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Quest Cluster Computing for the Amaral lab
Adam Pah

8.21.14
What is Quest
• Quest is the computing cluster that is administered by
Northwestern
• Quest is shared by all of Northweste...
What did we purchase
• We purchased 9 nodes to be added to Quest
• Since we purchased hardware we have a project group
tha...
How is Quest set up to handle all these users?
There are
log-in nodes
How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs
How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs
Jo...
How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs
Jo...
How is Quest set up to handle all these users?
There are
log-in nodes
And then
compute
nodes that
actually
execute jobs
Jo...
So what is Quest like?
SSH as:

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

[netid]@quest.it.northwestern.edu
So what is Quest like?
You will have a user directory, it is located at:
/home/[netid]
Your user directory is limited to 5...
So what is Quest like?
We also have a project directory, it is at:
/projects/b1022
Our project directory is limited to 432...
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 ad...
Getting the lab bashrc
Copyable:
$ cd ~
$ curl https://gist.githubusercontent.com/adamrpah/d0133fc9b36ad5854efe/raw/
aa282...
What python are we
using?
Quest has a number of
prepared “modules” for
researchers to use
What python are we
using?
Quest has a number of
prepared “modules” for
researchers to use
These “modules” are
prepackaged
...
What python are we
using?
Quest has a number of
prepared “modules” for
researchers to use
These “modules” are
prepackaged
...
What python are we
using?
This anaconda environment already has a lot of what we
use installed
What python are we
using?
This anaconda environment already has a lot of what we
use installed
I created a virtual environ...
What python are we
using?
This anaconda environment already has a lot of what we
use installed
I created a virtual environ...
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 abil...
How do I get files to Quest?
Two choices:
1) check out a repository
How do I get files to Quest?
Two choices:
1) check out a repository
2) SCP files
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 a...
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 a...
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 a...
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 a...
But what did all those options do?
The basics of that script are explained here:
Torque Job Submission
Options:
• —msub Qu...
But what did all those options do?
There are other options (that have Phoenix in mind)
but the other important one is:
• —...
That’s it! Life’s good!
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An overview of how the Amaral lab uses the Quest Cluster at Northwestern

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Quest overview

  1. 1. Quest Cluster Computing for the Amaral lab Adam Pah 8.21.14
  2. 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. 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. 4. How is Quest set up to handle all these users? There are log-in nodes
  5. 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. 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. 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. 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. 9. So what is Quest like? SSH as:
 [netid]@quest.it.northwestern.edu
  10. 10. So what is Quest like? SSH as:
 [netid]@quest.it.northwestern.edu
  11. 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. 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. 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. 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. 15. What python are we using? Quest has a number of prepared “modules” for researchers to use
  16. 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. 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. 18. What python are we using? This anaconda environment already has a lot of what we use installed
  19. 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. 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. 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. 22. How do I get files to Quest? Two choices: 1) check out a repository
  23. 23. How do I get files to Quest? Two choices: 1) check out a repository 2) SCP files
  24. 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. 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. 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. 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. 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. 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. 30. That’s it! Life’s good!

An overview of how the Amaral lab uses the Quest Cluster at Northwestern

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