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Con/boarding

This pages is intended for new employees of the Center for Open Neuroscience. Please note that some of the following links and resources are not publicly accessible.

Accounts

Github

Ask Yarik to add you to the CON Org.

Conventions

  1. Use https instead of ssh for git remotes to make the configuration more portable. You can switch to ssh for pushing by appending to your ~/.gitconfig

    [url "git@github.com:"]
   pushinsteadOf = https://github.com/
   pushinsteadOf = http://github.com/
[url "git@gitlab.com:"]
   pushInsteadOf = https://gitlab.com/
[url "git@bitbucket.org:"]
   pushinsteadOf = https://bitbucket.org/

  2. While you are modifying .gitconfig you might consider setting your default branch as well.

[init]
   defaultBranch = main

Chat clients

CON does not currently have a centralized IM infrastructure, there are however a number of per-project channels.

  1. CON-internal: by invitation (ask a colleague for the URL) after registering on matrix.io.
  2. DANDI slack workspace: registration comes with registering a user on https://dandiarchive.org. Then user needs to be invited to "internal" room.
  3. ReproNIM slack workspace (ask Yarik)
  4. DataLad matrix.io: public room, internal
  5. NWB slack workspace
  6. mattermost brainhack: for various open science projects

Calendar

  1. TODO: CON Calendar
  2. DANDI cal
  3. ReproNIM cal
  4. Datalad cal (I got a link for this but didn't have permissions, Yarik?)
  5. PBS Events Calendar (if you are local)

Drive

  1. Repronim grant directory

Compute

What are the appropriate uses of each box? How much does it cost to run things?

  1. Send desired login name and .pub portion of the SSH key to Yarik for development box(es): smaug, typhon, etc

    1. login to smaug: ssh -i /path/to/key me@smaug.dartmouth.edu -p $SOME_PORT

    2. login to typhon: ssh -i /path/to/key me@typhon.dartmouth.edu -p $SOME_PORT Note: When logging in from campus (use eduroam), SSH does not always work on typhon. Instead it is recommended to use ssh-agent and forward the authentication connection using -A

      1. (Assuming ssh-agent is running) ssh-add -t 3600 /path/to/key
      2. ssh-add -l should now show your fingerprint.
      3. SSH into smaug with connection forwarding: ssh -A me@smaug.dartmouth.edu -p $SOME_PORT
      4. Once on smaug ssh-add -l should now show the same fingerprint.
      5. From smaug, proceed to typhon with ssh me@typhon.dartmouth.edu -p $SOME_PORT

    3. You might benefit from specifying some details within your ~/.ssh/config for the given host(s):

      1. SOME_PORT so you don't need to enter it every time
      2. ForwardAgent is equivalent to -A
      3. ProxyJump allows you to jump automatically.
      Host smaug smaug.dartmouth.edu drogon drogon.dartmouth.edu typhon typhon.dartmouth.edu
   Port $SOME_PORT
   ForwardAgent yes

Host typhon typhon.dartmouth.edu
   ProxyJump smaug.dartmouth.edu

      With this ssh config in place, ssh typhon.dartmouth.edu would jump you over through smaug.

    4. If you need to use MacOS, ask Yarik to add your key to the Con Mac. Then you can add to your ssh config in smaug and login from there.

      Host conmac
  Hostname datalads-imac2.kiewit.dartmouth.edu
  AddKeysToAgent yes
  port 2223
  user yoh

  2. Get an account for the Discovery Cluster at Dartmouth and set up remote access to it

    1. Apply for Discovery Account
    2. The Discovery Cluster can be accessed off campus either via VPN or ProxyJump through ssh.
      1. To set up VPN, please visit the Services Portal for info.
      2. To set up ProxyJump through ssh, you must already have ssh access to a server on campus.
        • For example, if you already have ssh access to our server Smaug, you can set up ProxyJump by adding the following to your ~/.ssh/config file:
           Host smaug smaug.dartmouth.edu
       Hostname smaug.dartmouth.edu
       AddKeysToAgent yes
       IdentityFile <path to your private key>
       port <ssh port for Smaug>
       user <your username>

   Host discovery discovery.dartmouth.edu
       HostName discovery.dartmouth.edu
       PreferredAuthentications gssapi-with-mic,hostbased,keyboard-interactive,password
       ProxyJump smaug.dartmouth.edu
       ServerAliveInterval 30
       user <your user name at discovery>
    3. More information regarding the Discovery Cluster can be found at its documentation at Services Portal, Dartmouth Brain Imaging Center Handbook, and John Hudson's course notes.
    4. Request rc-DBIC group from Yarik. (Necessary to use Datalad) Be sure to follow this guide to use DBIC-installed git-annex. https://dbic-handbook.readthedocs.io/en/latest/mri/dataaccess.html#discovery-filesystem

  3. VNC is available on some of our servers

    To find out if a server provides VNC, try running vncserver --version. If the command returns information about a VNC server, VNC is available on the server. Once you have access to a server with VNC available, you can use VNC to access a desktop environment on the server by following these steps:

    1. Run vncpasswd to set a password to used for logging into VNC sessions (man vncpasswd for details)

      vncpasswd

    2. Run vncserver to start a TigerVNC desktop session (man vncserver for details)

      vncserver

      The started desktop session will be assigned an X display number that will be indicated in the output of the vncserver command.

    3. Each session is assigned a particular port number for network access. The port number is the X display number plus 5900. For example, if the X display number is 1, the port number will be 5901. Running vncserver -list will show the X display number and port number for each existing VNC session.

    4. To connect to the VNC session from your local machine, you will need a VNC client.

      If are using xtightvncviewer which has builtin SSH tunneling, you can connect to a VNC session directly.

      xtightvncviewer -via <username>@<server name>.dartmouth.edu localhost:<VNC assigned port number>

      If you are using a VNC client that does not have builtin SSH tunneling, you will need to create an SSH tunnel to the VNC server and then connect to the VNC session through the tunnel.

      1. Create an SSH tunnel to the VNC server

        ssh -L <local port number>:localhost:<VNC assigned port number> <username>@<server name>.dartmouth.edu

      2. Connect to the VNC session through the SSH tunnel using the VNC client on your local machine at localhost:<local port number>

      Where <VNC assigned port number> is the port number assigned to the VNC session on the server and <local port number> is the port number on your local machine that you want to use for the SSH tunnel. <server name> is the name of the server where the VNC session is running.

  4. ReproNim: request iam from David for AWS Access

  5. DANDI: request credentials for DANDI from Satra

Boilerplate

  1. Add yourself to whoweare to be displayed on the website.