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Table of Contents
Lab Machine Overview
Available Machines
These are the available lab machines:
- ultra
- 16 cores
- 125Gi RAM
- NVIDIA GeForce RTX 3090
- core
- cortex
- 4 cores
- 7.6Gi RAM
- No GPU
- form
- 20 cores
- 62Gi RAM
- NVIDIA TITAN Xp
- geometry
- 20 cores
- 62Gi RAM
- No GPU
Proxy Jumps (Gateways)
When connecting from home or outside the CIM network, you may need to go through one of these gateway servers first:
- barn
- cow
- pig
Remote Access Lab Machines
Direct Access (inside the lab)
Use XQuartz to enable graphical applications, else use Terminal.
ssh -X *yourusername*@*machinename*.cim.mcgill.ca # OR ssh -Y *yourusername*@*machinename*.cim.mcgill.ca # Admin access (more apps permitted)
Remote Access (outside the lab, from home)
First connect through a proxy jump (example using barn):
ssh -J *yourusername*@barn.cim.mcgill.ca *yourusername*@*machinename*.cim.mcgill.ca
General CIM Login
To access the CIM system without going to a specific machine:
ssh *yourusername*@barn.cim.mcgill.ca
Lab Machine Directory Structure
When using one of the lab machines, your home directory will be mounted at:
/home/leonardo/*yourusername*/src
Your home directory shares resources across all lab machines (ultra, core, etc), which is very convenient. However, your home directory is very small and will fill up quickly, slowing down all lab machines and eventually stop allowing processes to run. Therefore, store large file in either:
/usr/local/data/*yourusername* OR /usr/local/faststorage/*yourusername*
These directories are not shared across lab machines but can support large files.
Moving Files with SCP
Copying Files
Copy File from Local → Remote
scp /your/PC/path/to/file *yourusername*@*machinename*.cim.mcgill.ca:/home/leonardo/*yourusername*/src <code> === Copy File with ProxyJump (ie: copying files when outside of the lab)=== <code> scp -o ProxyJump=*yourusername*@barn.cim.mcgill.ca ./MeanCurvature/Data/PreprocessedVolumes/resampledUS.nii *yourusername*@ultra.cim.mcgill.ca:/home/leonardo/*yourusername*/src/OBNLM
Copying Folders
Copy Folder from Local → Remote
scp -r ./your/PC/path/to/folder *yourusername*@*machinename*.cim.mcgill.ca:/usr/local/data/*yourusername*/
Copy Folder from Remote → Local
scp -r *yourusername*@*machinename*.cim.mcgill.ca:/path/to/server/folder /path/to/local/folder
Mount Local Directory on Remote Machine
sshfs -o ProxyJump=*yourusername*@barn.cim.mcgill.ca *yourusername*@*machinename*.cim.mcgill.ca:/home/leonardo/*yourusername*/src */your/PC/path
Tip: Always replace *yourusername* with your CIM login and *machinename* with the specific machine name (ultra, core, cortex, form, geometry, etc.).
To get your CIM login account details, email Olivier St-Martin Cormier.
Available Machines
These are the available lab machines:
- ultra
- 16 cores
- 125Gi RAM
- NVIDIA GeForce RTX 3090
- core
- cortex
- 4 cores
- 7.6Gi RAM
- No GPU
- form
- 20 cores
- 62Gi RAM
- NVIDIA TITAN Xp
- geometry
- 20 cores
- 62Gi RAM
- No GPU
Proxy Jumps (Gateways)
When connecting from home or outside the CIM network, you may need to go through one of these gateway servers first:
- barn
- cow
- pig
Remote Access Lab Machines
Direct Access (inside the lab)
Use XQuartz to enable graphical applications, else use Terminal.
ssh -X *yourusername*@*machinename*.cim.mcgill.ca # OR ssh -Y *yourusername*@*machinename*.cim.mcgill.ca # Admin access (more apps permitted)
Remote Access (outside the lab, from home)
First connect through a proxy jump (example using barn):
ssh -J *yourusername*@barn.cim.mcgill.ca *yourusername*@*machinename*.cim.mcgill.ca
General CIM Login
To access the CIM system without going to a specific machine:
ssh *yourusername*@barn.cim.mcgill.ca
Lab Machine Directory Structure
When using one of the lab machines, your home directory will be mounted at:
/home/leonardo/*yourusername*/src
Your home directory shares resources across all lab machines (ultra, core, etc), which is very convenient. However, your home directory is very small and will fill up quickly, slowing down all lab machines and eventually stop allowing processes to run. Therefore, store large file in either:
/usr/local/data/*yourusername* OR /usr/local/faststorage/*yourusername*
These directories are not shared across lab machines but can support large files.
Moving Files with SCP
Copying Files
Copy File from Local → Remote
scp /your/PC/path/to/file *yourusername*@*machinename*.cim.mcgill.ca:/home/leonardo/*yourusername*/src <code> === Copy File with ProxyJump (ie: copying files when outside of the lab)=== <code> scp -o ProxyJump=*yourusername*@barn.cim.mcgill.ca ./MeanCurvature/Data/PreprocessedVolumes/resampledUS.nii *yourusername*@ultra.cim.mcgill.ca:/home/leonardo/*yourusername*/src/OBNLM
Copying Folders
Copy Folder from Local → Remote
scp -r ./your/PC/path/to/folder *yourusername*@*machinename*.cim.mcgill.ca:/usr/local/data/*yourusername*/
Copy Folder from Remote → Local
scp -r *yourusername*@*machinename*.cim.mcgill.ca:/path/to/server/folder /path/to/local/folder
Mount Local Directory on Remote Machine
sshfs -o ProxyJump=*yourusername*@barn.cim.mcgill.ca *yourusername*@*machinename*.cim.mcgill.ca:/home/leonardo/*yourusername*/src */your/PC/path
Tip: Always replace *yourusername* with your CIM login and *machinename* with the specific machine name (ultra, core, cortex, form, geometry, etc.).
To get your CIM login account details, email Olivier St-Martin Cormier.