First steps on Niagara - neuropsytox/Documentation GitHub Wiki
Logging into Niagara
Log in with your Compute Canada credentials:
You will need to setup SSH keys for Niagara, first see, https://docs.computecanada.ca/wiki/SSH_Keys
For more info on directories, modules, and running jobs in Niagara, see https://docs.scinet.utoronto.ca/index.php/Niagara_Quickstart. In general, the SciNet docs are very extensive, so any question you have regarding the Niagara cluster likely will have an answer there!
Setup the CoBrA lab software modules
Niagara has an extensive library of software you should learn how to navigate. The use a piece of software called environment-modules to manage it all, and there is a great write up on their wiki on how to use it.
The CoBrA lab has its own set of software you can use through the same "modules" system. Here's how you can get access to it:
cp /project/m/mchakrav/bashrc-template ~/.bashrcYou may get a warning that you are overwriting a file, this is okay and expected, select yes.source ~/.bashrcln -s $SCRATCH ~/scratch
Now CoBrALab modules are available for your account on Niagara. Note that you only need to do the above steps once, after that you should have access to the modules immediately after logging in.
Running module load cobralab/2019b is the most convenient way to load most of the core CoBrALab modules (such as minc-toolkit, RMINC) on Niagara.
Moving data to/from Niagara
This can be accomplished with rsync. The general format, as with any rsync command, is rsync [options] <source path> <destination path>. If you are moving files to/from your local machine, and either the source or destination is a remote server, the corresponding path will need to be prepended with the username and hostname used to access the remote server, i.e., [username@hostname]:.
Between your local machine and Niagara
On your local machine, run:
rsync -avz [email protected]:/path/to/files/on/remote /path/to/save/files/on/local
Don't forget to touch your files
find . -type f -exec touch {} +