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Contact Us
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Documentation

  • Requesting An Account
  • Get Started
    • Quick Start
    • Common Terms
    • HPC Resources
    • Theory of HPC
      • Overview of threads, cores, and sockets in Slurm for HPC workflows
    • Git Guide
  • Connecting to Unity
    • SSH
    • Unity OnDemand
    • Connecting to Desktop VS Code
  • Get Help
    • Frequently Asked Questions
    • How to Ask for Help
    • Troubleshooting
  • Cluster Specifications
    • Node List
    • Partition List
      • Gypsum
    • Storage
    • Node Features (Constraints)
      • NVLink and NVSwitch
    • GPU Summary List
  • Managing Files
    • Command Line Interface (CLI)
    • Disk Quotas
    • FileZilla
    • Globus
    • Scratch: HPC Workspace
    • Unity OnDemand File Browser
  • Submitting Jobs
    • Batch Jobs
      • Array Batch Jobs
      • Large Job Counts
      • Monitor a batch job
    • Helper Scripts
    • Interactive CLI Jobs
    • Unity OnDemand
    • Message Passing Interface (MPI)
    • Slurm cheat sheet
  • Software Management
    • Building Software from Scratch
    • Conda
    • Modules
      • Module Usage
    • Renv
    • Unity OnDemand
      • JupyterLab OnDemand
    • Venv
  • Tools & Software
    • ColabFold
    • R
      • R Parallelization
    • Unity GPUs
  • Datasets
    • AI and ML
      • AlpacaFarm
      • audioset
      • bigcode
      • biomed_clip
      • blip_2
      • coco
      • Code Llama
      • DeepAccident
      • DeepSeek
      • DINO v2
      • epic-kitchens
      • florence
      • gemma
      • glm
      • gpt
      • gte-Qwen2
      • ibm-granite
      • Idefics2
      • Imagenet 1K
      • inaturalist
      • infly
      • internLM
      • intfloat
      • lg
      • linq
      • Llama2
      • llama3
      • llama4
      • Llava_OneVision
      • Lumina
      • mims
      • mixtral
      • msmarco
      • natural-questions
      • objaverse
      • openai-whisper
      • Perplexity AI
      • phi
      • playgroundai
      • pythia
      • qwen
      • rag-sequence-nq
      • s1-32B
      • satlas_pretrain
      • scalabilityai
      • sft
      • SlimPajama
      • t5
      • Tulu
      • V2X
      • video-MAE
      • videoMAE-v2
      • vit
      • wildchat
    • Bioinformatics
      • AlphaFold3 Databases
      • BFD/MGnify
      • Big Fantastic Database
      • checkm
      • ColabFoldDB
      • Databases for ColabFold
      • dfam
      • EggNOG
      • EggNOG
      • GMAP-GSNAP database (human genome)
      • GTDB
      • Illumina iGenomes
      • Kraken2
      • MGnify
      • NCBI BLAST databases
      • NCBI RefSeq database
      • NCBI RefSeq database
      • Parameters of AlphaFold
      • Parameters of Evolutionary Scale Modeling (ESM) models
      • Parameters of Evolutionary Scale Modeling (ESM) models
      • PDB70
      • PINDER
      • PLINDER
      • Protein Data Bank
      • Protein Data Bank database in mmCIF format
      • Protein Data Bank database in SEQRES records
      • Tara Oceans 18S amplicon
      • Tara Oceans MATOU gene catalog
      • Tara Oceans MGT transcriptomes
      • Uniclust30
      • UniProtKB
      • UniRef100
      • UniRef30
      • UniRef90
      • Updated databases for ColabFold
    • Using HuggingFace Datasets

Documentation

  • Requesting An Account
  • Get Started
    • Quick Start
    • Common Terms
    • HPC Resources
    • Theory of HPC
      • Overview of threads, cores, and sockets in Slurm for HPC workflows
    • Git Guide
  • Connecting to Unity
    • SSH
    • Unity OnDemand
    • Connecting to Desktop VS Code
  • Get Help
    • Frequently Asked Questions
    • How to Ask for Help
    • Troubleshooting
  • Cluster Specifications
    • Node List
    • Partition List
      • Gypsum
    • Storage
    • Node Features (Constraints)
      • NVLink and NVSwitch
    • GPU Summary List
  • Managing Files
    • Command Line Interface (CLI)
    • Disk Quotas
    • FileZilla
    • Globus
    • Scratch: HPC Workspace
    • Unity OnDemand File Browser
  • Submitting Jobs
    • Batch Jobs
      • Array Batch Jobs
      • Large Job Counts
      • Monitor a batch job
    • Helper Scripts
    • Interactive CLI Jobs
    • Unity OnDemand
    • Message Passing Interface (MPI)
    • Slurm cheat sheet
  • Software Management
    • Building Software from Scratch
    • Conda
    • Modules
      • Module Usage
    • Renv
    • Unity OnDemand
      • JupyterLab OnDemand
    • Venv
  • Tools & Software
    • ColabFold
    • R
      • R Parallelization
    • Unity GPUs
  • Datasets
    • AI and ML
      • AlpacaFarm
      • audioset
      • bigcode
      • biomed_clip
      • blip_2
      • coco
      • Code Llama
      • DeepAccident
      • DeepSeek
      • DINO v2
      • epic-kitchens
      • florence
      • gemma
      • glm
      • gpt
      • gte-Qwen2
      • ibm-granite
      • Idefics2
      • Imagenet 1K
      • inaturalist
      • infly
      • internLM
      • intfloat
      • lg
      • linq
      • Llama2
      • llama3
      • llama4
      • Llava_OneVision
      • Lumina
      • mims
      • mixtral
      • msmarco
      • natural-questions
      • objaverse
      • openai-whisper
      • Perplexity AI
      • phi
      • playgroundai
      • pythia
      • qwen
      • rag-sequence-nq
      • s1-32B
      • satlas_pretrain
      • scalabilityai
      • sft
      • SlimPajama
      • t5
      • Tulu
      • V2X
      • video-MAE
      • videoMAE-v2
      • vit
      • wildchat
    • Bioinformatics
      • AlphaFold3 Databases
      • BFD/MGnify
      • Big Fantastic Database
      • checkm
      • ColabFoldDB
      • Databases for ColabFold
      • dfam
      • EggNOG
      • EggNOG
      • GMAP-GSNAP database (human genome)
      • GTDB
      • Illumina iGenomes
      • Kraken2
      • MGnify
      • NCBI BLAST databases
      • NCBI RefSeq database
      • NCBI RefSeq database
      • Parameters of AlphaFold
      • Parameters of Evolutionary Scale Modeling (ESM) models
      • Parameters of Evolutionary Scale Modeling (ESM) models
      • PDB70
      • PINDER
      • PLINDER
      • Protein Data Bank
      • Protein Data Bank database in mmCIF format
      • Protein Data Bank database in SEQRES records
      • Tara Oceans 18S amplicon
      • Tara Oceans MATOU gene catalog
      • Tara Oceans MGT transcriptomes
      • Uniclust30
      • UniProtKB
      • UniRef100
      • UniRef30
      • UniRef90
      • Updated databases for ColabFold
    • Using HuggingFace Datasets

On this page

  • SSH Connection to Unity
    • Error 1: ssh: Could not resolve hostname unity: Name or service not known
    • Error 2: permission denied (public key)
    • Error 3: Corrupted MAC on input
  • Job Management and File Storage
    • I got an error that said “disk quota exceeded.” What should I do?
    • When I try to queue a job, I get denied for MaxCpuPerAccount.
    • I have jobs in the queue, but I need to prioritize a specific job now. Can I do this without canceling the queued jobs?
    • I have too many jobs to run, and slurm won’t let me submit them all. I get an error for MaxJobCount or MaxJobSubmit. How can I work around this?
  1. Unity
  2. Documentation
  3. Get Help
  4. Troubleshooting

Troubleshooting

If you are running into errors that are not included in this page or in the rest of the documentation, please email hpc@umass.edu or join the Unity User Community Slack to chat with the Unity team and fellow Unity users.

SSH Connection to Unity

Unity relies on matching the public key stored in your Unity account to the private key on your host machine to authenticate SSH connections. Most connection errors come from not being able to match the keys appropriately.

Error 1: ssh: Could not resolve hostname unity: Name or service not known

This error occurs when your connection doesn’t understand what you mean by unity. This usually happens for one of two reasons:

  1. You haven’t yet set up your SSH config file (if that’s the case, see the SSH Documentation).
  2. You did set it up, but it’s misplaced or misnamed.

If you have created your SSH config, verify:

  1. It is a file (not directory) named config with no extension.
  2. It is located in the directory ~/.ssh/.

Error 2: permission denied (public key)

This problem means your SSH client and Unity can’t match the public key on Unity to the private key on your desktop.

First, verify that you’ve created SSH keys on the Unity portal or added an existing key to your Unity account. If you have done that, your SSH client must be configured to use your private key by specifying its location.

Additionally, ensure the following:

  • You are assigned to at least one PI group. We require at least one PI to endorse your account before you can use Unity. Request to join a PI on the My PIs page if needed.
  • Your login shell is valid. In Account Settings, try setting it to “/bin/bash” or “/bin/zsh”.
  • If you are a PI, do not use your PI group name as your login username (your login username should not start with pi_).

SSH can find keys with three methods:

  1. For keys with default names id_rsa, id_ecdsa, id_ed25519: Inside the standard ~/.ssh directory.
  2. From the IdentityFile <path to key> line in your SSH config file.
  3. With the ssh -i <path to key>... option on the command line.
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If you’re using the first two options but still get a permission denied error, try using the third option to verify that it’ll recognize the key. If this works, something’s wrong with your setup but not your key.

Error 3: Corrupted MAC on input

This issue affects Windows PowerShell users due to a known bug in PowerShell’s version of SSH. This bug causes connection issues with newer OpenSSH installations when using Microsoft’s SSH client included in PowerShell.

To fix this, Windows users using PowerShell SSH must add MACs hmac-sha2-512-etm@openssh.com to their ~/.ssh/config file, or use the flag option in your SSH command so that it reads ssh -m hmac-sha2-512-etm@openssh.com <rest of the cmd>.

Job Management and File Storage

I got an error that said “disk quota exceeded.” What should I do?

Move or delete some files to reduce your storage usage. For more information, see our documentation on disk quota management.

When I try to queue a job, I get denied for MaxCpuPerAccount.

Resource limits are set per lab, with 1000 concurrent CPUs and 64 concurrent GPUs shared across your entire PI group. If you encounter this error, adjust your usage or discuss resource allocations with your PI or the Unity team.

I have jobs in the queue, but I need to prioritize a specific job now. Can I do this without canceling the queued jobs?

You can de-prioritize your other queued jobs with scontrol update jobid=.... nice=100.

If it’s a short job, you can try the Quality of Service (QOS) to “jump the line” with a higher priority for a small, short job. (This does not always mean no wait, just a shorter wait, and depends on resource availability.) See the QOS announcement for details.

I have too many jobs to run, and slurm won’t let me submit them all. I get an error for MaxJobCount or MaxJobSubmit. How can I work around this?

Slurm has limits that are set to avoid either too many jobs being submitted at once or too many jobs running at once. To work around this, submit jobs as an array job instead.

Last modified: Tuesday, April 15, 2025 at 11:38 AM. See the commit on GitLab.
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