🖥 Computers @NeuroPoly#

Poly-Grames#

Poly-Grames Network Account#

A Poly-Grames network account is required to have access to various computation resources available in the laboratory.

In order to request a Poly-Grames network account you need to have your Polytechnique ID number, which you get during your onboarding.

Note

If you want to find out who is behind u/pXXXXXX Grames account, type this:

getent passwd <GRAMES_ACCOUNT>

To list all lab members:

getent group neuropoly | cut -f 4 -d : | tr , '\n' | xargs -n1 getent passwd | less

Home folder#

Every GRAMES account has a school-wide personal home folder. It is backed-up nightly.

macOS

Open Finder
CMD+K
for students:
1. smb://hvclusterfs.grames.polymtl.ca/usagers/etudiants/USERNAME
for personnel:
1. smb://hvclusterfs.grames.polymtl.ca/usagers/personnels/USERNAME

Poly-Grames Groups#

The list permissions for shared folders on duke are available here.

Connect to Poly-Grames Server#

Use Microsoft Remote Desktop Connection on creer51, creer52, creer53.

Computer : creer51.grames.polymtl.ca

Username: grames\your_polygrames_username

Password: your_polygrames_password

List of Computers at NeuroPoly#

Are you new to NeuroPoly and looking for a desk and a station? Please check the list of Desktop/Server/Clusters computers and Printers so you can pick one that is free. If you’d like a particular desk and someone else is using a station remotely, please ask the admins to move the station to another location.

If you prefer to work on your laptop, please let the admins know and we will give you a screen you can connect your laptop to.

VPN#

When working remotely from off-campus you need to use the VPN.

To connect to the VPN, you need to have an account with École Polytechnique, specifically with CAS. Students should already have this. Consultants and Research Associates will need to have an account created for them. This should have happened during your onboarding.

You can change your password at Gestion des Codes. Also, you can double-check you have VPN access by looking for VPN_* = Actif here.

The VPN is a Cisco AnyConnect server. For Linux and macOS you can reach it by first installing a VPN client such as openconnect (recommended) or Cisco AnyConnect Secure Mobility Client (if openconnect is not available for your OS/distro):

MacOS

brew install openconnect

Open your Keychain program and click ‘+’ to add a new item:

Name: poly-vpn
Account: your YOUR_CAS_USERNAME (corresponds to your GRAMES username)
Password: enter your password here.

Note: the new item has to be added as an application password to your login Keychain (i.e., not to your iCloud Keychain).

Then, create the following script:

#!/bin/bash
# vpn.sh

set -eo pipefail

USER="<YOUR_CAS_USERNAME>"
PASS="$(security find-generic-password -a "${USER}" -s poly-vpn -w)"
GROUP=PolySSL # or PolyInvites, depending on your account's status
echo -n "$PASS" | sudo openconnect -u "$USER" --authgroup "$GROUP" --passwd-on-stdin --reconnect-timeout 20 ssl.vpn.polymtl.ca

To connect to the VPN, you need to run:

./vpn.sh

Linux

apt install openconnect

Then, create the following script:

#!/bin/bash
# vpn.sh

set -eo pipefail

USER="<YOUR_CAS_USERNAME>"
PASS="<YOUR_CAS_PASSWORD>"
GROUP=PolySSL # or PolyInvites, depending on your account's status
echo -n "$PASS" | sudo openconnect -u "$USER" --authgroup "$GROUP" --passwd-on-stdin ssl.vpn.polymtl.ca

To connect to the VPN, you need to run:

./vpn.sh

Windows

Please follow the official steps from PolyMTL (French or English.

In case the above links ever break, the steps are:

Install “Cisco AnyConnect Secure Mobility Client”.
- NB: This software is licensed to organizations, so the download page will typically be behind some sort of authentication. Right now, you have to download it from the “Utilisation du Service” section of this page, which requries you to sign in with your CAS account.
Run the newly-installed Cisco AnyConnect Secure Mobility Client program.
Configure the VPN:
- Enter the server address: ssl.vpn.polymtl.ca
- In the “Group” drop-down list, choose the profile: PolySSL
- Identify yourself with the username and password of your CAS account (e.g. p123123)
Click “Accept”. You’re connected! :)

Connect to NeuroPoly Computers#

Locally#

To log into a local station at NeuroPoly use your GRAMES account.

SSH (command line)#

Once the VPN connection established, connect via ssh using the STATION you want:

 ssh <POLYGRAMES_USERNAME>@<STATION>.neuro.polymtl.ca

Note: For Windows systems, you can install Microsoft’s ssh package, WSL, PuTTY, or cmder.

Optionally, this shortcut. It allows you to just type ssh <STATION> and be connected:

cat >~/.ssh/config_neuropoly <<EOF
# GPU servers
Match Host romane,rosenberg,bireli
HostName %h.neuro.polymtl.ca

# CPU servers
Match Host joplin,abbey,tristano
HostName %h.neuro.polymtl.ca

# Workstations
Match Host ferguson,davis
HostName %h.neuro.polymtl.ca

# data servers
Match Host data
HostName %h.neuro.polymtl.ca

Match Host data.neuro.polymtl.ca
User git
PreferredAuthentications publickey

Match host *.neuro.polymtl.ca
User <POLYGRAMES USERNAME> # fill in your username and remove this comment
# passwords are required to access /mnt/duke: https://github.com/neuropoly/computers/issues/90:
PreferredAuthentications password
EOF

echo 'Include ~/.ssh/config_neuropoly' >> ~/.ssh/config

Add this to your ~/.ssh/config to make multiple ssh connections faster and without retyping your password:

Host *
ControlMaster auto
ControlPath ~/.ssh/%r@%h:%p
ControlPersist 3s

SFTP (Mount a remote station)#

ssh also allows accessing remote files, via sftp.

The best way to do this is sshfs, which makes them appear as if they were a drive on your computer:

Install sshfs, if not yet installed:

Linux

sudo apt install -y sshfs

mac (Monterey and after)

Follow this procedure.

mac (Before Monterey)

brew install --cask osxfuse
brew install sshfs

Then mount the folder

mkdir cluster_folder
sshfs <USERNAME>@<STATION>: cluster_folder

If you use ~ or nothing (as shown) after the :, the connection will be relative to to your remote home directory, e.g.

sshfs <USERNAME>@<STATION>:~/project1/ cluster_folder

will attach the remote /home/GRAMES.POLYMTL.CA/$USER/project1/ to the local ./cluster_folder, and

sshfs <USERNAME>@<STATION>:project1/ cluster_folder

will do the exact same.

However if you use / after the :, the mount will be relative to the remote root directory, e.g.

sshfs <USERNAME>@<STATION>:/tmp/ cluster_folder

will attach the remote /tmp/ to the local ./cluster_folder

Note

If you are experiencing mounting issues on macOs, this might help.

VNC (graphical interface)#

macOS

Open Finder
Click Cmd+K
In the “Server Address”, type (using the STATION you want): vnc://STATION.neuro.polymtl.ca
You can use your local/network account information or the shared account credentials

PC/Linux

Establish a VNC connection using vinaigre.
In the “Server Address”, type (using the STATION you want): vnc://STATION.neuro.polymtl.ca
You can use the password from shared account credentials

Linux stations#

On Linux targets, a VNC server needs to be started manually before the above instructions will work.

Create configuration file under ~/.vnc/xstartup with the following contents:

 #!/bin/sh
 # Uncomment the following two lines for normal desktop:
 unset SESSION_MANAGER
 unset DBUS_SESSION_BUS_ADDRESS
 startxfce4 &
 [ -x /etc/vnc/xstartup ] && exec /etc/vnc/xstartup
 [ -r $HOME/.Xresources ] && xrdb $HOME/.Xresources
 xsetroot -solid grey
 vncconfig -iconic &

Give the right permissions to the file ~/.vnc/xstartup

 chmod +x ~/.vnc/xstartup

Start VNC server

 vncserver -geometry 1600x1200 :<PORT_NUMBER>

Note: To list all running vncservers, use: ps -ef | grep vnc`

After starting the vncserver, connect to it as above.

Note

Note:

On the first start of the vncserver, you will have to set a personal password for your vnc session
The resolution can be defined by changing the value of the -geometry flag.

Stop VNC server - mandatory at the end of your session

 vncserver -kill :<PORT_NUMBER>

Language#

The default interface on our systems is français. To use another language, set your LANG environment variable:

echo 'export LANG=en_CA.UTF-8' >> ~/.profile

Logout and back in again and apps should now be in English (or the other language code you chose).

CPU/GPU Clusters#

The following CPU and GPU clusters are available for internal use at NeuroPoly.

Warning

Please indicate in NeuroPoly’s “Computer resource” calendar if you plan to launch intensive calculations on a computer. These are shared resources, so it helps to know which computer is being used and by who, in order to prioritize tasks and make the best of our resources. Your calendar entry could span several days, and should specify your name and the ID or number of GPU/CPU used. Example: julien@rosenberg:gpu[4,5], or naga@joplin:cpu[n=20] If you don’t have writing permission on this calendar please post a request on Slack #computer.

rosenberg#

Spec	Description
Model	8 x P100 GPU
OS	Ubuntu 18.04.2
Hostname	`rosenberg.neuro.polymtl.ca`
VNC

By default, the root (OS and home folder) mount point is on the NVME disk
Shared scratch located under /scratch. Please clean the unnecessary data after you finish the processing.
How to use GPU Clusters at NeuroPoly
- Video tutorial to get started

For system administrators: Please log all the changes on the station by updating the ansible scripts from neuropoly/computers.

bireli#

Spec	Description
Model	2 x Tesla GPU
OS	Ubuntu 16.04
Hostname	`bireli.neuro.polymtl.ca`
VNC	NeuroPoly Internal Document: Bireli TeamViewer Credentials

Add event to the computer calendar
Use your Poly-Grames account to connect on the machine
How to use GPU Clusters at NeuroPoly

joplin#

Spec	Description
Model	64-core CPU
OS	Ubuntu 20.04.4
Hostname
VNC

The server is bound to the GRAMES domain.

Connect to the server via ssh using the Poly-Grames account.

To access the sct_testing_management development webpage use the username: sct_test_user; passwd: management.

For fast I/O, use the NVMe hard drive, which is automatically mounted on your home at: ~/data_nvme_XXX (XXX being your GRAMES matricule). If there is no more space on this disk, use /mnt/extrassd1/.

abbey#

Spec	Description
Model	Xeon 12-core
OS	Ubuntu 20.04.3
Hostname
Credentials	NeuroPoly Internal Document: Abbey Teamviewer Credentials

fitzgerald#

Spec	Description
Model
OS	Windows 7
Hostname
Credentials	NeuroPoly Internal Document: Fitzgerald TeamViewer Credentials

tristano#

Spec	Description
Model	Mac Mini
OS	Ubuntu 16.04
Hostname
Credentials	NeuroPoly Internal Document: Tristano VNC Credentials

For SCT database interface use: SCT annotations

vnmrj#

Spec	Description
Model	PC Intel Duo Quad Core
OS	RedHat
Hostname
Credentials	NeuroPoly Internal Document: VNMRJ VNC Credentials

idea3t#

Spec	Description
Purpose	Programming pulse sequences within the Siemens IDEA environment for VE11C (Prisma)
Model	PC
OS	Windows 10 (Connect with Microsoft Remote Desktop)
Hostname	`idea3t.neuro.polymtl.ca`
Credentials	NeuroPoly Internal Document: Idea3t Remote Credentials

Warning

Possible error: “The certificate or associated chain is not valid.”
Solution: Install remote Desktop v10 or higher (v8 does not work)

idea7t#

Spec	Description
Purpose	Programming pulse sequences within the Siemens IDEA environment for VE12U (Terra)
Model	PC
OS	Windows 10 (Connect with Microsoft Remote Desktop)
Hostname	`idea7t.neuro.polymtl.ca`
Credentials	NeuroPoly Internal Document: Idea7t Remote Credentials

peterson#

Spec	Description
Purpose	EM simulation with CST
Model	PC, NVIDIA RTX A6000 (1x)
OS	Windows 10 (Connect with Microsoft Remote Desktop)
Hostname	`peterson.grames.polymtl.ca`
Credentials	<GRAMES_USERNAME>/<GRAMES_PASSWORD>

node006 (Poly-Grames)#

Spec	Description
Purpose	EM simulation with CST
Model	PC, NVIDIA Tesla V100S-PCIE-32GB (1x)
OS	Windows 10 (Connect with Microsoft Remote Desktop)
Hostname	`node006.grames.polymtl.ca`
Credentials	<GRAMES_USERNAME>/<GRAMES_PASSWORD>

node007 (Poly-Grames)#

Spec	Description
Purpose	EM simulation with CST
Model	PC, NVIDIA Tesla V100S-PCIE-32GB (1x)
OS	Windows 10 (Connect with Microsoft Remote Desktop)
Hostname	`node007.grames.polymtl.ca`
Credentials	<GRAMES_USERNAME>/<GRAMES_PASSWORD>

Connect to the Polytechnique public disk#

Finder –> Go –> Connect to server Server address:

smb://genie06.polymtl.ca/public

Then enter your ID and password at poly.

Retrieve an old backup#

duke (/mri, /projects, /sct_testing) is backed up on grappelli every evening at 21:00 EST. In order to retrieve old backup you have to contact Jean-Sébastien Décarie.

Software Installed#

Installed on each station (local)#

MRI#

FSL
ANTS
FreeSurfer
mricron (for dcm2nii conversion)
Osirix
ITKsnap
MITKworkbench
Diffusion Toolkit (with quicklook plugin) + Trackvis

Programming#

git
source tree –> visualiser of git
Xcode (with command line tools)
PyCharm (Python editor)
Sublime Text (code editor)

Misc#

Google Sketchup
Google Chrome
VirtualBox
Endnote
Dropbox
X11 Quartz
Microsoft suite (Installation kit can be found on the GRAMES server. Please see section below.)
Matlab (Installation kit can be found on the GRAMES server. Please see section below.)
Slack
NDP view
QuickLook:
- Nifti viewer
Tanguy’s app to open Nifti files with FSLview

To access software from the department (Matlab, Microsoft Office, etc.), connect to:

smb://hcifst.grames.polymtl.ca/tools

Scheduled reboots#

Each computer has a regular unattended upgrade that forces a reboot once a week. The date and time of the next reboot will be indicated in a message when you log in. Do try and consider this when starting your computations. If you started a long computation that you think will be interupted by the scheduled reboot, you can contact the admins in the #computers Slack channel to request that the reboot be exceptionally delayed.

Admins: Documentation on the standard operating procedure for delaying scheduled reboots is described here.

Admin#

Technical details about station management and documentation is found on this repository.

🖥 Computers @NeuroPoly

Page Contents

🖥 Computers @NeuroPoly#

Poly-Grames#

Poly-Grames Network Account#

Home folder#

Poly-Grames Groups#

Connect to Poly-Grames Server#

List of Computers at NeuroPoly#

VPN#

Connect to NeuroPoly Computers#

Locally#

SSH (command line)#

SFTP (Mount a remote station)#

VNC (graphical interface)#

Linux stations#

Language#

CPU/GPU Clusters#

rosenberg#

bireli#

joplin#

abbey#

fitzgerald#

tristano#

vnmrj#

idea3t#

idea7t#

peterson#

node006 (Poly-Grames)#

node007 (Poly-Grames)#

Connect to the Polytechnique public disk#

Retrieve an old backup#

Software Installed#

Installed on each station (local)#

MRI#

Programming#

Misc#

Scheduled reboots#

Admin#