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Supercomputing Demonstration

Getting things onto and off of summit

Method 3: Filezilla from Summit Users Guide

  • Install Filezilla on your workstation.
  • Launch Filezilla, then choose “File → Site Manager…”
  • Choose “New Site”, enter a name (i.e. Summit) in the My Sites list, and then enter the following information:
    • Host: login.rc.colorado.edu
    • Protocol: choose “SFTP – SSH File Transfer Protocol”
    • Logon Type: Normal
    • User: eName@colostate.edu
    • Password: ePassword,push (where “push” is a literal string. Don’t forget the comma “,”).
  • Then click OK. This step saves the profile information for Summit.
  • To use Filezilla, choose “File → Site Manager…”. In the My Sites list choose the profile name for Summit (i.e. Summit), and click Connect. Immediately, the DUO application on your cell phone should prompt you to “Approve” the request. You will then be connected to Summit in sftp mode. A file list in your Summit home directory should display in the “Remote Site” area of Filezilla. At this point you can “drag-and-drop” files to/from Summit.

A demonstration of submitting big jobs on summit

We are going to use the program bowtie to align some short sequence reads to the genome.

To use multiple cores, match -ntasks with the number of threads your program uses.

###################
#!/bin/bash
#SBATCH --job-name=bowtie
#SBATCH --nodes=1
#SBATCH --ntasks=4

#execute a bowtie command
bowtie -p 4 /pathToIndex/ce11 seqFile1.fastq outFileName.sam

###################

In the above example the number of ntasks matches the number after -p in the bowtie command.

Not all software is designed to run on multiple cores. Look for options such as -p, -n, or -T and look for terms called parallel, multiple cores, multiple threads in the instructions.

By using multiple cores, you can really speed up your jobs, do many jobs in parallel, and make your computing much more efficient.

This is what happened when I used 1 - 24 cores for the bowtie command.

Upcoming Summit Workshop

“Getting Started on Summit” Workshop
Wednesday Sept. 20, 10am-noon
Morgan Library Event Hall #167
Colorado State University

Summit best practices

  • Consult the Support materials at RC Boulder and Colostate
  • Ask for help by e-mailing: rc-help@colorado.edu
  • Sign up for announcements by e-mailing: rc-announce-join@colorado.edu
  • Reference Summit in your research publications. citation details here
wiki/supercomputingdemo.txt · Last modified: 2017/08/31 09:32 by erin