Bug #2274
closed
Added by Melody Campbell about 12 years ago.
Updated about 11 years ago.
Affected Version:
Appion/Leginon 2.1.0
Description
I just wanted to point out a couple of things about the RCT interface in appion:
1. Once the spider RCT model jobs finish, the 3d density cannot be downloaded through the web-interface, though they can be through a terminal.
2. The RCT model jobs submitted through appion specify 2 nodes but dmitry mentioned the jobs can only use one node at a time, therefore there is an extra node simply being
3. The 3d volume snapshots are not consistently displayed, sometimes you see them, but other times they are just black boxes. I can't find any correlation as to why or why this happens, as jobs run in the same session from the same alignment in succession will yield a mix of images vs. black boxes
4. It has been brought up that it would be useful to be able to see the 2D class chosen in the summary page with the snapshots of the 3d model.
Thanks, and let me know if i can help with or test anything (:
Hi could we please have the RCT reconstructions defaulted to 1 node instead of 2 (point 2 as described above)?
Also, points 3 and 4 would be nice too, but not as important.
Thanks!
Hi,
It would be really great if the job file created for RCT jobs could specify 1 node with 4 processors instead of 2 nodes. The routine uses only 1 node, so when a job is created in appion it takes up an extra node for absolutely no reason (the job will not run any faster) thereby contributing to the guppy queues, unless each job file created is manually changed.
I imagine the change that is needed would be from this:
#PBS -l nodes=2:ppn=4
to this:
#PBS -l nodes=1:ppn=4
I would really appreciate it if this change could be made.
Please let me know if there is anything I can do to help.
Thanks,
Melody
Hi Amber,
You mentioned it would help to have a test session for this issue with all the stacks and particles set up. A good session you can use is this one:
13mar22c
If you go to "90 complete" under "Particle Clustering" then you will see a bunch of 2D class averages select one of them (any of them) and then click "Create RCT Volume." You can leave all the default parameters as is, just put in a mask radius (ex 75) and a mass (ex 150) and then it should run. You'll see in the created job file it will request 2 nodes instead of 1 node. That is all that needs to be changed.
Thanks.
Melody
- Status changed from New to In Test
- Assignee changed from Amber Herold to Melody Campbell
Melody, go ahead and give the rct volume and try and let me know if correctly requests the nodes and ppn as you have specified.
- Status changed from In Test to Closed
Hi Amber, it asks for the correct number of nodes now, thanks!
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