Problems and Technical Issues with Rosetta@home

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Marcin

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Message 107596 - Posted: 27 Oct 2022, 19:53:49 UTC - in response to Message 107594.  

Rosetta is out of work, DENIS has a model problem, COSMO has a SSL problem, what else is going on out there with problems? Seems like you need 12 projects to get 8 of them with work at any given time.

Einstein@Home seems to have a LOAD of arecibo WU's since they have a new PhD there now crunching the data
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Jean-David Beyer

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Message 107597 - Posted: 27 Oct 2022, 19:55:27 UTC - in response to Message 107536.  

Multithreaded CPU applications can use multiple CPU cores at once if the application is written to allow this. The main restriction on these is that no two virtual cores within a physical core can execute an instruction at the same time. However, main memory speed is usually such that any virtual core waiting on a main memory access will not have to wait any longer if another virtual core for that physical core can get its inputs from a cache instead of main memory.

My processor has 16 cores and currently I allow 11 of them to run boinc tasks. Currently, the work is like this:

    PID    PPID USER      PR  NI S    RES  %MEM  %CPU  P     TIME+ COMMAND                                                   
 276543   18589 boinc     39  19 R 411784   0.6  99.0  0 365:00.07 ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x+ 
 272100   18589 boinc     39  19 R 334292   0.5  99.2 15 398:23.28 ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x+ 
 278211   18589 boinc     39  19 R 329396   0.5  99.5  8 332:35.08 ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x+ 
 282712   18589 boinc     39  19 R 329016   0.5  99.5  1 239:43.68 ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x+ 
 294398   18589 boinc     39  19 R 117612   0.2  98.5 11   1:34.50 ../../projects/www.worldcommunitygrid.org/wcgrid_opn1_au+ 
 294358   18589 boinc     39  19 R 114536   0.2  99.2 13   2:33.49 ../../projects/www.worldcommunitygrid.org/wcgrid_opn1_au+ 
 294415   18589 boinc     39  19 R 113492   0.2  98.6  5   1:02.63 ../../projects/www.worldcommunitygrid.org/wcgrid_opn1_au+ 
 289788   18589 boinc     39  19 R  73000   0.1  99.3  4  92:44.43 ../../projects/www.worldcommunitygrid.org/wcgrid_mcm1_ma+ 
  18589       1 boinc     30  10 S  39016   0.1   0.2  8  39924:11 /usr/bin/boinc   <---<<< BOINC CLIENT                                  
 292098   18589 boinc     39  19 R   7136   0.0  99.3  3  43:46.18 ../../projects/milkyway.cs.rpi.edu_milkyway/milkyway_1.4+ 
 293586   18589 boinc     39  19 R   6996   0.0  99.2  6  12:04.72 ../../projects/milkyway.cs.rpi.edu_milkyway/milkyway_1.4+ 
 293296   18589 boinc     39  19 R   4876   0.0  99.6  2  18:16.38 ../../projects/universeathome.pl_universe/BHspin2_20_x86+ 


Only a little over 11% of cache references are misses. Other tasks, expecially N216 CPDN tasks hit the cache very hard.

# perf stat -aB -e cache-references,cache-misses
 Performance counter stats for 'system wide':

     5,688,852,727      cache-references                                            
       632,547,182      cache-misses              #   11.119 % of all cache refs    

      61.181304830 seconds time elapsed


Computer 5910575
Computer information

CPU type 	GenuineIntel
Intel(R) Xeon(R) W-2245 CPU @ 3.90GHz [Family 6 Model 85 Stepping 7]
Number of processors 	16

Operating System 	Linux Red Hat Enterprise Linux
Red Hat Enterprise Linux 8.6 (Ootpa) [4.18.0-372.26.1.el8_6.x86_64|libc 2.28]
BOINC version 	7.20.2
Memory 	63772.81 MB
Cache 	16896 KB   <---<<<

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Message 107598 - Posted: 28 Oct 2022, 7:57:42 UTC - in response to Message 107595.  

Rosetta has run out of work about two days ago, always check the server status page in case you don't get work, usually you'll find the reason there.

Do You think it is an intermittent shortage or is the project heading into a sunset?
As far as I know, the WU supply with Rosetta tasks has been intermittent since a while, that does not need to mean, they will shut down soon. It just means they have no work right now, this might happen at any project.
.
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Sid Celery

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Message 107599 - Posted: 28 Oct 2022, 9:37:42 UTC - in response to Message 107598.  
Last modified: 28 Oct 2022, 9:43:23 UTC

Rosetta has run out of work about two days ago, always check the server status page in case you don't get work, usually you'll find the reason there.

Do You think it is an intermittent shortage or is the project heading into a sunset?
As far as I know, the WU supply with Rosetta tasks has been intermittent since a while, that does not need to mean, they will shut down soon. It just means they have no work right now, this might happen at any project.

There really is nothing quite so tiresome as random people claiming the project is going to close down because they had a period with no tasks.

A reminder of the status of the project posted here 28-Sep-2022
There are plans for more python tasks, but we are still working on creating the new disk image for the VM.
This image will likely be larger in size since we hope to run some of the latest deep-learning based methods for protein design and validation.

Computing resources are still very much in high demand within the Baker Lab and IPD so Rosetta@home will definitely help once we can get the latest software set up and running.

Also, the standard rosetta application is currently being worked on for an update.
The IPD has hired a software developer specifically to help expedite this.

I am not sure about timelines at the moment but hopefully there should be updates to both projects/apps within the next month or so.

David Kim

If an update to the VM for python tasks and taking a developer on to update the Rosetta app is a sign of heading into a sunset, then yes.
More obviously it's the opposite, so no.

Since that statement was originally posted we've had the largest drop of new tasks for quite some time.
It's always difficult to hold people to timelines on a project that's always been at the cutting edge, so while I'd hope we'll see something in November, it might be more realistic to expect something this side of the new year. It gets here when it gets here
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Message 107600 - Posted: 28 Oct 2022, 10:26:23 UTC - in response to Message 107599.  

If an update to the VM for python tasks and taking a developer on to update the Rosetta app is a sign of heading into a sunset, then yes.
More obviously it's the opposite, so no.

Since that statement was originally posted we've had the largest drop of new tasks for quite some time.
It's always difficult to hold people to timelines on a project that's always been at the cutting edge, so while I'd hope we'll see something in November, it might be more realistic to expect something this side of the new year. It gets here when it gets here


The death of Ralph@home is not a good sign...
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Sid Celery

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Message 107601 - Posted: 28 Oct 2022, 11:33:35 UTC - in response to Message 107599.  

There really is nothing quite so tiresome as random people claiming the project is going to close down because they had a period with no tasks.

Not sure as the front page and server status page haven't been updated quite yet, but another batch of tasks seem to be coming through
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Sid Celery

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Message 107602 - Posted: 28 Oct 2022, 11:36:54 UTC - in response to Message 107600.  
Last modified: 28 Oct 2022, 11:37:21 UTC

The death of Ralph@home is not a good sign...

Can something that was never really alive be said to have died?
I never joined it. If I had, I'm not sure I'd ever have noticed.
Unless there was ever some golden era I'm completely unaware of over the last 14 years
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Message 107603 - Posted: 28 Oct 2022, 11:57:57 UTC - in response to Message 107602.  

The death of Ralph@home is not a good sign...

Can something that was never really alive be said to have died?
I never joined it. If I had, I'm not sure I'd ever have noticed.


No, no, i'm wrong!!
Today, just for curiosity, i opened the link and Ralph is online!
After months is back!
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kotenok2000
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Message 107605 - Posted: 28 Oct 2022, 12:09:41 UTC - in response to Message 107603.  
Last modified: 28 Oct 2022, 12:11:29 UTC

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Message 107607 - Posted: 28 Oct 2022, 13:57:04 UTC - in response to Message 107605.  

Bu last workunit was returned at 07-31
https://grafana.kiska.pw/d/boinc/boinc?orgId=1&var-project=Ralph@Home&from=now-6M&to=now


That's not a problem.
Ralph has not a lot of work
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Message 107608 - Posted: 28 Oct 2022, 16:37:31 UTC
Last modified: 28 Oct 2022, 16:42:16 UTC

wow..17 tasks available..whoopie!
Where do you see the so called upcoming RAH stuff?
I looked randomly up to page 17 of Robetta and all I see is neural network stuff.
So either I am looking in the wrong place or something does not add up.
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.clair.

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Message 107610 - Posted: 28 Oct 2022, 23:57:13 UTC - in response to Message 107600.  

The death of Ralph@home is not a good sign...

"This parrot is dead"
Errm . .
Oh .
sorry wrong forum .
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Sid Celery

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Message 107611 - Posted: 29 Oct 2022, 0:09:28 UTC - in response to Message 107601.  

There really is nothing quite so tiresome as random people claiming the project is going to close down because they had a period with no tasks.

Not sure as the front page and server status page haven't been updated quite yet, but another batch of tasks seem to be coming through

Very small - maybe 50-60k. Not even enough to fill all cores at any one time.
Ah well, something.
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Message 107612 - Posted: 29 Oct 2022, 8:20:19 UTC - in response to Message 107611.  

There really is nothing quite so tiresome as random people claiming the project is going to close down because they had a period with no tasks.

Not sure as the front page and server status page haven't been updated quite yet, but another batch of tasks seem to be coming through

Very small - maybe 50-60k. Not even enough to fill all cores at any one time.
Ah well, something.



The majority of the work goes to their 3 channel deep learning system.
That's what I saw on Robetta at least.
Robetta is the system that feeds all systems right? There is no separate system that feeds here?
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Message 107613 - Posted: 29 Oct 2022, 13:13:10 UTC - in response to Message 107612.  

[snip]
The majority of the work goes to their 3 channel deep learning system.
That's what I saw on Robetta at least.
Robetta is the system that feeds all systems right? There is no separate system that feeds here?

Robetta is a system that allows people outside their campus to enter work. This creates workunits with names that start with rb_ .
Work can also be created on campus, giving workunits with names that don't start with rb_ and at least used to be most of what was available.
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Message 107614 - Posted: 29 Oct 2022, 14:27:18 UTC - in response to Message 107613.  

[snip]
The majority of the work goes to their 3 channel deep learning system.
That's what I saw on Robetta at least.
Robetta is the system that feeds all systems right? There is no separate system that feeds here?

Robetta is a system that allows people outside their campus to enter work. This creates workunits with names that start with rb_ .
Work can also be created on campus, giving workunits with names that don't start with rb_ and at least used to be most of what was available.



ok, so short of clicking every workunit or whatever...how can you tell at a glance what is going to come here?
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Message 107615 - Posted: 29 Oct 2022, 14:32:04 UTC - in response to Message 107614.  

There is show names link at rosetta results page.
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Sid Celery

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Message 107616 - Posted: 30 Oct 2022, 0:19:49 UTC - in response to Message 107612.  

There really is nothing quite so tiresome as random people claiming the project is going to close down because they had a period with no tasks.

Not sure as the front page and server status page haven't been updated quite yet, but another batch of tasks seem to be coming through

Very small - maybe 50-60k. Not even enough to fill all cores at any one time.
Ah well, something.

The majority of the work goes to their 3 channel deep learning system.
That's what I saw on Robetta at least.
Robetta is the system that feeds all systems right? There is no separate system that feeds here?

You never seem to get tired of whining about something, do you
I thought you were going to leave
The latter would be preferable if the former is the only thing you ever have to say
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Sid Celery

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Message 107617 - Posted: 31 Oct 2022, 3:24:41 UTC - in response to Message 107611.  

There really is nothing quite so tiresome as random people claiming the project is going to close down because they had a period with no tasks.

Not sure as the front page and server status page haven't been updated quite yet, but another batch of tasks seem to be coming through

Very small - maybe 50-60k. Not even enough to fill all cores at any one time.
Ah well, something.

Maybe another 100k went through a few hours ago, but they seem to have all been picked up already.
Regular tasks, even if never quite sufficient to last
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Message 107619 - Posted: 31 Oct 2022, 18:49:59 UTC - in response to Message 107617.  

Not sure as the front page and server status page haven't been updated quite yet, but another batch of tasks seem to be coming through

Very small - maybe 50-60k. Not even enough to fill all cores at any one time.
Ah well, something.

Maybe another 100k went through a few hours ago, but they seem to have all been picked up already.
Regular tasks, even if never quite sufficient to last

On this page you can easily see if some tasks are available and how the supply was in the past 90 days.
.
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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