Laura’s Notebook: Pre-spawn plumbing update

Just a quick update on some plumbing that needs to be done prior to getting my animals in buckets to spawn:

Several parts that I need were out of stock @ Harrington so I ordered them to be delivered to the hatchery- they’ll get there on Tuesday. This sets me back a few days. I’ll go out on Tuesday to do as much as I can, and then will hopefully finish up the gluing on Wednesday after class. At the earliest I’ll have animals in their spawning buckets on Thursday.

I’ve been watching the pH & temp via the updates, and pH is hovering around 7.58, temp between 13.8-14.5. PSRF is lowering their heated line to 14degC on May 1st – since that’s 10 days away (and since my animals are currently at ~14) I think it’s wise to just condition them at 14.

from The Shell Game

Top on Hyak Execute nodes: It is possible!

In talking with the Hyak IT people, I stumbled on a useful ability! Running Top (activity monitor for you mac people) on execute nodes. It’s super simple. You just ssh in to the execute node from your mox login node.

For example. Im currently running PBJelly on execute node N2185. You can find this information via the scontrol show job JOBID command.

From there, in your mox login node you just ssh via ssh NODE (ex. ssh n2185 with no user credentials. This gives you shell access to the execute node as things are running. Also, it should give us direct access to the local node scratch directory, which shouldn’t have file number limitations like the /gscratch/

This also revealed some disappointing CPU usage for PBJelly. It’s essentially running single threaded, event though it was told not to. Going to have to try parallel-sql or GNU-parallel next time.

Also, got a time extension on our PBJelly run (These have to be given by people with admin privileges) up to the scheduled Hyak downtime. Fingers crossed it will finish.