1. Maxwell Compute Cluster
Dr. Sophie Shaw
CGEBM Bioinformatician

2. What We’re Going To Do Maxwell – what it is and how to connect.
The available queues.
How to load modules.
How to run a job.
How to monitor a job.
File transfer to/from
Maxwell.
Galaxy

3. Maxwell University of Aberdeen Compute Cluster Shared resource
Lots of users all running programs at the same time

4. How Maxwell Works Login 1 Login 2 Scheduler Node 1 Node 2 Node 3
Login node
these are machines to log in to
give access to the cluster
used by many people
not for “heavy” compute
Node
a “normal” machine in the cluster
can have multiple users at the same time
where jobs are run
Job
a piece of compute work submitted to the cluster by a user
Node 1
Node 2
Node 3
Node 4
Node 5
Node 6

5. How Maxwell Works Login 1 Login 2 Scheduler Sophie Node 1 Node 2

6. How Maxwell Works Login 1 Login 2 Scheduler Tony Naveed Tony Sophie
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Node 2
Node 3
Node 4
Node 5
Node 6

7. How Maxwell Works Eduardo Login 1 Login 2 Scheduler Tony Naveed Tony
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Node 2
Node 3
Node 4
Node 5
Node 6

8. How Maxwell Works Eduardo Login 1 Login 2 Scheduler Tony Naveed Tony
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Node 6

9. How Maxwell Works Antonio Login 1 Login 2 Scheduler Tony Naveed Tony
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Node 6

10. Nodes 30 nodes with 185GB or 300GB of RAM (split between UOA and OGTC)
1 very high memory node with 3TB of RAM (32GB per processor core)
7 GPU nodes allowing software with GPU capacities to run
Verify this? Think it’s less

11. Connecting to Maxwell
Command line connections can be made via SSH (putty on Windows, terminal on MacOS).
Graphical connections can be made via X2Go.

12. Connect with PuTTY
Desktop
Common Applications
Internet
Services

14. Host: maxlogin1.abdn.ac.ukOR
Host: maxlogin2.abdn.ac.uk
Port: 22
Make sure connection type is SSH
Then Click ‘Open’

15. At this prompt, click “Yes”

16. Enter your username and then your password

17. You’re now connected to a login node and you’re ready to submit jobs!

18. Connect with X2Go
Desktop
All Disciplines
Plant & Soil Science

19. Don’t Panic!
Drag this warning to one side – it won’t go away but it’s not important!
Cancel this warning. It may pop up more than once!

20. Don’t Panic! Finally select “Ok” with this warning.
These are all related to being able to hear sound on the Maxwell – which we don’t need!

21. New Session

22. Session Name – something sensible!
Host: maxlogin1.abdn.ac.uk OR
Host: maxlogin2.abdn.ac.uk
Your Username
Make sure the session type is KDE
(XCFE and MATE also work)
Then Click ‘OK’

23. Your connection has now appeared in the top right hand corner.
Make sure that sound is “Disabled”. If it says “Enabled”, just click on the word to change it.
This should prevent any more annoying pop-ups!

24. Click Here

25. Log in using your password

26. At this prompt click “Yes”
In the bottom left corner, click on the “Start” button.
Search for Terminal.
Select the top option “Terminal”.

27. You’re now connected to a login node and you’re ready to submit jobs!

28. Any Questions So Far?

29. Common Unix Commands PROGRAM pwd ls cd mkdir man mv rm –i cp tar
gunzip
head
tail
more
less
cat
wc –l
grep
USE
Print present working directory
List contents
Change directory
Make directory
Open manual page
Move (or rename) file
Remove file (FOREVER!)
Copy file
Archive/Unarchive file
Unzip .gz file
Look at the top 10 lines of a file
Look at the bottom 10 lines of a file
Shows content of a file one full screen at a time
Shows content of a file one full screen at a time – allows searching
Shows an entire file at once/combine files
Counts the number of lines in a file
Searches for and prints the lines containing a specified pattern

30. Software on Maxwell
The Maxwell Team have more than 150 commonly used software pre-installed.
These are listed on the website.
To use it, all you need to do is load this into your environment
To list the modules available:
$ module avail
To load a module:
$ module load <name>
For example, to load the module for blast version 2.9.0:
Mention modules available.
$ module load blast-2.9.0
To unload a module:
$ module unload <name>
To list all the modules you have loaded:
$ module list

31. How Maxwell Works Login 1 Login 2 Scheduler Tony Naveed Tony Sophie
Alex
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Node 1
Node 2
Node 3
Node 4
Node 5
Node 6

32. The Queues
The sinfo command tells us about all of the queues and worker nodes that we can use:
UoA and OGTC both have dedicated queues.
You’ll only see the information of the queues that you can use.
Spot queues allow you use to all of the queues if they are available.
HOWEVER if a job is submitted by a user with priority, your job maybe be terminated on
the spot queues.

33. To Submit a Job to the Queue
You need to write a bash script! Top line
#!/bin/bash
This needs to contain some lines of info at the start
These lines all start #SBATCH
Lines beginning with #SBATCH are read by the scheduler as instructions
Examples:
Specify the queue that you want to use
#SBATCH --partition=uoa-compute
Specify the amount of time allocated to the job (hh:mm:ss)
#SBATCH --time=24:00:00
Specify the amount of memory per cpu to allocate to the job
#SBATCH --mem-per-cpu=1000

34. To Submit a Job to the Queue
More Examples:
Send an when a job ends, aborts or stops
#SBATCH --mail-type=ALL
The address to send this to
#SBATCH
To submit a batch job
#SBATCH --array=1-10
To submit a job using parallelisation
#SBATCH --ntasks=8
#SBATCH --cpus-per-task=1000

35. To Submit a Job to the Queue
To submit the job
$ sbatch scriptfile.sh
To monitor the progress of the job
$ squeue
Each job gets
a unique ID
You can see
the script
name here
Status – R if
running, PD
if waiting

36. Let’s Put this into Practice
As a group, we’ll all submit a job to Maxwell.
This will be using blastx to search for alignments of a number of
reads (in fasta format) in the E. coli genes from strain K12 (from NCBI).
If you want to learn more about blast, load the module
$ module load blast-2.9.0
And then read the blast manual
(there is a manual for each type of blast)
$ blastx -help

37. Let’s Put this into Practice
Make a directory to contain the files:
$ mkdir ~/Blast_Run
$ cd ~/Blast_Run
Copy the following four files:
$ cp /uoa/scratch/shared/cgebm/Unix_Workshop/sequences.fasta ./
$ cp /uoa/scratch/shared/cgebm/Unix_Workshop/ecolidb.phr ./
$ cp /uoa/scratch/shared/cgebm/Unix_Workshop/ecolidb.pin ./
$ cp /uoa/scratch/shared/cgebm/Unix_Workshop/ecolidb.psq ./
The sequences.fasta files contains the nucleotide sequence of genes of
interest in fasta format.
The ecolidb.* files contains the amino acid sequences of all E. coli genes
from the K12 strain. This has then been formatted ready for use with blastx.

38. Let’s Put this into Practice
Open nano
$ nano
It’s a bash script so we need this line
uoa-compute queue
Run for a maximum of 15 minutes
Using 1 Gb maximum of memory per cpu
Send an if the jobs stops
To this address

39. Let’s Put this into Practice
Make sure the module is loaded
Then you just need to type what you would have typed on the command line – running blastx against the ecolidb database, with sequences.fasta as the query, only report hits with an evalue cut off of 1e-06 to blast_results.txt
Finally save the script as submit_blast.sh (Ctrl+O) and exit nano (Ctrl+X).

40. Let’s Put this into Practice
Check you have the correct files in your directory:
$ ls
ecolidb.phr ecolidb.pin ecolidb.psq sequences.fasta submit_blast.sh
Submit the job
$ sbatch submit_blast.sh
You’ll get a job ID – note this down
Monitor the job progress
$ squeue
This should take about five minutes to run
Once finished, use more to take a look at the results file (just the top!)

41. How do we know the job was successful?!
Once a job is complete, we can use the ID to check basic facts about the run
$ sacct –j JOBID
State should be COMPLETED.
ExitCode should be 0.
Any other number means that the job failed!

42. What if a job fails? Return to Blast_Run directory and list your files
ecolidb.phr ecolidb.pin ecolidb.psq sequences.fasta slurm out
submit_blast.sh
You’ve got an extra file!
This contains all of the text which is normally output to screen whilst a program runs.
Often this is a great place to start to look at why a job has failed.
BUT it doesn’t always tell you!

43. Interactive Jobs Typing $ salloc --partition=uoa-compute
Opens up an interactive instance of node.
Here you are working in an allocated amount of space on a node. This can be customised.
Jobs can be run using the command line here and do not need to be submitted.
This is ideal for using things such as R which require an interactive environment.
Once you’re finished, remember to exit the node! Do this by typing:
$ exit
You’ll see a little message saying that you have logged out.

44. Old Maxwell vs. New Maxwell
Handy link for converting SGE commands (old Maxwell) to Slurm commands (new Maxwell):

45. Any Questions So Far?

46. Transferring Files To/From Maxwell
Desktop
Common Applications
Internet
Services

47. Transferring Files To/From Maxwell
Host: maxlogin1.abdn.ac.uk OR
Host: maxlogin2.abdn.ac.uk
Your Username
Your Password
UPDATE SCREENSHOT
Then Login

48. Transferring Files To/From Maxwell
At this message, select “Yes”

49. Transferring Files To/From Maxwell
THIS IS YOUR COMPUTER
THIS IS MAXWELL
Right click on the file you want to move and select “Upload” or “Download”

50. Any Questions So Far?

51. What is Galaxy?
Graphical user interface for our high performance compute cluster.
A lot of bioinformatics software doesn’t work on Windows PCs – needs linux.
Galaxy is an alternative to
command line.
Restricted parameters.

52. Connecting to Galaxy
Go to the Browser on your Computer (Internet Explorer or Google Chrome)
Navigate to “maxgalaxy.abdn.ac.uk”
Login with your UoA username and Password (e.g. s10ss5)

53. Connecting to Galaxy
You’re now ready to start using Galaxy!

54. Any Questions So Far?