Minirosetta 3.73-3.78

Message boards : Number crunching : Minirosetta 3.73-3.78

To post messages, you must log in.

Previous · 1 · 2 · 3 · 4 · 5 . . . 11 · Next

AuthorMessage
B.Rothbaecher

Send message
Joined: 2 Jun 12
Posts: 7
Credit: 1,101,835
RAC: 0
Message 79454 - Posted: 28 Jan 2016, 21:45:05 UTC

ID: 79454 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Trotador

Send message
Joined: 30 May 09
Posts: 66
Credit: 49,588,981
RAC: 52,190
Message 79455 - Posted: 28 Jan 2016, 23:05:36 UTC - in response to Message 79454.  

I\'ve several WUs which end with error \"Error reading and gzipping output datafile: default.out\".

https://boinc.bakerlab.org/rosetta/result.php?resultid=789266189
https://boinc.bakerlab.org/rosetta/result.php?resultid=789264562
https://boinc.bakerlab.org/rosetta/result.php?resultid=789264561
https://boinc.bakerlab.org/rosetta/result.php?resultid=789175516
https://boinc.bakerlab.org/rosetta/result.php?resultid=789173393


This is occurring with the new WUs starting with 2wcd_, I do not know if any of them is finishing without this error. Moreover, these WUs have very large memory usage, this mornig I had to abort one that was over 20 GB although all the rest are below 1 GB so far
ID: 79455 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Trotador

Send message
Joined: 30 May 09
Posts: 66
Credit: 49,588,981
RAC: 52,190
Message 79457 - Posted: 29 Jan 2016, 6:45:08 UTC - in response to Message 79455.  

I\'ve several WUs which end with error \"Error reading and gzipping output datafile: default.out\".

https://boinc.bakerlab.org/rosetta/result.php?resultid=789266189
https://boinc.bakerlab.org/rosetta/result.php?resultid=789264562
https://boinc.bakerlab.org/rosetta/result.php?resultid=789264561
https://boinc.bakerlab.org/rosetta/result.php?resultid=789175516
https://boinc.bakerlab.org/rosetta/result.php?resultid=789173393


This is occurring with the new WUs starting with 2wcd_, I do not know if any of them is finishing without this error. Moreover, these WUs have very large memory usage, this mornig I had to abort one that was over 20 GB although all the rest are below 1 GB so far


These units are definitively causing problems, cancelling them.
ID: 79457 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
krypton
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 16 Nov 11
Posts: 108
Credit: 2,164,309
RAC: 1
Message 79458 - Posted: 29 Jan 2016, 8:23:52 UTC

Thank you Trotador and B.Rothbaecher, I\'ve informed the group about the error!
ID: 79458 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
kipnis
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 29 Jan 16
Posts: 1
Credit: 45,501
RAC: 0
Message 79459 - Posted: 29 Jan 2016, 17:19:28 UTC

Jobs starting from 2wcd_ are intended to perform \"fold and dock\" simulations of a native protein forming large oligomeric complexes. These simulation should allow identification of key features responsible for oligomerization and modifications necessary to convert 12mer to higher order oligomeric states. It looks like the monomer is too big for the protocol to be run without any modification. Sorry, Trotador, for any trouble.
ID: 79459 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Trotador

Send message
Joined: 30 May 09
Posts: 66
Credit: 49,588,981
RAC: 52,190
Message 79460 - Posted: 29 Jan 2016, 19:25:33 UTC - in response to Message 79459.  

Jobs starting from 2wcd_ are intended to perform \"fold and dock\" simulations of a native protein forming large oligomeric complexes. These simulation should allow identification of key features responsible for oligomerization and modifications necessary to convert 12mer to higher order oligomeric states. It looks like the monomer is too big for the protocol to be run without any modification. Sorry, Trotador, for any trouble.


Thanks for the explanation, no issue in finding problems when crunching. The computation error ocurred in all my hosts that received these units (and all the wingmen) but I see the memory problem only in one of them and maybe it is host related and not these wus. Will you rebuilt the wus for further tests? It seems an interesting simulation.


ID: 79460 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 670
Credit: 5,240,248
RAC: 7,685
Message 79461 - Posted: 30 Jan 2016, 0:32:12 UTC
Last modified: 30 Jan 2016, 0:37:43 UTC

Oddball results from this task after restarting from a checkpoint - both Outcome: Success, and error messages at the end of the log file:

http://boinc.bakerlab.org/rosetta/result.php?resultid=789657365

Could you check if 3.71 restarts from checkpoints correctly, and if it reports correctly whether the task reports success properly?
ID: 79461 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Natalie de Clare

Send message
Joined: 27 Feb 12
Posts: 4
Credit: 670,812
RAC: 0
Message 79462 - Posted: 30 Jan 2016, 11:54:37 UTC

The blue background is stupid and I do not like it at all. If you are going to change that then have an option for blue and black otherwise I am just not going to use it anymore.
ID: 79462 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 631
Credit: 1,813,948
RAC: 2,558
Message 79463 - Posted: 30 Jan 2016, 22:36:22 UTC - in response to Message 79462.  

The blue background is stupid and I do not like it at all.


Please, use other terms.
ID: 79463 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Jonathan Jeckell

Send message
Joined: 17 Dec 05
Posts: 7
Credit: 3,470,565
RAC: 1,362
Message 79470 - Posted: 3 Feb 2016, 0:55:22 UTC

Not sure if this is directly due to the application upgrade or not, but seems to correlate to when I started having some issues.

I\'m running a few laptops using Linux on USB sticks and now In the last few days BOINC takes an insufferably long time to start while it tells me \"please wait.\" I took a look tonight and top showed the client and Rosetta were barely using the processor. Once in a while one of the Rosetta apps would bounce up to 100% for a bit and then subside. I have the client set to max out the processor and memory using all cores without restriction. No other processes are coming close to using a significant portion of the processor, and nothing indicates the USB bandwidth is the issue.
ID: 79470 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 670
Credit: 5,240,248
RAC: 7,685
Message 79471 - Posted: 3 Feb 2016, 5:30:56 UTC - in response to Message 79451.  


No, i will not move. I have a weak and unstable internet connection. I do not waste internet traffic with a shorter runtime and disk space as well.


@sinspin, I would just point out that if files already exist on your host as you receive new work, then they do not have to be downloaded. However, if the host completes all tasks that need a file, the file is deleted.


Mod.Sense, that appears to be due to a new BOINC feature that I had not noticed before. When I checked several months ago, anything downloaded to the project directory was almost always kept for YEARS, such as versions of minirosetta that had been superseded years ago, and doing a Reset project only downloaded another copy each each of the files previously in the project directory.

Also, it appears that not all BOINC projects are set up to use this feature yet; some of the other projects my computers participate in still have files in their project directories that were superseded years ago.

It\'s good to see this feature used; more BOINC projects should use it.


ID: 79471 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Wiktor Jezioro | lakewik.pl

Send message
Joined: 22 Feb 15
Posts: 4
Credit: 17,409,243
RAC: 41
Message 79472 - Posted: 3 Feb 2016, 18:26:03 UTC

Hello!

I have error processing units of the series: if32_4_0044_r1_partial_fold_and_dock_nat_cst

Example: https://boinc.bakerlab.org/rosetta/workunit.php?wuid=716899628

The workunits of this batch processing are over 5 hours and haven\'t checkpoints

Thanks
ID: 79472 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator
Project administrator

Send message
Joined: 22 Aug 06
Posts: 3434
Credit: 0
RAC: 0
Message 79477 - Posted: 4 Feb 2016, 15:55:32 UTC - in response to Message 79471.  


Mod.Sense, that appears to be due to a new BOINC feature that I had not noticed before.


The project files get an additional attribute (sticky) which indicates they should be kept regardless of the current tasks. This is used for files that all tasks use. That way if all tasks for a given project are completed at some point in time, you won\'t have to download the always (or often) needed files with the next tasks.

My comments were more about other files that are more task specific. If you get another task later that requires the same file, a cache in a proxy or having another task on-board already that uses the same file will avoid another download.

Rosetta Moderator: Mod.Sense
ID: 79477 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator
Project administrator

Send message
Joined: 22 Aug 06
Posts: 3434
Credit: 0
RAC: 0
Message 79478 - Posted: 4 Feb 2016, 15:56:25 UTC - in response to Message 79470.  

Not sure if this is directly due to the application upgrade or not, but seems to correlate to when I started having some issues.

I\'m running a few laptops using Linux on USB sticks and now In the last few days BOINC takes an insufferably long time to start while it tells me \"please wait.\" I took a look tonight and top showed the client and Rosetta were barely using the processor. Once in a while one of the Rosetta apps would bounce up to 100% for a bit and then subside. I have the client set to max out the processor and memory using all cores without restriction. No other processes are coming close to using a significant portion of the processor, and nothing indicates the USB bandwidth is the issue.


Is it possible the tasks ran more than normal memory and the machine is swapping to death? Do you have a swap space somewhere other than the USB?
Rosetta Moderator: Mod.Sense
ID: 79478 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Jonathan Jeckell

Send message
Joined: 17 Dec 05
Posts: 7
Credit: 3,470,565
RAC: 1,362
Message 79488 - Posted: 5 Feb 2016, 22:16:04 UTC - in response to Message 79478.  

Not sure if this is directly due to the application upgrade or not, but seems to correlate to when I started having some issues.

I\'m running a few laptops using Linux on USB sticks and now In the last few days BOINC takes an insufferably long time to start while it tells me \"please wait.\" I took a look tonight and top showed the client and Rosetta were barely using the processor. Once in a while one of the Rosetta apps would bounce up to 100% for a bit and then subside. I have the client set to max out the processor and memory using all cores without restriction. No other processes are coming close to using a significant portion of the processor, and nothing indicates the USB bandwidth is the issue.


Is it possible the tasks ran more than normal memory and the machine is swapping to death? Do you have a swap space somewhere other than the USB?


No, it\'s all on USB because of the transitory nature of my possession of these machines. But I will look into getting some hard drives for this purpose instead of the USB sticks. Since nobody else jumped in on the problem, I must be the only one experiencing this (vs a general bug) and this must be the issue. Thanks!
ID: 79488 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Natalie de Clare

Send message
Joined: 27 Feb 12
Posts: 4
Credit: 670,812
RAC: 0
Message 79489 - Posted: 6 Feb 2016, 2:20:42 UTC - in response to Message 79463.  

The blue background is stupid and I do not like it at all.


Please, use other terms.


I will use whatever terms I desire to use.
ID: 79489 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jesse Viviano

Send message
Joined: 14 Jan 10
Posts: 40
Credit: 740,619
RAC: 995
Message 79490 - Posted: 6 Feb 2016, 3:31:39 UTC

I can confirm that work unit 717556481 crashes due to out of memory errors in both results, and I suspect that work units 717556482 and 717556497 will also fail due to the same reason once the computers assigned these work units return their results because my computer also had the same errors in these work units. Their names are of the form 02_2016_(one numeral and then three letters)_backrub_design_(six numerals)_(one or more numerals).
ID: 79490 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 670
Credit: 5,240,248
RAC: 7,685
Message 79491 - Posted: 6 Feb 2016, 3:54:54 UTC - in response to Message 79489.  

The blue background is stupid and I do not like it at all.


Please, use other terms.


I will use whatever terms I desire to use.


Fine if you then let everyone else use those same terms to describe you.
ID: 79491 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
sinspin

Send message
Joined: 30 Jan 06
Posts: 25
Credit: 6,106,189
RAC: 0
Message 79492 - Posted: 6 Feb 2016, 22:44:00 UTC - in response to Message 79491.  

The blue background is stupid and I do not like it at all.


Please, use other terms.


I will use whatever terms I desire to use.


Fine if you then let everyone else use those same terms to describe you.


I am sure, stupid is not the right description. But, for whatever reason was it necessary to change to blue?
Screensaver background should be as dark as possible. There is no way to say, this wtfs blue is dark enough. Only black is it!

Please change back to black or give us an option to change it by ourself.
ID: 79492 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile robertmiles

Send message
Joined: 16 Jun 08
Posts: 670
Credit: 5,240,248
RAC: 7,685
Message 79493 - Posted: 7 Feb 2016, 2:20:20 UTC

If I was still using screensavers, I\'d want an option to choose some main color other than blue. I\'ve read that seeing blue tends to keep people awake for at least half an hour after they see much of it, and I don\'t find much to do in the half hour between the time I turn the monitors of my computers off and the time I go to bed.
ID: 79493 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Previous · 1 · 2 · 3 · 4 · 5 . . . 11 · Next

Message boards : Number crunching : Minirosetta 3.73-3.78



©2017 University of Washington
http://www.bakerlab.org