🖥 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
Password#
Important
Once in a while, you are requested to change your password. To do so, log onto another machine (eg bireli
, joplin
) and use the command passwd
to change your password.
Home folder#
Every GRAMES account has a school-wide personal home folder. It is backed-up nightly.
Open Finder
CMD+K
for students:
smb://hvclusterfs.grames.polymtl.ca/usagers/etudiants/USERNAME
for personnel:
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):
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 "$GROUP" --passwd-on-stdin --reconnect-timeout 20 ssl.vpn.polymtl.ca
To connect to the VPN, you need to run:
./vpn.sh
apt install openconnect
Then, create the following script:
#!/bin/bash
# vpn.sh
set -eo pipefail
USER="<YOUR_CAS_USERNAME>"
PASS="<YOUR_CAS_PASSWORD>"
GROUP=PolySSL # or PolyInvites, depending on your account's status
echo -n "$PASS" | sudo openconnect -u "$USER" --authgroup "$GROUP" --passwd-on-stdin --reconnect-timeout 20 ssl.vpn.polymtl.ca
To connect to the VPN, you need to run:
./vpn.sh
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:
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)#
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
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 the ticket tracker.
rosenberg#
Spec |
Description |
---|---|
Model |
8 x P100 GPU |
OS |
Ubuntu 18.04.2 |
Hostname |
|
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.
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 |
|
VNC |
Add event to the computer calendar
Use your Poly-Grames account to connect on the machine
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 |
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 |
For SCT database interface use: SCT annotations
vnmrj#
Spec |
Description |
---|---|
Model |
PC Intel Duo Quad Core |
OS |
RedHat |
Hostname |
|
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 |
|
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 |
|
Credentials |
peterson#
Spec |
Description |
---|---|
Purpose |
EM simulation with CST |
Model |
PC, NVIDIA RTX A6000 (1x) |
OS |
Windows 10 (Connect with Microsoft Remote Desktop) |
Hostname |
|
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 |
|
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 |
|
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 neuropoly-admin@liste.polymtl.ca 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.