| tags |
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ggg, ggg2024, ggg201b |
[toc]
Lab for Fri, Jan 12th, 2024.
- Up front questions:
- Welcome & intro
- Brief syllabus overview and discussion of topics
- Please check that you've gotten an e-mail from me with farm account information!
- subject should be "farm account information for GGG 201b lab"
- username: datalab-xx
- password: <some nonsense string>
- (if you are in GGG 298, use same account as for that class)
- if you haven't gotten this e-mail, contact me at ctbrown@ucdavis.edu!
- How sequencing data analysis fits into biology research - discussion & whiteboarding
For HW 0, you might find the Happy Belly Bioinformatics UNIX Crash Course helpful.
You might be interested in workshops 1 through 5 of Intro to Remote Computing. Warning, this was written mostly by Titus ;). There are video recordings available.
You might also be interested in the Grad Pathways Microcredentialing in Research Computing - (link). Hit me up by e-mail if you're interested!
DataLab runs a bunch of workshops that you might be interested in, as does the Genome Center Bioinformatics Core. The DataLab workshops are free, the GC ones are not. This course will prepare you well, and/or complement, these workshops!
The book Bioinformatics Data Skills is an excellent reference that is worth buying if you are looking to invest ;).
Using the login information I sent you for farm, please follow the appropriate set of instructions for your platform:
Instructions for Mac OS, Linux, and WSL
Instructions for Windows and MobaXterm
Once you log in successfully...
You should be at a prompt that says datalab-XX@farm:~$ .
Things to try:
- log out and log back in a few times to make sure you've got it! You can log out by typing
exit. - log in simultaneously a few times by using a new window or windows.
Copy & paste the following command at the command prompt:
srun -p high2 --time=3:00:00 --nodes=1 --cpus-per-task 1 --mem 5GB --pty /bin/bash
This asks for three hours of access to one computer and one CPU, reserving 5 GB of memory for your use. The -p high2 says to ask for it with high priority, while the --pty /bin/bash asks for an interactive terminal as opposed to running a specific program.
You should see output that looks like this:
srun: job 9312054 queued and waiting for resources srun: job 9312054 has been allocated resources
but with different numbers ;).
And you should end up at a prompt that looks something like this:
datalab-02@cpu-3-64:~$
but again, with different numbers.
What you've done here is reserve a specific chunk of compute time for your sole private use on farm. After 3 hours, your reservation will be cancelled and whatever you're running will be stopped. You can also give up your reservation early by logging out.
Now run:
module load rstudio-server
followed by:
module load R
followed by:
rstudio-launch
The first command sets up your account to use the RStudio Server software.
The second command sets up your account to use a specific version of R.
The third command runs RStudio Server on farm.
You should see output that looks like this;
Run the following command in a new terminal on your computer:
ssh -L50700:cpu-3-64:50700 datalab-02@farm.hpc.ucdavis.eduThen, on your computer, navigate your browser to:
URL: http://localhost:50700 Username: datalab-02 Password: attention-plausible-overripe-sliceable-vacant-imprintNOTE: Using R at /share/apps/conda/environments/r-4.2.3/bin/R.
Find the ssh command above that starts with ssh -L. We'll need to run that on your laptop, so, copy it into your copy/paste buffer.
If you're on Mac OS X, Linux, or WSL: open a new terminal prompt and paste in the command. You may need to enter your datalab password from my e-mail again.
If you're on MobaXterm, open a shell window, and paste in the command. You shouldn't need a password this time.
Leaving that all running, open a browser and paste in the URL from your ssh window. It should start with http://localhost.... You'll need to enter your account name and the password output by RStudio (NOT the one in my e-mail).
If all goes well... you should see an RStudio window!