The document discusses Quest, the computing cluster at Northwestern University. It summarizes that the Amaral lab purchased 9 nodes to add to Quest, giving the lab 108 simultaneous jobs. It provides instructions for setting up accounts on Quest, including downloading a bashrc file, using the Anaconda Python environment, submitting jobs via a generate_qsub script, and getting help installing additional packages.

1. Quest Cluster Computing for the Amaral lab
Adam Pah
8.21.14

2. What is Quest
• Quest is the computing cluster that is administered by
Northwestern
• Quest is shared by all of Northwestern
• There are two ways to get time on Quest:
• Get an allocation of hours
• Purchase hardware to be added to Quest
• We purchased hardware to be added to Quest

3. What did we purchase
• We purchased 9 nodes to be added to Quest
• Since we purchased hardware we have a project group
that will be everyone in the lab
• Each node has:
• 12 cores per node
• 128 GB RAM per node
• So we can run 108 simultaneous jobs as a project group

4. How is Quest set up to handle all these users?
There are
log-in nodes

5. How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs

6. How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs
Jobs are submitted on log-in nodes to a “scheduler”

7. How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs
Jobs are submitted on log-in nodes to a “scheduler”
The “scheduler” finds a free compute node and runs the job

8. How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs
Jobs are submitted on log-in nodes to a “scheduler”
The “scheduler” finds a free compute node and runs the job
For us, it will find a free spot in the hardware that we purchased

9. So what is Quest like?
SSH as:
[netid]@quest.it.northwestern.edu

10. So what is Quest like?
SSH as:
[netid]@quest.it.northwestern.edu

11. So what is Quest like?
You will have a user directory, it is located at:
/home/[netid]
Your user directory is limited to 50 GB and not backed up

12. So what is Quest like?
We also have a project directory, it is at:
/projects/b1022
Our project directory is limited to 432 GB and it is
shared by *EVERYONE* in the lab

13. So how do I set up my user on Quest?
Quest isn’t the same as every other computer we have in
the lab and there are some adjustments
I already created a bashrc, some shortcuts, and a script to
make it as much like using phoenix as possible
So the first thing to do is get the bashrc that the lab will use

14. Getting the lab bashrc
Copyable:
$ cd ~
$ curl https://gist.githubusercontent.com/adamrpah/d0133fc9b36ad5854efe/raw/
aa282448ae924592452c952f25632a27361deff6/amaral_quest_bashrc > .bashrc
$ source ~/.bashrc
This puts LabTools on your path
(LabTools is our projects folder)
It also sets up aliases so mercurial
and python will work

15. What python are we
using?
Quest has a number of
prepared “modules” for
researchers to use

16. What python are we
using?
Quest has a number of
prepared “modules” for
researchers to use
These “modules” are
prepackaged
programming
environments for a
number of languages/
use cases

17. What python are we
using?
Quest has a number of
prepared “modules” for
researchers to use
These “modules” are
prepackaged
programming
environments for a
number of languages/
use cases
We’re using Anaconda

18. What python are we
using?
This anaconda environment already has a lot of what we
use installed

19. What python are we
using?
This anaconda environment already has a lot of what we
use installed
I created a virtual environment and added in the few
missing packages that we use

20. What python are we
using?
This anaconda environment already has a lot of what we
use installed
I created a virtual environment and added in the few
missing packages that we use
To use this python on a log-in node or test to make sure a
package is installed just do:
Note that the “actpy”
command is unique
and requires our lab
bashrc

21. What if I need a package installed?
Let myself, Nick, Joao, or June know and we’ll take care
of it to the best of our ability
Anaconda uses pip to install packages, so almost all
packages are good to go
However, this means that any package that won’t install
cleanly with pip is now suspect!
We can ask the Quest team to take care of it, but that will
take time

22. How do I get files to Quest?
Two choices:
1) check out a repository

23. How do I get files to Quest?
Two choices:
1) check out a repository
2) SCP files

24. How do I submit a job to Quest to run?
Actually, it’s pretty simple.
I wrote a script that is in LabTools that abstracts away any
differences on Quest
1) Navigate to directory with python code

25. How do I submit a job to Quest to run?
Actually, it’s pretty simple.
I wrote a script that is in LabTools that abstracts away any
differences on Quest
1) Navigate to directory with python code
2) Submit the job with the “generate_qsub” script

26. How do I submit a job to Quest to run?
Actually, it’s pretty simple.
I wrote a script that is in LabTools that abstracts away any
differences on Quest
1) Navigate to directory with python code
2) Submit the job with the “generate_qsub” script
3) Check that the job is running with “qstat”

27. How do I submit a job to Quest to run?
Actually, it’s pretty simple.
I wrote a script that is in LabTools that abstracts away any
differences on Quest
1) Navigate to directory with python code
2) Submit the job with the “generate_qsub” script
3) Check that the job is running with “qstat”
4) Enjoy!

28. But what did all those options do?
The basics of that script are explained here:
Torque Job Submission
Options:
• —msub Quest uses the Moab scheduler, this makes a
moab submission file. This option is MANDATORY when
using Quest
• —execute With this option the generate_qsub script will
submit the job to the scheduler automatically
• —temporary This option will remove the submission
scripts

29. But what did all those options do?
There are other options (that have Phoenix in mind)
but the other important one is:
• —kwargs This option takes in command arguments that
your code uses

30. That’s it! Life’s good!