Problems and Technical Issues with Rosetta@home

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.clair.

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Message 106372 - Posted: 10 Jun 2022, 0:15:56 UTC

one of the `fun` things about the Linux command line is the `kill` command
A great way to deal will zombie processes
and rosetta workunits .
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Mr P Hucker
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Message 106373 - Posted: 10 Jun 2022, 0:34:09 UTC
Last modified: 10 Jun 2022, 0:34:40 UTC

You mean exactly like pressing "end task" in Windows Task Manager?

And wouldn't you be better letting Boinc kill it? Then it knows to start another one.
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Michael E.@ team Carl Sagan

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Message 106374 - Posted: 10 Jun 2022, 2:59:27 UTC - in response to Message 106367.  

I did an experiment with one of these tasks that seem to never finish. I let it run. Elapsed time is now 4 days 5:12:xx hours with 00:00:01 seconds remaining. I am curious if it will ever finish and was curious about what the credits might look like, but the task took too long.

The Rosetta BOINC status says the task has: "timed out - no response". Task id is: aagb-FPS_pp-mNMPHE-mACPenC13T-B3LEU_pp_3_2601503_6_0

As Sid says, if the time needed for a "Rosetta python projects 1.03 (vbox64)" is much more than is expected, stop the task.
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Message 106375 - Posted: 10 Jun 2022, 7:06:37 UTC - in response to Message 106278.  

Ah, this is the problem. The Python book has only one use:


It's a pity, the new version of Python seems great
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.clair.

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Message 106377 - Posted: 10 Jun 2022, 18:34:58 UTC - in response to Message 106373.  

You mean exactly like pressing "end task" in Windows Task Manager?
And wouldn't you be better letting Boinc kill it? Then it knows to start another one.

Yes , true , and it iz wot I do , Just commenting and being a silly bint .
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Message 106378 - Posted: 10 Jun 2022, 23:45:46 UTC - in response to Message 106375.  

Ah, this is the problem. The Python book has only one use:
It's a pity, the new version of Python seems great
PyPy ROTFPMSL! Is that the one for kids?
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Mr P Hucker
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Message 106379 - Posted: 10 Jun 2022, 23:46:33 UTC - in response to Message 106377.  

You mean exactly like pressing "end task" in Windows Task Manager?
And wouldn't you be better letting Boinc kill it? Then it knows to start another one.

Yes , true , and it iz wot I do , Just commenting and being a silly bint .
You sound like a fun bint, what are you wearing? ;-)
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.clair.

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Message 106380 - Posted: 11 Jun 2022, 0:24:36 UTC - in response to Message 106379.  
Last modified: 11 Jun 2022, 0:27:29 UTC

You mean exactly like pressing "end task" in Windows Task Manager?
And wouldn't you be better letting Boinc kill it? Then it knows to start another one.

Yes , true , and it iz wot I do , Just commenting and being a silly bint .
You sound like a fun bint, what are you wearing? ;-)

At the moment I am not wearing my one piece `avatar` na`vi suit , with tail , though the hair is real ,
I never was as good looking as Neytiri , or blue ;-)
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Mr P Hucker
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Message 106381 - Posted: 11 Jun 2022, 0:40:11 UTC - in response to Message 106380.  

You mean exactly like pressing "end task" in Windows Task Manager?
And wouldn't you be better letting Boinc kill it? Then it knows to start another one.

Yes , true , and it iz wot I do , Just commenting and being a silly bint .
You sound like a fun bint, what are you wearing? ;-)

At the moment I am not wearing my one piece `avatar` na`vi suit
If you're not wearing it then.... oh!

, with tail , though the hair is real ,I never was as good looking as Neytiri , or blue ;-)
I'm not so sure that's a suit. Isn't that just her natural skin?
https://james-camerons-avatar.fandom.com/wiki/Na%27vi
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Sid Celery

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Message 106382 - Posted: 11 Jun 2022, 7:59:08 UTC - in response to Message 106374.  

I did an experiment with one of these tasks that seem to never finish. I let it run. Elapsed time is now 4 days 5:12:xx hours with 00:00:01 seconds remaining. I am curious if it will ever finish and was curious about what the credits might look like, but the task took too long.

The Rosetta BOINC status says the task has: "timed out - no response". Task id is: aagb-FPS_pp-mNMPHE-mACPenC13T-B3LEU_pp_3_2601503_6_0

As Sid says, if the time needed for a "Rosetta python projects 1.03 (vbox64)" is much more than is expected, stop the task.

I'm rarely confident of anything regarding computers, but because I work away 2-4 consecutive days every week I routinely come back to one or two tasks in progress for whole days.
With one solitary exception, they show reduced CPU runtimes of 1 or 2hrs down to as little as 20-something seconds. Not one ever restarts once stalled
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Message 106385 - Posted: 12 Jun 2022, 3:08:05 UTC

You might be able to leave it running more than the number of cores you have, then if some stall your PC is still flat out while you're away. Not sure if you can do this for tasks designed for a single core, but I do it with multicore Cosmology tasks:

<app_config>
   <app_version>
       <app_name>camb_boinc2docker</app_name>
       <plan_class>vbox64_mt</plan_class>
       <avg_ncpus>5</avg_ncpus>
       <cmdline>--nthreads 6</cmdline>
   </app_version>
</app_config>


This tells the actual app to use 6 cores per task, but the Boinc scheduler they only use 5.

Or perhaps there's another way to tell Boinc you have more cores than you really do?
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Message 106390 - Posted: 15 Jun 2022, 6:46:18 UTC

I just got back from vacation and restarted my system. I didn't check it and today I did and I see this stupid project dropped me from VM jobs until I reset it again a bit ago. This project really enjoys kicking people off its VM stuff.
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Message 106391 - Posted: 15 Jun 2022, 7:37:54 UTC - in response to Message 106390.  

I just got back from vacation and restarted my system. I didn't check it and today I did and I see this stupid project dropped me from VM jobs until I reset it again a bit ago. This project really enjoys kicking people off its VM stuff.
I keep getting kicked off on a machine that never fails a VB task. It doesn't make sense.
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Message 106392 - Posted: 15 Jun 2022, 22:41:11 UTC - in response to Message 106391.  

I just got back from vacation and restarted my system. I didn't check it and today I did and I see this stupid project dropped me from VM jobs until I reset it again a bit ago. This project really enjoys kicking people off its VM stuff.
I keep getting kicked off on a machine that never fails a VB task. It doesn't make sense.



Nothing here makes sense anymore....new normal I guess.
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Message 106393 - Posted: 16 Jun 2022, 4:54:59 UTC

I await to see what happens when we get them all done, only two thirds of a million left, it used to be 15 million.
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Message 106409 - Posted: 21 Jun 2022, 9:46:19 UTC

559,612 as of 21 Jun. I'm sure they're slowing down. Maybe they're sneaking more in?
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Message 106417 - Posted: 26 Jun 2022, 13:45:04 UTC

No idea where to put this comment and I didn't want to start a new topic.
WCG forum has come back - but no sign of any tasks - and a couple of things have been said.
It's now apparent to me that the people taking over WCG are virtually a one-man-band (ok, a three-man-band) so expectations from that project in future are tending to zero for me.

And a brief article on the Open Pandemics project while it was under the auspices of IBM make it clear that they've achieved the square root of f'all after two years.

I get the feeling everyone's wasting their time. Distributed Computing seems to be heading downhill at a rate of knots.
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Message 106418 - Posted: 26 Jun 2022, 13:54:41 UTC - in response to Message 106417.  

No idea where to put this comment and I didn't want to start a new topic.
WCG forum has come back - but no sign of any tasks - and a couple of things have been said.
It's now apparent to me that the people taking over WCG are virtually a one-man-band (ok, a three-man-band) so expectations from that project in future are tending to zero for me.

And a brief article on the Open Pandemics project while it was under the auspices of IBM make it clear that they've achieved the square root of f'all after two years.

I get the feeling everyone's wasting their time. Distributed Computing seems to be heading downhill at a rate of knots.
Bullshit. Just because one project is slow doesn't mean the whole lot are no good. Pick the one you trust.

I do like the three man band reference though. I reckon it must be to take 4 months just to copy some data to a new server. Total and utter incompetance.

WCG is almost running actually, I managed to persuade 9 devices to attach a couple of days ago, and now 3 of them have acknowledged the name of the project. Just waiting on my username, previous credits, then a work unit. Give the hamster a chance! My main gripe is you can't complain in their forums. Anything remotely against them gets you banned instantly.

In the meantime I've been doing Folding at Home since it has biology on GPUs.
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Message 106419 - Posted: 26 Jun 2022, 18:56:45 UTC - in response to Message 106417.  
Last modified: 26 Jun 2022, 19:07:19 UTC

I get the feeling everyone's wasting their time. Distributed Computing seems to be heading downhill at a rate of knots.

I have my own reservations too. For one thing, the molecular docking technique (both SiDock and OPN) has not yet been shown to result in a cure of anything that I have seen, just a lot of candidates for trials.
Maybe Scripps can make OPN fly. They are working hard on it.

And Rosetta is mostly out of it for us crunchers, though they continue their very innovative work in-house.

For BOINC, try TN-Grid or QuChemPedIA.
https://gene.disi.unitn.it/test/index.php
https://quchempedia.univ-angers.fr/athome/

But for the really most innovative science, and plenty of work for both CPUs and GPUs, there is only one: Folding@home.
https://foldingathome.org/start-folding/?lng=en

It is not a BOINC project, and the Linux client is a bit of a kludge (I have posted on it), but they are working on a new one.
https://foldingforum.org/viewtopic.php?p=356367#p356367
And they keep advancing their technology with new compute cores for CPU and GPU.

Molecular dynamics (MD), is very compute-intensive. But it yields very accurate results that no other technique can do.
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Message 106420 - Posted: 26 Jun 2022, 19:09:34 UTC - in response to Message 106419.  

I get the feeling everyone's wasting their time. Distributed Computing seems to be heading downhill at a rate of knots.

I have my own reservations too. For one thing, the molecular docking technique (both SiDock and OPN) has not yet been shown to result in a cure of anything that I have seen, just a lot of candidates for trials.
You have to eliminate the wrong things to find the right thing.
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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