3. Perform 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:
~/lsf-conf.rc, which configures some useful LSF settings
bashto automatically load
~/lsf-conf.rcwhen you log on to Compute1
~/interactive.bsub, which is a simple interactive job script
If you need help any any point in this section, please contact Liam Bindle.
Before proceeding, log on to Compute1:
$ ssh email@example.com
[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/
[wustlkey@compute1-client-1 ~]$ vim lsf-conf.rc
MY_PROJECTS_DIR so that it points to your project directory (it needs to be the absolute path).
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
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
~/.bashrc to do this automatically. Open
[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 $HOME/lsf-conf.rc fi
This snippet will automatically load your LSF settings when you log on to Compute1.
Now, check that your LSF settings are being auto-loaded properly. To do this, log off and then log back in (this is to trigger the automatic-loading of your LSF settings).
[wustlkey@compute1-client-1 ~]$ exit $ ssh firstname.lastname@example.org [wustlkey@compute1-client-1 ~]$
Then check that
MY_PROJECTS_DIR was automatically set.
[wustlkey.bindle@compute1-client-1 ~]$ echo $MY_PROJECTS_DIR /storage1/fs1/rvmartin/Active/wustlkey
3.3. Download starter job¶
interactive.bsub. This is a basic interactive job script. In the future, you can expand on it as you need,
but in the next section we will use it to get familiar with Compute1.
[wustlkey@compute1-client-1 ~]$ wget -q https://raw.githubusercontent.com/Atmospheric-Composition-Analysis-Group/compute1/master/interactive.bsub