Posts by dekim

1) Message boards : News : Rosetta version 4.20 released for testing (Message 6821)
Posted 3 May 2020 by Profile dekim
Post:
I'd restart the client and if there's still an issue, try aborting them.
2) Message boards : News : Scheduler update for more accurate job cache (Message 6816)
Posted 3 May 2020 by Profile dekim
Post:
Michael, please see my post below. This discrepancy was due to a server configuration that I recently removed which should fix the discrepancy for new jobs. The deadlines should be 3 days and should match what is on the website for new jobs.
3) Message boards : News : Rosetta version 4.20 released for testing (Message 6814)
Posted 3 May 2020 by Profile dekim
Post:
Is it making any progress with the downloads?
4) Message boards : News : Scheduler update for more accurate job cache (Message 6813)
Posted 3 May 2020 by Profile dekim
Post:
The BOINC client progress and remaining time estimates can be off and irregular. You can ignore those estimates and assume the jobs will run close to the cpu run time preference which defaults to 1 hour on Ralph and 8 hours on R@h.

I updated the title of this news thread since it was a bit misleading initially. A run time estimate (job duration) is calculated within the scheduler code to determine how many jobs to send to a host (and thus how many jobs to cache). This estimate is now based on the user run time preference. This change does not affect the progress and remaining time estimates displayed by the client. These values can be off and irregular due to the random nature of the modeling algorithms and checkpoint frequency, and can be ignored.
5) Message boards : News : Scheduler update for more accurate job cache (Message 6811)
Posted 2 May 2020 by Profile dekim
Post:
I figured out the issue causing the discrepancy. It should be fixed now with new work units. I previously added a "report_grace_period" param in the server config a while back that added 6 days to the normal 3 day deadline and that longer deadline is what is showing on the web site. I took that config param out so now there is no longer a grace period. Our R@h project does not have a grace period set in the config.

How many concurrent jobs are running on your host? 6? Assuming all jobs run for 1 hour, how many will not make the 3 day deadline? I can add a factor that increases the job duration which will produce a smaller cache, if necessary to help satisfy the deadlines.
6) Message boards : News : Scheduler update for more accurate job cache (Message 6808)
Posted 2 May 2020 by Profile dekim
Post:
I just got 159 Ralph@home tasks which estimate that they will take ~1 hour which does not seem possible. I'm almost certain I won't be able to meet the deadline - also the deadline shown on the RALPH website is different than what I see in my BOINC manager.


That doesn't sound good. How many cpu's? What do the website and manager show for deadlines? Maybe I need to reduce the duration calculation a bit to hopefully prevent this from happening.
7) Message boards : News : Scheduler update for more accurate job cache (Message 6806)
Posted 2 May 2020 by Profile dekim
Post:
We updated the scheduler to use the optional user defined cpu run time preference for the estimated run time. Hopefully this should produce a more accurate job cache. Please post issues regarding this updae in the discussion.
8) Message boards : News : Rosetta version 4.20 released for testing (Message 6805)
Posted 2 May 2020 by Profile dekim
Post:
Did this host previously run ok?
9) Message boards : News : Rosetta version 4.18 released for testing (Message 6802)
Posted 2 May 2020 by Profile dekim
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Done.
10) Message boards : News : Rosetta version 4.20 released for testing (Message 6799)
Posted 1 May 2020 by Profile dekim
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Thanks! I'm very happy that these updates will prevent a ton of disk usage and cpu waste.
11) Message boards : News : Rosetta version 4.20 released for testing (Message 6797)
Posted 1 May 2020 by Profile dekim
Post:
I was not able to reproduce the extraction issues so if anyone notices this issue on their host, please report back here and maybe we can work together to come up with a fix. You will know that your host is having the issue if the "Peak disk usage" is close to 1gig and if you see a file ending with ".is_bad" in the project directory.
12) Message boards : News : Rosetta version 4.20 released for testing (Message 6796)
Posted 1 May 2020 by Profile dekim
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I updated most of the R@h apps to 4.20. The remaining platforms will get updated later today.
13) Message boards : News : Rosetta version 4.20 released for testing (Message 6794)
Posted 1 May 2020 by Profile dekim
Post:
I'll send out more tasks. It would be nice to have more android and linux-arm devices in the test pool.

I'm still seeing some "finish file present too long" errors.
14) Message boards : News : Rosetta version 4.20 released for testing (Message 6793)
Posted 1 May 2020 by Profile dekim
Post:
Things are looking pretty good so far with this latest version. I'm going to look into the extraction issue to see if I can reproduce the behavior and come up with a fix, but if I don't make much progress today, then I'll go ahead and release this version on R@h. Thanks for all your feedback, and suggesting this change.
15) Message boards : News : Rosetta version 4.20 released for testing (Message 6791)
Posted 1 May 2020 by Profile dekim
Post:
Detaching from the project, cleaning out the project directory, and then reattaching the project would hopefully solve this rare issue. I don't think it is a general issue but this needs more investigation.
16) Message boards : News : Rosetta version 4.20 released for testing (Message 6778)
Posted 1 May 2020 by Profile dekim
Post:
I noticed a few hosts had issues extracting into the project directory so instead of just failing, this option allows them to continue on with the previous method of extracting into the run directory. I'm not sure what exactly caused it, one was a permissions issue and another was missing files, but rare.
17) Message boards : News : Rosetta version 4.20 released for testing (Message 6775)
Posted 1 May 2020 by Profile dekim
Post:
This version includes a fallback to the original method of extracting into the slot directory for each job if extracting into the project directory fails.

Please provide feedback in the discussion thread.
18) Message boards : News : Rosetta version 4.18 released for testing (Message 6772)
Posted 30 Apr 2020 by Profile dekim
Post:
Just for fun, a reminder for those who are opening up the graphics window, you can change the display by pressing the keys:

's' to change the side chain display, for example to show amino acid side chains in stick, spheres, etc.
'b' to change the backbone display, for example to show the backbone in cartoon, spheres, etc.
'c' to change the color display, for example for the COVID-19 interface designs, you can color by chain to see the COVID-19 spike domain and the designed mini-protein.

Keep in mind that the graphics may not immediately respond and the display can randomly change.
19) Message boards : News : Rosetta version 4.18 released for testing (Message 6771)
Posted 30 Apr 2020 by Profile dekim
Post:
That's normal
20) Message boards : News : Rosetta version 4.18 released for testing (Message 6768)
Posted 30 Apr 2020 by Profile dekim
Post:
The improvements in this update include:

1. The use of a lock file so only one job extracts the database into the project directory while other jobs wait, including graphics. Once the database is extracted, all jobs read the same database.

2. Checkpointing added to the Rosetta comparative modeling method.

Please test these updates and let us know if there are any issues. Thanks!


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