Minirosetta 3.59

Message boards : Number crunching : Minirosetta 3.59

To post messages, you must log in.

1 · 2 · Next

AuthorMessage
Profile David E K
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 1 Jul 05
Posts: 985
Credit: 2,630,856
RAC: 1,168
Message 78312 - Posted: 15 Jun 2015, 19:01:10 UTC

This version includes a relatively recent sync with the Rosetta source. New and updated protocols and code refactoring efforts have been made in this version since it has been quite a while since the last update. These include protocols for modeling cyclic peptides, ab initio modeling starting from an extended chain in the hybridize protocol (RosettaCM), etc. Please report issues regarding this update in this thread.
ID: 78312 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
TPCBF

Send message
Joined: 29 Nov 10
Posts: 108
Credit: 2,150,359
RAC: 2,683
Message 78314 - Posted: 16 Jun 2015, 2:46:15 UTC

Those WUs seem to have some serious problems, at least here on my Windows 8.1 laptop (4core i3, 8GB of RAM)
They just rack up a few minutes of CPU time before kind of stopping, just \"real\" time advancing but with no apparent processing happening for hours...
And when restarting BOINC, they might pretend to work for a (very) short time, then crapping out with \"Computation Error\"...

Ralf
ID: 78314 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
P . P . L .

Send message
Joined: 20 Aug 06
Posts: 581
Credit: 4,865,274
RAC: 0
Message 78315 - Posted: 16 Jun 2015, 10:30:18 UTC
Last modified: 16 Jun 2015, 10:31:01 UTC

Yea, the graphics window finally works under Ubuntu after how many years I\'ve lost count.

As for the tasks, I haven\'t seen any problems with the ones running on my rigs.
ID: 78315 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile David E K
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 1 Jul 05
Posts: 985
Credit: 2,630,856
RAC: 1,168
Message 78317 - Posted: 16 Jun 2015, 16:34:27 UTC - in response to Message 78314.  

Those WUs seem to have some serious problems, at least here on my Windows 8.1 laptop (4core i3, 8GB of RAM)
They just rack up a few minutes of CPU time before kind of stopping, just \"real\" time advancing but with no apparent processing happening for hours...
And when restarting BOINC, they might pretend to work for a (very) short time, then crapping out with \"Computation Error\"...

Ralf



Are you seeing this problem with all WUs? There doesn\'t seem to be a general issue as far as I can tell so far.
ID: 78317 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator
Project administrator

Send message
Joined: 22 Aug 06
Posts: 3417
Credit: 0
RAC: 0
Message 78319 - Posted: 16 Jun 2015, 21:28:37 UTC - in response to Message 78317.  

Those WUs seem to have some serious problems, at least here on my Windows 8.1 laptop (4core i3, 8GB of RAM)
They just rack up a few minutes of CPU time before kind of stopping, just \"real\" time advancing but with no apparent processing happening for hours...
And when restarting BOINC, they might pretend to work for a (very) short time, then crapping out with \"Computation Error\"...

Ralf



Are you seeing this problem with all WUs? There doesn\'t seem to be a general issue as far as I can tell so far.


Their first WU seems to have failed with an error about getting lock on lockfile:
http://boinc.bakerlab.org/rosetta/result.php?resultid=739734418
Starting work on structure: _00001
[2015- 6-15 16: 8:27:] :: BOINC:: Initializing ... ok.
Can\'t acquire lockfile - exiting
FILE_LOCK::unlock(): close failed.: No error
[2015- 6-15 16: 9:10:] :: BOINC:: Initializing ... ok.
Can\'t acquire lockfile - exiting
FILE_LOCK::unlock(): close failed.: No error
...and it repeats about every 45 seconds.
Rosetta Moderator: Mod.Sense
ID: 78319 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
TPCBF

Send message
Joined: 29 Nov 10
Posts: 108
Credit: 2,150,359
RAC: 2,683
Message 78320 - Posted: 17 Jun 2015, 0:00:56 UTC - in response to Message 78317.  

Those WUs seem to have some serious problems, at least here on my Windows 8.1 laptop (4core i3, 8GB of RAM)
They just rack up a few minutes of CPU time before kind of stopping, just \"real\" time advancing but with no apparent processing happening for hours...
And when restarting BOINC, they might pretend to work for a (very) short time, then crapping out with \"Computation Error\"...

Ralf



Are you seeing this problem with all WUs? There doesn\'t seem to be a general issue as far as I can tell so far.
Not all, but still weird. 6 other tasks seemed to have finished today fine, though I see messages about \"exit status 0\" and \"you might have to reset the project if this continues\" in the logs.

Ralf
ID: 78320 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
nanoprobe

Send message
Joined: 5 Apr 09
Posts: 8
Credit: 381,804
RAC: 0
Message 78322 - Posted: 17 Jun 2015, 20:07:37 UTC

Just started running this project again after a long hiatus. The tasks I\'m getting are taking about 24 hours each on a 2600k. Is that normal?
ID: 78322 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
SDotloe

Send message
Joined: 16 Mar 15
Posts: 1
Credit: 45,350,100
RAC: 0
Message 78323 - Posted: 17 Jun 2015, 21:59:42 UTC - in response to Message 78322.  

Just started running this project again after a long hiatus. The tasks I\'m getting are taking about 24 hours each on a 2600k. Is that normal?


Might be your cpu runtime preference. Otherwise, they shouldn\'t run that long.
ID: 78323 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
nanoprobe

Send message
Joined: 5 Apr 09
Posts: 8
Credit: 381,804
RAC: 0
Message 78324 - Posted: 18 Jun 2015, 0:06:05 UTC - in response to Message 78323.  

Just started running this project again after a long hiatus. The tasks I\'m getting are taking about 24 hours each on a 2600k. Is that normal?


Might be your cpu runtime preference. Otherwise, they shouldn\'t run that long.

Runtime preferences are 100% 24/7/365
ID: 78324 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile David E K
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 1 Jul 05
Posts: 985
Credit: 2,630,856
RAC: 1,168
Message 78325 - Posted: 18 Jun 2015, 1:16:14 UTC - in response to Message 78324.  

Just started running this project again after a long hiatus. The tasks I\'m getting are taking about 24 hours each on a 2600k. Is that normal?


Might be your cpu runtime preference. Otherwise, they shouldn\'t run that long.

Runtime preferences are 100% 24/7/365


That was me accidentally logged in as SDotloe. I meant the CPU runtime preference. When you login, go to your preferences, particularly the \"Resource share and graphics: Rosetta@home preferences\".

There\'s a \"Target CPU run time\" option. I wonder if that is set to 24 hours. If so, set it to your preferable run time. If it is not set and is the default then maybe you have some long running work units.
ID: 78325 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
nanoprobe

Send message
Joined: 5 Apr 09
Posts: 8
Credit: 381,804
RAC: 0
Message 78326 - Posted: 18 Jun 2015, 1:28:07 UTC - in response to Message 78325.  

Just started running this project again after a long hiatus. The tasks I\'m getting are taking about 24 hours each on a 2600k. Is that normal?


Might be your cpu runtime preference. Otherwise, they shouldn\'t run that long.

Runtime preferences are 100% 24/7/365


That was me accidentally logged in as SDotloe. I meant the CPU runtime preference. When you login, go to your preferences, particularly the \"Resource share and graphics: Rosetta@home preferences\".

There\'s a \"Target CPU run time\" option. I wonder if that is set to 24 hours. If so, set it to your preferable run time. If it is not set and is the default then maybe you have some long running work units.

CPU target runtime is set to 1 day and the tasks are taking 1 day. Is there any correlation there? I\'m going to change it and see what happens.
ID: 78326 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator
Project administrator

Send message
Joined: 22 Aug 06
Posts: 3417
Credit: 0
RAC: 0
Message 78328 - Posted: 19 Jun 2015, 0:24:26 UTC - in response to Message 78326.  

CPU target runtime is set to 1 day and the tasks are taking 1 day. Is there any correlation there? I\'m going to change it and see what happens.


Yep. The only other \"catch\" is that you can set it differently for each \"venue\" if you like. So you have to make the change to the settings for the venue that the PC is configured to be a part of.
Rosetta Moderator: Mod.Sense
ID: 78328 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
nanoprobe

Send message
Joined: 5 Apr 09
Posts: 8
Credit: 381,804
RAC: 0
Message 78329 - Posted: 20 Jun 2015, 18:44:08 UTC - in response to Message 78328.  

CPU target runtime is set to 1 day and the tasks are taking 1 day. Is there any correlation there? I\'m going to change it and see what happens.


Yep. The only other \"catch\" is that you can set it differently for each \"venue\" if you like. So you have to make the change to the settings for the venue that the PC is configured to be a part of.

Changed CPU runtime to 4 hours and tasks are now taking 4-5 hours. Thanks for the help.
Curious as to why you have a CPU runtime option? I don\'t think I\'ve seen that on any other project that I\'ve run.
ID: 78329 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Timo
Avatar

Send message
Joined: 9 Jan 12
Posts: 174
Credit: 13,073,983
RAC: 18,149
Message 78330 - Posted: 21 Jun 2015, 15:09:41 UTC - in response to Message 78329.  
Last modified: 21 Jun 2015, 15:11:02 UTC

Curious as to why you have a CPU runtime option? I don\'t think I\'ve seen that on any other project that I\'ve run.


Great question. Setting a longer run-time actually means that each WU you crunch will run more decoys (more searches through different paths of confirmation-space) for the same core model/protein/data set. Many thousands of decoys are needed for obtaining an accurate prediction of a single protein.

As an example only; Setting a short runtime like 3 hours may compute 2-3 decoys for a given target model. Setting a longer runtime like 10 hours would compute say 8-12 decoys for the same target model. Either way, thousands of computations are needed for a given target, so what is the advantage? Well, there are hundreds of different core models running on Rosetta at any given time, so setting a longer runtime means that your WU will work with the SAME core model for a bit longer, and this means that some core datasets can be reused by the same WU. This all results in saving some bandwidth / less pestering of the project server/less overhead switching out the core targets and datasets, etc.

It\'s akin to telling the computer to concentrate on a certain task for longer rather than jumping between tasks and having to load new datasets/bug the server/etc. Thus, longer runtimes mean less overhead and more efficiency.
ID: 78330 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
sgaboinc

Send message
Joined: 2 Apr 14
Posts: 170
Credit: 125,409
RAC: 0
Message 78334 - Posted: 22 Jun 2015, 15:19:24 UTC

i\'m doing a first run via 3.59 on opensuse linux 13.2, thanks much for adding the show graphics feature in 3.59 for linux, this is truly a cool/great feature :)


ID: 78334 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
TPCBF

Send message
Joined: 29 Nov 10
Posts: 108
Credit: 2,150,359
RAC: 2,683
Message 78375 - Posted: 29 Jun 2015, 21:47:22 UTC - in response to Message 78320.  

Those WUs seem to have some serious problems, at least here on my Windows 8.1 laptop (4core i3, 8GB of RAM)
They just rack up a few minutes of CPU time before kind of stopping, just \"real\" time advancing but with no apparent processing happening for hours...
And when restarting BOINC, they might pretend to work for a (very) short time, then crapping out with \"Computation Error\"...

Ralf



Are you seeing this problem with all WUs? There doesn\'t seem to be a general issue as far as I can tell so far.
Not all, but still weird. 6 other tasks seemed to have finished today fine, though I see messages about \"exit status 0\" and \"you might have to reset the project if this continues\" in the logs.

Ralf
Ok, here we go again. Yesterday, two WU crapped out after stopping and restarting BOINC a couple of times with computation error. Today (actually, since last night) there are again two WUs that start fine, then just rack up \"real time\" without doing anything past the last check point in terms of CPU time, just blocking two cores on this CPU for no good reason at all...

Ralf
ID: 78375 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Ryan

Send message
Joined: 17 Aug 09
Posts: 2
Credit: 1,156,245
RAC: 1,374
Message 78382 - Posted: 30 Jun 2015, 16:13:57 UTC

Ever since the new update launch, BOINC freezes during the transition from one Rosetta Mini app to another. The only way I have found to stop this is to suspend one app to allow the other to run. This is becoming rather frustrating, because instead of running in the background I have to continually monitor the new downloads to the system. Even if it is not or cannot fixed I am going to continue to run this appilication as I believe it.

Thanks, Ryan
ID: 78382 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Ryan

Send message
Joined: 17 Aug 09
Posts: 2
Credit: 1,156,245
RAC: 1,374
Message 78383 - Posted: 30 Jun 2015, 16:15:25 UTC - in response to Message 78375.  

Those WUs seem to have some serious problems, at least here on my Windows 8.1 laptop (4core i3, 8GB of RAM)
They just rack up a few minutes of CPU time before kind of stopping, just \"real\" time advancing but with no apparent processing happening for hours...
And when restarting BOINC, they might pretend to work for a (very) short time, then crapping out with \"Computation Error\"...

Ralf



Are you seeing this problem with all WUs? There doesn\'t seem to be a general issue as far as I can tell so far.
Not all, but still weird. 6 other tasks seemed to have finished today fine, though I see messages about \"exit status 0\" and \"you might have to reset the project if this continues\" in the logs.

Ralf
Ok, here we go again. Yesterday, two WU crapped out after stopping and restarting BOINC a couple of times with computation error. Today (actually, since last night) there are again two WUs that start fine, then just rack up \"real time\" without doing anything past the last check point in terms of CPU time, just blocking two cores on this CPU for no good reason at all...

Ralf


This is exactly what is happening to me!!!
ID: 78383 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator
Project administrator

Send message
Joined: 22 Aug 06
Posts: 3417
Credit: 0
RAC: 0
Message 78385 - Posted: 30 Jun 2015, 17:50:32 UTC

Please report which BOINC version is installed and which host you are making yout observations on.
Rosetta Moderator: Mod.Sense
ID: 78385 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
TPCBF

Send message
Joined: 29 Nov 10
Posts: 108
Credit: 2,150,359
RAC: 2,683
Message 78387 - Posted: 30 Jun 2015, 18:54:42 UTC - in response to Message 78385.  

Please report which BOINC version is installed and which host you are making yout observations on.
BOINC 7.4.42 on Windows 8.1/64(4core i3/8GB of RAM).

Task ID 742059437 and Task ID 742059580.

After restarting BOINC 3 or 4 times and shutdown and restart my laptop half a couple times since yesterday, right now both WUs are currently continuing working again, but I have the feeling that they will stop and do the same thing all over again in a while...

Ralf


ID: 78387 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
1 · 2 · Next

Message boards : Number crunching : Minirosetta 3.59



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