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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
      • biomed_clip
      • blip_2
      • blip_2
      • coco
      • Code Llama
      • DeepAccident
      • DeepSeek
      • DINO v2
      • epic-kitchens
      • florence
      • gemma
      • gpt
      • gte-Qwen2
      • ibm-granite
      • Idefics2
      • Imagenet 1K
      • inaturalist
      • infly
      • instruct-blip
      • intfloat
      • LAION
      • linq
      • llama
      • Llama2
      • llama3
      • llama4
      • Llava_OneVision
      • Lumina
      • mixtral
      • msmarco
      • natural-questions
      • objaverse
      • openai-whisper
      • pythia
      • qwen
      • R1-1776
      • rag-sequence-nq
      • red-pajama-v2
      • s1-32B
      • satlas_pretrain
      • scalabilityai
      • SlimPajama
      • t5
      • Tulu
      • V2X
      • video-MAE
      • videoMAE-v2
      • vit
      • wildchat
    • Bioinformatics
      • AlphaFold3 Databases
      • BFD/MGnify
      • Big Fantastic Database
      • checkm
      • ColabFoldDB
      • dfam
      • EggNOG
      • EggNOG
      • gmap
      • GMAP-GSNAP database (human genome)
      • GTDB
      • igenomes
      • Kraken2
      • MGnify
      • NCBI BLAST databases
      • NCBI RefSeq database
      • NCBI RefSeq database
      • Parameters of Evolutionary Scale Modeling (ESM) models
      • params
      • PDB70
      • PDB70 for ColabFold
      • 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
      • biomed_clip
      • blip_2
      • blip_2
      • coco
      • Code Llama
      • DeepAccident
      • DeepSeek
      • DINO v2
      • epic-kitchens
      • florence
      • gemma
      • gpt
      • gte-Qwen2
      • ibm-granite
      • Idefics2
      • Imagenet 1K
      • inaturalist
      • infly
      • instruct-blip
      • intfloat
      • LAION
      • linq
      • llama
      • Llama2
      • llama3
      • llama4
      • Llava_OneVision
      • Lumina
      • mixtral
      • msmarco
      • natural-questions
      • objaverse
      • openai-whisper
      • pythia
      • qwen
      • R1-1776
      • rag-sequence-nq
      • red-pajama-v2
      • s1-32B
      • satlas_pretrain
      • scalabilityai
      • SlimPajama
      • t5
      • Tulu
      • V2X
      • video-MAE
      • videoMAE-v2
      • vit
      • wildchat
    • Bioinformatics
      • AlphaFold3 Databases
      • BFD/MGnify
      • Big Fantastic Database
      • checkm
      • ColabFoldDB
      • dfam
      • EggNOG
      • EggNOG
      • gmap
      • GMAP-GSNAP database (human genome)
      • GTDB
      • igenomes
      • Kraken2
      • MGnify
      • NCBI BLAST databases
      • NCBI RefSeq database
      • NCBI RefSeq database
      • Parameters of Evolutionary Scale Modeling (ESM) models
      • params
      • PDB70
      • PDB70 for ColabFold
      • 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

  • Open CLI and navigate to a directory
  • Copy files to your Unity home directory
    • SCP
    • RSYNC
  1. Unity
  2. Documentation
  3. Managing Files
  4. Command Line Interface (CLI)

Manage files using the Command Line Interface (CLI)

After successfully connecting to Unity with OpenSSH, you can manage your Unity files using the Command Line Interface (CLI). The CLI is a program that allows you to interact with the computer operating system by inputting lines of text called command-lines.

You can use the CLI to copy or upload files to your Unity home directory. The CLI also allows you to conveniently copy a whole directory (folder).

The instructions below will guide you through opening the CLI, navigating to a directory, and copying files to your Unity home directory using the commands scp and rsync.

stylus_note
In order to reference unity and copy files to your Unity home directory using scp and rsync, you must configure the OpenSSH config file to contain the information for host unity.
warning

Windows users using PowerShell SSH only 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>.

This is necessary due to a known bug in Microsoft’s SSH library which causes problems connecting to newer OpenSSH installs from Microsoft’s SSH client included in PowerShell.

Open CLI and navigate to a directory

  1. Go to your computer’s application search menu and search for “Terminal” or “Command prompt”. Once opened, the CLI typically looks like a plain window with a text area that is mostly empty besides one small line of text.

  2. Once you have your CLI open, navigate to the directory containing the files you want to upload. Experienced CLI users might choose to use absolute paths in their commands and skip this step.

To navigate to a directory, in your CLI use the command cd followed by the path to the directory:

# Windows
cd C:/Users/YOUR_NAME/Desktop
# Linux
cd /home/$USER/Desktop
# Mac
cd /Users/YOUR_NAME/Desktop

The code example above assumes that the files you want to upload are located in your desktop directory. In the Windows example, the drive you want to copy from is the C drive. If they are located somewhere else, you must change the path used above.

report
If your file name contains spaces, you will have to put it in quotes.

Copy files to your Unity home directory

There are multiple commands you can use to copy your files to your Unity home directory, including scp and rsync.

For a simple and straightforward copy, you can use the scp command without installing anything. For recurring tasks and synchronizing files over a network, you can use the rsync command. To use rsync, you must install the utility on your Linux or Mac.

SCP

OpenSSH comes with the scp command, which is similar to cp (copy) but with the added benefit of referencing the OpenSSH config file (~/.ssh/config).

The scp command allows you to use unity as part of the command because the OpenSSH config file contains the connection information for host unity. If the OpenSSH config file does not contain the connection information for host unity, you must configure the OpenSSH config file to have that information in order to use unity in your commands.

The following code example shows how to use scp to copy a single file or an entire directory into your Unity home directory:

# single file
scp FILE_NAME unity:~

# entire directory
scp -r DIRECTORY_NAME unity:~

You could also upload the files to a different location on the Unity filesystem as long as you have the correct permissions.

stylus_note
The recursive flag
-r in many commands is short for ‘recursive,’ which means that the command will apply to all files and subdirectories under that directory to ensure that all contained files are accounted for.
stylus_note
Home directory shortcut

~ in the CLI is a shortcut for your home directory path.

Your home directory path, or ~, is:

  • C:/Users/YOUR_NAME in Windows
  • /home/YOUR_NAME in Linux
  • /Users/YOUR_NAME in Mac.

RSYNC

Linux and Mac users can install and use the command rsync to copy their files.

Similarly to scp, the rsync command references the OpenSSH config file. If the OpenSSH config file does not contain the connection information for host unity, you must configure the OpenSSH config file to have that information in order to use unity in your commands.

The rsync command also comes with many useful options. For example, using the -tlp flags ensures that timestamps, relative links, and permissions are preserved, respectively.

The following code example shows how to use rsync to copy a single file or an entire directory into your Unity home directory:

# single file
rsync -tlp FILE_NAME unity:~

# entire directory
rsync -rtlp DIRECTORY_NAME unity:~
Last modified: Thursday, March 13, 2025 at 10:08 AM. See the commit on GitLab.
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