Large proteins

Message boards : Number crunching : Large proteins

To post messages, you must log in.

Previous · 1 · 2 · 3 · Next

AuthorMessage
Admin
Project administrator

Send message
Joined: 1 Jul 05
Posts: 4805
Credit: 0
RAC: 0
Message 94938 - Posted: 19 Apr 2020, 20:26:10 UTC

After talking to the researcher whose jobs are the 12v1n_ batch, we decided to cancel the remaining jobs. The majority of these jobs have completed successfully.
ID: 94938 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 94946 - Posted: 19 Apr 2020, 22:17:24 UTC - in response to Message 94916.  

We may consider boosting credits for these jobs.

I'm not so interested in credits. I'm interested in scientific results.
And i'm interested that R@H can use my pc as better as possible.
ID: 94946 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1562
Credit: 16,340,194
RAC: 16,878
Message 94949 - Posted: 19 Apr 2020, 23:09:03 UTC - in response to Message 94946.  

We may consider boosting credits for these jobs.
I'm not so interested in credits.
But many people are. And these Tasks are important, so they need to be run & not aborted because they may stop other Tasks from running at the time. The possible extra Credit will just offset any loss in Credit from other Tasks not being able to run at that time.
So overall, it will still be the same -with mostly the same Credit awarded with the odd peak & dip here & there.
Grant
Darwin NT
ID: 94949 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Feet1st
Avatar

Send message
Joined: 30 Dec 05
Posts: 1755
Credit: 4,690,520
RAC: 0
Message 94953 - Posted: 19 Apr 2020, 23:31:33 UTC - in response to Message 94949.  

If you are also crunching small memory tasks, such as WCG, what loss of credit exists?
Add this signature to your EMail:
Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
ID: 94953 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1562
Credit: 16,340,194
RAC: 16,878
Message 94955 - Posted: 19 Apr 2020, 23:43:39 UTC - in response to Message 94953.  

If you are also crunching small memory tasks, such as WCG, what loss of credit exists?
Overall, other projects won't be affected- Resource share settings take care of that.
The only impact will be on Rosetta Credit, as other Rosetta work won't be able to be done at the same tame as these Tasks are being processed. Some systems won't be affected (humongous amounts of RAM, resulting in a good RAM to thread ratio), many systems will be affected (much lower RAM to thread ratio), other systems hardly affected (few cores/threads reasonable amount of RAM so a good RAM to thread ratio), others not affected at all (not enough RAM to be allocated the Tasks).
Grant
Darwin NT
ID: 94955 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1562
Credit: 16,340,194
RAC: 16,878
Message 94956 - Posted: 20 Apr 2020, 0:07:17 UTC

One more thought- a 32bit programme can address 4GB of RAM, so those programmes will still be able to process the new Work Units.
However a 32bit OS such as Windows can only access up to 3.6GB (and often less with PCIe cards in the system) due to reserved addresses- so these Tasks can only go to 64bit OS systems.
Yes, they often won't need the full 4GB, but if they get over 3GB, then there won't be enough left for the OS and and much else and a lot of drive thrashing will follow.
Grant
Darwin NT
ID: 94956 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 94976 - Posted: 20 Apr 2020, 9:19:43 UTC - in response to Message 94949.  

I'm not so interested in credits.
But many people are.

I know, i know.

And these Tasks are important, so they need to be run & not aborted because they may stop other Tasks from running at the time.

If one of these "big wus" goes in "waiting for memory", a volunteers must be present to solve the situation (or, maybe, the wus will go on deadline).

I think that these new wave should be treated carefully and gently.
A lot of people have hesitations about introducing 64bit native windows client or introducing SSEx/Avx extensions, but i think this change have more impact on volunteers
ID: 94976 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 94977 - Posted: 20 Apr 2020, 9:22:15 UTC - in response to Message 94956.  

Yes, they often won't need the full 4GB, but if they get over 3GB, then there won't be enough left for the OS and and much else and a lot of drive thrashing will follow.

If i'm not wrong, you are skeptical about 64 bit windows native client...
Now the situation is turning into a mandatory condition
ID: 94977 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Grant (SSSF)

Send message
Joined: 28 Mar 20
Posts: 1562
Credit: 16,340,194
RAC: 16,878
Message 94979 - Posted: 20 Apr 2020, 9:59:51 UTC - in response to Message 94977.  

Yes, they often won't need the full 4GB, but if they get over 3GB, then there won't be enough left for the OS and and much else and a lot of drive thrashing will follow.

If i'm not wrong, you are skeptical about 64 bit windows native client...
Now the situation is turning into a mandatory condition
No, the 32bit client will have no problem with the new 4GB Tasks. So there is still no need for a 64bit client.
However 32bit operating systems will have problems.
Grant
Darwin NT
ID: 94979 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Bryn Mawr

Send message
Joined: 26 Dec 18
Posts: 381
Credit: 11,631,984
RAC: 11,243
Message 94980 - Posted: 20 Apr 2020, 10:17:18 UTC - in response to Message 94976.  

I'm not so interested in credits.
But many people are.

I know, i know.

And these Tasks are important, so they need to be run & not aborted because they may stop other Tasks from running at the time.

If one of these "big wus" goes in "waiting for memory", a volunteers must be present to solve the situation (or, maybe, the wus will go on deadline).

<snip>


Must is a bit strong, yes, a waiting for memory could last all day but more likely an hour and if the deadline does loom it will, presumably, be given priority.
ID: 94980 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 94983 - Posted: 20 Apr 2020, 11:31:22 UTC - in response to Message 94979.  

However 32bit operating systems will have problems.

Dismiss support to 32 bit OS.
It's time to.
ID: 94983 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 94984 - Posted: 20 Apr 2020, 11:35:32 UTC - in response to Message 94980.  

Must is a bit strong, yes, a waiting for memory could last all day but more likely an hour and if the deadline does loom it will, presumably, be given priority.

I see a lot of "probably", "presumably", etc about this new app
ID: 94984 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 94985 - Posted: 20 Apr 2020, 11:38:33 UTC - in response to Message 94955.  

Some systems won't be affected (humongous amounts of RAM, resulting in a good RAM to thread ratio), many systems will be affected (much lower RAM to thread ratio), other systems hardly affected (few cores/threads reasonable amount of RAM so a good RAM to thread ratio), others not affected at all (not enough RAM to be allocated the Tasks).

All these situations will be automaticaly managed by R@H servers?

P.S. Seems like a little "nightmare".
And a nightmare rejects new volunteers.
ID: 94985 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Bryn Mawr

Send message
Joined: 26 Dec 18
Posts: 381
Credit: 11,631,984
RAC: 11,243
Message 94987 - Posted: 20 Apr 2020, 12:17:57 UTC - in response to Message 94984.  

Must is a bit strong, yes, a waiting for memory could last all day but more likely an hour and if the deadline does loom it will, presumably, be given priority.

I see a lot of "probably", "presumably", etc about this new app


Because until it is here and running there is a lot of uncertainty at to how it will run in practice.
ID: 94987 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Admin
Project administrator

Send message
Joined: 1 Jul 05
Posts: 4805
Credit: 0
RAC: 0
Message 95000 - Posted: 20 Apr 2020, 18:20:44 UTC

I want to make this clear since there is some mis-information going around. These long, up to 2000 residue, sequences that are sometimes, but not often, submitted to Robetta, our protein structure prediction server, have been around for a while now. They are nothing new, may or may not be related to COVID-19, and are rare. We have just adjusted the logic to make sure these jobs are assigned with enough memory and time to complete . The vast majority of jobs have a smaller memory footprint of less than 2g and produce models at timescales in minutes and not hours.

Run times and memory usage may vary but a typical 2000 residue Rosetta comparative modeling job from Robetta (these jobs are rare) took a little over an hour to produce 1 model and used 1.8 gigs of RAM on our local cluster.

These jobs should not be confused with the problematic cyclic peptide jobs (which have been canceled) that users reported sometimes taking longer than the cpu run time preference to complete. This also was a rare event and likely due to random trajectories that were not passing model quality filtering criteria. These cyclic peptide jobs have a small memory footprint and can produce models at a faster pace.

These issues highlight the fact that Rosetta@home runs a variety of protocols for modeling and design, the result of which can be seen from the variety of research publications and projects related to diseases such as COVID-19 and cancer, vaccine development, nano-materials, cellular biology, structural biology, environmental sciences, and the list goes on. These are within the Baker lab and IPD, but there are also researchers around the world using the Robetta structure prediction server for a vast variety of research.
ID: 95000 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 95012 - Posted: 20 Apr 2020, 20:07:16 UTC - in response to Message 95000.  

I want to make this clear since there is some mis-information going around. These long, up to 2000 residue, sequences that are sometimes, but not often, submitted to Robetta, our protein structure prediction server, have been around for a while now. They are nothing new, may or may not be related to COVID-19, and are rare. We have just adjusted the logic to make sure these jobs are assigned with enough memory and time to complete . The vast majority of jobs have a smaller memory footprint of less than 2g and produce models at timescales in minutes and not hours.

I'm here since 2005 and, even with this big wus (i don't think to have hw capable) i will be here.
You're doing GREAT work.
And i will continue to ask for the SSEx/AVX extensions :-P
ID: 95012 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jim1348

Send message
Joined: 19 Jan 06
Posts: 881
Credit: 52,257,545
RAC: 0
Message 95014 - Posted: 20 Apr 2020, 20:46:32 UTC - in response to Message 95012.  

And i will continue to ask for the SSEx/AVX extensions :-P

You are a good man. But I don't believe for a minute that you have given up on GPUs.
ID: 95014 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1924
Credit: 9,040,415
RAC: 8,687
Message 95030 - Posted: 21 Apr 2020, 5:40:49 UTC - in response to Message 95014.  

You are a good man. But I don't believe for a minute that you have given up on GPUs.

Despite i continue to write on the Ralph@Home's opencl thread, during the years i became skeptical.

But, maybe trRosetta... :-O
ID: 95030 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Michael H.W. Weber
Avatar

Send message
Joined: 18 Sep 05
Posts: 13
Credit: 6,672,462
RAC: 0
Message 95049 - Posted: 21 Apr 2020, 15:42:31 UTC

Just a short note on large RAM requiring tasks:
I consider it mandatory that in order to distribute such tasks there needs to be a new, separate RAM threshold setting in the project's preference section that requires manual activiation before such tasks are going to be send to the corresponding machines.

While it appears to work that systems not meeting the PHYSICAL RAM requirements of a project do indeed not get such tasks, it is similarly known that the determination of REMAINING RAM (while other tasks are already progressing) lacks reliability in the BOINC ecosystem (to say the least).
A lot of people run BOINC on unattended machines and are not checking these for days or even weeks and I am not sure whether to date a majority of these even has (the small) amount of 16 GB of RAM.

You may say "there will be only few of these". I am sure, I will get them all at once on the same machine. ;-)

Michael.

P.S.: Rosetta already has an EXTREMELY annoying issue with RAM management due to the sending of new WUs with deadlines dating BEFORE those of RAH tasks already running on the same system: the tasks in progress go on hold and the newly loaded ones bloat the RAM.
President of Rechenkraft.net e.V.

http://www.rechenkraft.net - The world's first and largest distributed computing association. We make those things possible that supercomputers don't.
ID: 95049 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
CIA

Send message
Joined: 3 May 07
Posts: 100
Credit: 21,059,812
RAC: 0
Message 95051 - Posted: 21 Apr 2020, 16:53:53 UTC
Last modified: 21 Apr 2020, 16:54:08 UTC

Have the larger ones started coming out? This beast ran for 18 hours and only had one decoy: https://boinc.bakerlab.org/rosetta/result.php?resultid=1156094562
ID: 95051 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Previous · 1 · 2 · 3 · Next

Message boards : Number crunching : Large proteins



©2024 University of Washington
https://www.bakerlab.org