Assignment 4 Repo and RCC Accounts

tabinks commented 7 years ago

Repo: https://classroom.github.com/assignment-invitations/287b1b6a6889885960328fb09be3bc77

Assignment: http://uchicago.bio/sessions/session4/MPCS56420-2016-Autumn-Assignment4.ipynb

I've got word that your RCC accounts will be activated tomorrow. I will post here with instructions on how to login.

tabinks commented 7 years ago

Log in to RCC

From a terminal login using ssh

ssh <cnetid>@midway.rcc.uchicago.edu

Download Files

Query sequence file

wget http://uchicago.bio/sessions/session4/protein1.fasta

Sbatch script to launch a blastp job on a single node. Note that it uses a database that is located on a shared directory on RCC.

wget https://raw.githubusercontent.com/uchicago-bio/RCC-Utilities/master/single-node-blast.sbatch

Run the Script

From the command line:

sbatch single-node-blast.sbatch <some-unique-text-to-identify-this-job>

Adjust the number of threads

This task is running on a single node, but we will vary the number of threads that are used. Do runs with 1,2,4,8,16 threads. The Sandy Bridge chips in our allocation have 16 cores.

#SBATCH --cpus-per-task=1

fungedwin commented 7 years ago

Might be too early, but I'm still having trouble logging into RCC, it says permission denied after I try to enter my password.

tabinks commented 7 years ago

@fungedwin I'm looking into it.

uchicago-bio / 2016-Autumn-Forum