3. First Time Setup#


This section uses terminology that you might not be familiar with. Please refer to the glossary for definitions.

This section describes the steps to set up your environment on Compute1, so you can start using it effectively. By the end of this section you will have:

  1. created ~/lsf-conf.rc, which configures some useful LSF settings

  2. configured bash to automatically load ~/lsf-conf.rc when you log on to Compute1

  3. created ~/interactive.bsub, which is a simple interactive job script

If you need help any any point in this section, please contact Yidan Tang.

Before proceeding, log on to Compute1:

$ ssh wustlkey@compute1-client-1.ris.wustl.edu

3.1. Create lsf-conf.rc#

Here, you are going to create lsf-conf.rc. This file sets environment variables that configure some useful LSF settings. Make sure you are logged on to Compute1 and in your $HOME directory.

Download our lsf-conf.rc template:

[wustlkey@compute1-client-1 ~]$ wget -q https://raw.githubusercontent.com/Atmospheric-Composition-Analysis-Group/compute1/master/lsf-conf.rc

Next, find your project directory. Do this by listing the contents of /storage1/fs1/rvmartin/Active/, and noting the directory that looks like it is yours (it is most likely your WUSTL key):

[wustlkey@compute1-client-1 ~]$ ls /storage1/fs1/rvmartin/Active/

Open lsf-conf.rc

[wustlkey@compute1-client-1 ~]$ vim lsf-conf.rc

and add an environment variable at the bottom:

export MY_PROJECTS_DIR=/storage1/fs1/rvmartin/Active/wustlkey

Make sure MY_PROJECTS_DIR points to your project directory (it needs to be the absolute path). Save lsf-conf.rc.

Now, you can load these setting like so:

[wustlkey@compute1-client-1 ~]$ source lsf-conf.rc


MY_PROJECTS_DIR is the only variable you need to modify in lsf-conf.rc.

3.2. Auto-load LSF Settings#

You are going to want to source lsf-conf.rc everytime you log on to Compute1. Therefore, you can add some lines to ~/.bashrc to do this automatically. Open ~/.bashrc:

[wustlkey@compute1-client-1 ~]$ vim .bashrc

and add the following at the bottom

# Source ~/lsf-conf.rc we land on a head node
if $(hostname | grep -q "compute1-client"); then
    source $HOME/lsf-conf.rc

This snippet will automatically load your LSF settings when you log on to Compute1.

Now, check that your LSF settings are being auto-loaded properly. To do this, log off and then log back in (this is to trigger the automatic-loading of your LSF settings).

[wustlkey@compute1-client-1 ~]$ exit
$ ssh wustlkey@compute1-client-1.ris.wustl.edu
[wustlkey@compute1-client-1 ~]$

Then check that MY_PROJECTS_DIR was automatically set.

[wustlkey.bindle@compute1-client-1 ~]$ echo $MY_PROJECTS_DIR

3.3. Download Starter Job#

Lastly, download interactive.bsub. This is a basic interactive job script. In the future, you can expand on it as you need, but in the next section we will use it to get familiar with Compute1.

[wustlkey@compute1-client-1 ~]$ wget -q https://raw.githubusercontent.com/Atmospheric-Composition-Analysis-Group/compute1/master/interactive.bsub