We will be using the SUMMIT supercomputer for this class. SUMMIT is a joint venture between Colorado State University and CU Boulder and is sponsored jointly by those institutes and by a grant from the National Science Foundation.
To test whether you can access summit,
$ ssh -l <youreID@colostate.edu> login.rc.colorado.edu # Prompted for Password: <your eID Password>,push #Note, you won't see anything being typed # Switch to your cell phone and OK the transaction using DUO Key OR #Prompted for Password: <your eID password>,<duoKEY>
Quick Tip: When you type your password, you won't see anything appear on the screen. This is for security reasons.
EXAMPLE: Here is an example of Sansa Stark logging on. Her eID e-mail is
firstname.lastname@example.org and her password is
$ ssh -l email@example.com login.rc.colorado.edu Password: thepacksurvives,push
Great! Now that we know you can access summit, let's test whether you can successfully use its features.
FIRST, let's move to an scompile node.
$ ssh scompile
This moves us off the login node and onto a compile node.
SECOND, let's move into scratch/summit where we can start a directory for this class.
$ cd /scratch/summit/<youreID@colostate.edu> # substitute in your e-mail $ mkdir DSCI512_RNAseq $ cd DSCI512_RNAseq $ mkdir PROJ01_testsummit $ cd PROJ01_testsummit
THIRD, let's explore some test software that David has written for us.
In a separate tab or window, open this github link: https://github.com/meekrob/summit-rna-seq-setup
github is an amazing version control platform used for developing software, collaborating on software, and much much more. David has written some code on his github repository that we can download into our directory on Summit, execute, and use. This download process is called cloning.
To clone, select the clone or download then click on the little clipboard icon to save the URL address to your clipboard.
Switch to your terminal, and type…
$ git clone <CTRL + V> #Paste the URL address
We can now follow the instructions for test use on David's repository in the README documentation. The instructions tell us to do the following…
$ cd summit-rna-seq-setup $ make setup
Did it work? Raise your hand if you got an error.
No error? Congratulations! You can successfully use SUMMIT!
Review: Feel like you need a refresher on SUMMIT? Please review the following previous lectures from DSCI510 Linux: