User Tools

Site Tools


wiki:testingsummit

Testing SUMMIT

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,

  1. Open your terminal.
  2. Log into summit using secure shell:
$ 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 sstark@colostate.edu and her password is thepacksurvives

$ ssh -l sstark@colostate.edu 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:

INTRO TO SUPERCOMPUTING

USING SUMMIT

Return to RNA-seq Schedule

wiki/testingsummit.txt · Last modified: 2018/11/06 06:28 by erin