will rise in priority as it waits so it will start eventually. To request an estimate from the queueing system of your start time, run squeue -u <mst3k> --start (substitute your own login for mst3k).

How can I check when my job will start?


squeue -j <jobid> --start

Slurm will provide an estimate of the day and time your job will start.

Why was my job killed?

Usually this is because you inadvertently submitted the job to run in a location that the compute nodes can’t access or is temporarily unavailable. If your jobs exit immediately this is usually why. Other common reasons include using too much memory, too many cores, or running past a job’s timelimit.

You can run sacct:

[aam2y@udc-ba36-27:/root] sacct
       JobID    JobName  Partition    Account  AllocCPUS      State ExitCode
------------ ---------- ---------- ---------- ---------- ---------- --------
159637       ompi_char+   parallel  hpc_admin         80  COMPLETED      0:0
159637.batch      batch             hpc_admin          1  COMPLETED      0:0
159637.0          orted             hpc_admin          3  COMPLETED      0:0
159638       ompi_char+   parallel  hpc_admin        400    TIMEOUT      0:1
159638.batch      batch             hpc_admin          1  CANCELLED     0:15
159638.0          orted             hpc_admin         19  CANCELLED  255:126

If it’s still not clear why your job was killed, please contact us and send us the output from sacct.

Why can’t I submit jobs anymore?

In order to be allowed to submit jobs, you must not be overallocated with your /scratch usage and you must have some remaining service units. There is a limit of 10 TB of space used per user in each /scratch directory and if you exceed either of those limits, you will not be able to run jobs until you clean up. To check whether this is the case, run


If you have not exceeded the limits on /scratch, check whether your account has allocation units remaining by running


Why do I get sbatch error: Batch script contains DOS line breaks

If you use a Windows editor to create Slurm batch scripts, when you try to run them you may encounter an error

sbatch: error: Batch script contains DOS line breaks (\r\n)
sbatch: error: instead of expected UNIX line breaks (\n).

Windows and Linux use different conventions to mark the end of each line. Many applications on Rivanna, such as compilers, Matlab, etc., understand Windows end-of-line markers, but the shell does not. This is easy to fix by running the dos2unix commmand

dos2unix myscript.slurm

It will not hurt to run dos2unix on a file that doesn’t need it. Sometimes you get {^M} character at the end of every line when the file was imported from Windows environment. dos2unix usually takes care of the problem, but not 100% all the time.

How do I check the efficiency of my completed jobs?

Run the command seff on the Slurm job ID:

udc-ba34-36-deepLearning$seff 40330441
Job ID: 40330441
Cluster: shen
User/Group: teh1m/users
State: COMPLETED (exit code 0)
Nodes: 1
Cores per node: 2
CPU Utilized: 00:15:14
CPU Efficiency: 89.08% of 00:17:06 core-walltime
Job Wall-clock time: 00:08:33
Memory Utilized: 6.89 GB
Memory Efficiency: 58.76% of 11.72 GB

The output of this command is also contained in the email sent by Slurm once your job completes.

Storage Management

What storage options are available to me to use on Rivanna?

All users are provided a 50-GB home directory for longer-term storage. This directory provides “snapshots” though it is not backed up. Each user also is provided 10TB of temporary “scratch” storage accessible as /scratch/$USER where $USER will stand for your ID. Scratch storage is fast but is not backed up in any way.

If the free storage is not sufficient, you need snapshots of your files, or you wish to share space among a research group, the group should lease storage.

Why should I use /scratch storage?

Scratch storage is fast and provides a large quantity of free space. However, there are limits on the number of files and the amount of space you may use. This is to maintain the stability and performance of the system. Please review our scratch filesystem policy for details. If you use or expect to use a large number of files please contact us.

How do I obtain leased storage?

Research Computing offers two tiers of leased storage, Research Standard and Research Project. Please see our storage page for details.

How do I check my disk usage?

Run hdquota on a Rivanna frontend.

How do I check my /scratch usage on Rivanna?

Run the command sfsq:


If you have used up too much space, created too many files, or have “old” files you may be regarded as “overallocated”. Please note that if you are overallocated, you won’t be able to submit any new jobs until you clean up your /scratch folder.

If I’m over my disk quota in either in my /home directory or my /scratch directory, how can I determine my disk usage?

You can run the following command from your /home or /scratch directory to see how your disk usage is distributed across subdirectories, and where you need to remove files. You can increase max-depth to go further down in the directory structure.

du . -h  --max-depth=1|sort -h -r

If I’m over my file limit in /scratch, how can I determine where all the files are located?

From your /scratch directory, run the following command to determine where you need to remove files.

find . -type f | cut -d/ -f2 | sort | uniq -c

How long can I store files in /scratch?

/scratch is designed to serve as fast, temporary storage for running jobs, and is not long-term storage. For this reason, files are periodically marked for deletion from all /scratch directories. Please review the /scratch filesystem policy for more details. Store longer-term files in your home directory or purchased storage.

How do I share data in my /scratch or leased storage with a colleague?

To share data from your /scratch directly with any other user, use Globus sharing. If your colleague also has an account on Rivanna, he or she does not need to set up a personal endpoint but can simply log into the uva#main-DTN endpoint and navigate to his or her /scratch directory to transfer the files.

If you wish to share data in leased space with a member of your group, be sure that permissions are set so that the group member can access your subdirectory. The college can then simply use the data directly, or copy it elsewhere. If you wish to share data from your leased storage to a colleague who is not a member of the group, use Globus sharing in the same manner as sharing /scratch.

Data Transfer

How do I transfer data from UVA Box to my /scratch directory on Rivanna?

Log into Rivanna using the web-based FastX and launch the MATE Desktop interface. Then from the top menu bar, open firefox through the FastX desktop, in the upper right hand corner of the browser window you should see 3 horizontal bars. Click on that and then select Preferences from the drop down window. In the new window scroll down until you see Downloads and select ‘Always ask you where to save files’. Then when you go to Box to download, a new window will pop up and if you click on ‘Other locations’, you can navigate to your scratch directory.

How do I transfer data from my /scratch directory on Rivanna to my UVA Box account?

Log into Rivanna using the web-based FastX and launch the MATE Desktop interface. Then from the top menu bar, open firefox through the FastX desktop and log into your UVA Box account. Once logged in to box, click on the New + button (upper right) to upload a file/folder. In the left sidebar of the new window, select Other Locations/Computer/scratch/ to navigate to your scratch directory and select the files/folders you want to upload to your box account.

What Linux commands can I use to transfer files to/from Rivanna?

Smaller files can be transferred to/from Rivanna using scp, sftp, and rsync as well as standard FTP tools.

Larger files should be moved using Globus.

Read more about data transfer.

I need to push and commit code changes from Rivanna account to my GitHub account. How do I set that up?

You must first generate an ssh key and then copy it to your git repository. Here are the instructions for generating the ssh key and what to do on your git page:

  1. To generate an ssh key, see the following link: ssh key generation

  2. Click on the drop-down menu next to my Git profile picture in the upper right corner; Select Settings; Click on SSH and GPG keys in the left column; Click on the New SSH Key button and followed the directions to upload your ssh key. Make sure that the ssh key is in your authorized_keys file in your .ssh directory on Rivanna.

  3. The next step is to clone the repository using the ssh link. If you have already cloned the repository using the http link and made a number of changes to your files, you won’t want to redo them. Rename the directory that was created when you first cloned the repository. Then, re-clone the repository using the ssh link and copy all of the files you had changed to the new directory. Finally, push those changes back to the repository.

Other Questions

What if my question doesn’t appear here? Take a look at our User Guide. If your answer isn’t there, contact us.