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David E K Profile
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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.

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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

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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.
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Message 78317 - Posted 16 Jun 2015 16:34:27 UTC - in response to Message ID 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.

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Message 78319 - Posted 16 Jun 2015 21:28:37 UTC - in response to Message ID 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.
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Message 78320 - Posted 17 Jun 2015 0:00:56 UTC - in response to Message ID 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

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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?

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Message 78323 - Posted 17 Jun 2015 21:59:42 UTC - in response to Message ID 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.

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Message 78324 - Posted 18 Jun 2015 0:06:05 UTC - in response to Message ID 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

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Message 78325 - Posted 18 Jun 2015 1:16:14 UTC - in response to Message ID 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.

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Message 78326 - Posted 18 Jun 2015 1:28:07 UTC - in response to Message ID 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.

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Message 78328 - Posted 19 Jun 2015 0:24:26 UTC - in response to Message ID 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.
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nanoprobe

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Message 78329 - Posted 20 Jun 2015 18:44:08 UTC - in response to Message ID 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.

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Message 78330 - Posted 21 Jun 2015 15:09:41 UTC - in response to Message ID 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.

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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 :)


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Message 78375 - Posted 29 Jun 2015 21:47:22 UTC - in response to Message ID 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

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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

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Message 78383 - Posted 30 Jun 2015 16:15:25 UTC - in response to Message ID 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!!!

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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.
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Message 78387 - Posted 30 Jun 2015 18:54:42 UTC - in response to Message ID 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


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Message 78420 - Posted 7 Jul 2015 20:13:23 UTC - in response to Message ID 78387.

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





The first task looks to be completed, the second failed with:

[2015- 7- 3 19:15: 0:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting
FILE_LOCK::unlock(): close failed.: No error
[2015- 7- 3 19:15:42:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting


not sure what is causing this. maybe someone else could chime in.

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Message 78421 - Posted 7 Jul 2015 22:44:26 UTC - in response to Message ID 78420.

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





The first task looks to be completed, the second failed with:

[2015- 7- 3 19:15: 0:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting
FILE_LOCK::unlock(): close failed.: No error
[2015- 7- 3 19:15:42:] :: BOINC:: Initializing ... ok.
Can't acquire lockfile - exiting


not sure what is causing this. maybe someone else could chime in.




Here is some advice I found on an archive copy of the BOINC wiki:

This Message means that the BOINC Client Software has tried to acquire the "Lock File" but was unable to obtain an exclusive access to this file. This can occur for the following reasons:


  • A previous copy of the BOINC Client Software is still running, or
  • The BOINC Client Software did not exit cleanly and the "Lock File" is still present and is marked as "read only".


The cure for this is to make sure that no copy of the BOINC Manager and BOINC Daemon is running, and then to delete the "Lock File".

You may have to change the permissions on the file to remove it. Restarting your computer after removing the "Lock File" will allow the BOINC Client Software to create a new copy of the "Lock File".

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Message 78446 - Posted 14 Jul 2015 22:47:04 UTC

On Ubuntu Linux kernel update to 4.2RC kernel (latest testing version) causes all Rosetta tasks (currently running and new ones) to fail with "Compute error". Reverting to current stable 3.19 kernel version (officially provided by Ubuntu repositories) appears to fix it. I encountered no similar behavior from other projects I run.

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Message 78511 - Posted 28 Jul 2015 1:53:46 UTC
Last modified: 28 Jul 2015 1:58:09 UTC

Getting a lot of errors on these tasks.

Edit // I've taken the rig that started getting all these errors since it got new work this morning off rosetta.


C3C3P213xtal_3fuy_3nz2_004017_0005_0001.pdb_150726UN_15_07_09_24_22_globalDocking_2_SAVE_ALL_OUT_276123_35_0



<core_client_version>7.2.42</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)


SIGSEGV: segmentation violation
Stack trace (14 frames):
[0xccc64cf]
[0xf7736410]
[0xcce9213]
[0xcce2ade]
[0xcce47ec]
[0xccebcd4]
[0xccec12a]
[0xccd3229]
[0xccd33c9]
[0xccd0144]
[0xccd107d]
[0x80534f9]
[0xcd5e0d8]
[0x8048131]

Exiting...

</stderr_txt>
____________


Sid Celery

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Message 78534 - Posted 3 Aug 2015 2:10:36 UTC
Last modified: 3 Aug 2015 2:14:46 UTC

Compute error on this task:

jr6mer_rd2_0182__fold_SAVE_ALL_OUT_276187_1934_0

ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() );
ERROR:: Exit from: ..\..\..\src\protocols\simple_moves\FragmentMover.cc line: 301
std::cerr: Exception was thrown:


[ERROR] EXCN_utility_exit has been thrown from: ..\..\..\src\protocols\simple_moves\FragmentMover.cc line: 301
ERROR: Assertion failure: runtime_assert( ( begin + size - 1 ) <= pose.total_residue() );


Also:
jr3_0019__fold_SAVE_ALL_OUT_276302_72_0

Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
Setting up folding (abrelax) ...
ERROR:: Exit from: ..\..\..\src\core\scoring\dssp\PairingsList.cc line: 85
std::cerr: Exception was thrown:


[ERROR] EXCN_utility_exit has been thrown from: ..\..\..\src\core\scoring\dssp\PairingsList.cc line: 85

____________

svincent

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Message 78545 - Posted 6 Aug 2015 17:29:23 UTC

FFD__5strand14helixWYY_filteredloops_321_0001_dock_PD1CancerImmunotherapy_15_08_07_40_34_globalDocking_4_SAVE_ALL_OUT_277259_19

crashed immediately on Linux (nothing useful in stderr): it also crashed on a Windows machine

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Message 78551 - Posted 6 Aug 2015 21:44:18 UTC - in response to Message ID 78545.

FFD__5strand14helixWYY_filteredloops_321_0001_dock_PD1CancerImmunotherapy_15_08_07_40_34_globalDocking_4_SAVE_ALL_OUT_277259_19

crashed immediately on Linux (nothing useful in stderr): it also crashed on a Windows machine


------------------------------------------------

I,ve had a few of those error as well.

____________


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Message 78553 - Posted 7 Aug 2015 1:01:26 UTC - in response to Message ID 78511.

Hi P.P.L.,

Just to check, did your edit indicate that the errors were somehow resolved?
I submitted those C3C3P2123xtal_ jobs and most of them seem to have worked...

Looking forward to your response,
natteruw



Getting a lot of errors on these tasks.

Edit // I've taken the rig that started getting all these errors since it got new work this morning off rosetta.


C3C3P213xtal_3fuy_3nz2_004017_0005_0001.pdb_150726UN_15_07_09_24_22_globalDocking_2_SAVE_ALL_OUT_276123_35_0



<core_client_version>7.2.42</core_client_version>
<![CDATA[
<message>
process exited with code 193 (0xc1, -63)


SIGSEGV: segmentation violation
Stack trace (14 frames):
[0xccc64cf]
[0xf7736410]
[0xcce9213]
[0xcce2ade]
[0xcce47ec]
[0xccebcd4]
[0xccec12a]
[0xccd3229]
[0xccd33c9]
[0xccd0144]
[0xccd107d]
[0x80534f9]
[0xcd5e0d8]
[0x8048131]

Exiting...

</stderr_txt>

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Message 78554 - Posted 7 Aug 2015 5:03:45 UTC
Last modified: 7 Aug 2015 5:09:59 UTC

Hi natteruw.

The problem was that there was a bad kernel update that seemed to cause those errors, a few days later they put out a fix for whatever the problem was.

I've put that rig back on Rosetta and it's still going fine now, it was only the one AMD rig for some reason, my other Intel rigs didn't have any problems.

Thanks for asking. :)
____________


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Message 78571 - Posted 12 Aug 2015 12:48:45 UTC

Two validate errors in quick succession. One with a very obvious problem, the other without one I can spot:

FFD__5strand14helixWYR_filteredloops_243_0001_dock_PD1CancerImmunotherapy_15_08_07_40_27_localDocking_9_SAVE_ALL_OUT_277200_4_1

util.cc line: 131

ERROR: Attempting to auto-detect interface partner chains, however the pose contains no jumps.
ERROR:: Exit from: ..\..\..\src\protocols\docking\util.cc line: 131

ERROR: Attempting to auto-detect interface partner chains, however the pose contains no jumps.
ERROR:: Exit from: ..\..\..\src\protocols\docking\util.cc line: 131

ERROR: Attempting to auto-detect interface partner chains, however the pose contains no jumps.
ERROR:: Exit from: ..\..\..\src\protocols\docking\util.cc line: 131

...& repeat...


HH7SRPEG_SiliCar9_F6A_relax_SAVE_ALL_OUT_277610_16_1
======================================================
DONE :: 99 starting structures 1201 cpu seconds
This process generated 99 decoys from 99 attempts
======================================================
BOINC :: WS_max 2.19148e+008

Not sure if that last line is an error of sorts
____________

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