Running some tasks on qiime2 while our computer is off

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#1

Hi there! I am running the DADA2 command to denoise some sessile samples but it takes a while... I have added threads with --p-n-threads command but it's still long...So, does it exist a command to run a task while the computer is off?

Thank you!

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#3

Hi @LillyBouvarel,

Welcome to the :qiime2: forum!

I don't know of a solution that works when the computer is fully off. However, I used to run a lot of computation over night on a laptop that sat by my bed. (I do not recommend that, but it happened.) I had a Mac and used a program called amphetamine (there are similar versions called taurine and maybe caffeine) that kept my computer "awake" for a set duration of time or until I turned the program off. I'd start my long running commands, lock the screen, turn off the brightness, plugin in the computer, and go about my evening. The next morning, stuff would hopefully :crossed_fingers: be done.

The other option is to buy time on a computer elsewhere. Amazon has some relatively cheap computation, or you might be able to get some super computer time from an institutional or national resource. On those machines, you start the job, and can walk away. If you set things up correctly, you could even configure it to send you an e-mail when you're done. (This option is probably best discussed with the people running your supercomputer center, since its going to depend on your system)

Best,
Justine

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#7

Hi @jwdebelius!

Thanks for your response! I finally found a command to run a task even if we are disconnected from our session!
I used : " nohup sh your_bash_script.sh & " and it works! You'll get this: [1] task ID (number). Nohup will run your bash file and put all the messages relative to the task your're running in a file called : nohup.out. If you want to know if your task is still running, you just have to write "top". If you want to stop it : "kill" + task ID.

Hope it will help you!

Best,
Lilly

2 Likes
#8

Hi @LillyBouvarel,

I'm glad you found a solution that works for you! I shoudl have asked about your system. (If its a server, I also like "tmux" to keep sessions running.)

Best,
Justine

2 Likes