Minirosetta v1.47 bug thread.

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Profile Paul D. Buck

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Message 58216 - Posted: 29 Dec 2008, 2:41:56 UTC - in response to Message 58215.  
Last modified: 29 Dec 2008, 3:05:54 UTC

On the i7 about the time of the failures I know there was a period where there were 4 or more Rosetta tasks running at the same time. Perhaps there is an upper limit on the number of simultaneous incarnations that can be run at the same time?

Well, I put the i7 into NNT until I can get an answer on this. I hate to waste my time crashing tasks ... or trying to baby sit the machines ...


I've noticed that for the more memory demanding BOINC projects, there often is a limit on how many incarnations will run at the same time, especially if you enable the Leave In Memory option but make no effort to increase the amount of swap space they can use. Before I increased the upper limit on swap space on my machine, only one minirosetta workunit would run at a time on my dual CPU core machine; now I often see a minirosetta workunit running on each of the CPU cores.


According to my Task manager my peak was 3.9 G with limit 5G so, I did not even get close. I have 3G normal RAM (well, 6 actually, but XP can only "see" 3 G) so ...

Well, I will try to increase the swap file, but, have suspended work on this machine till the project says something... over half the tasks failed with this one error and I am still waiting to see what happens to the last task ... it has been running with 11 min to go for a couple hours now ... if the % Complete was not slowly rising I would have killed it by now ... the main reason I am letting it run is that curiosity overwhelms me as to if it is going to fail with the same error after eating up 10 or more hours of my time or not ...

Oh, man, this is worse... I had nearly 10 hours on the clock. Changed the memory settings to increase the possible size of the swap file (even though it had 2G never used) and after a reboot, the task ended with 8 hours clock time. It looks like it is valid ... but that tells me that I just wasted nearly 2 hours on a task that should have ended ...

{edit add} The tasks that ended badly *MAY* have all been suspended. I cannot say for sure that they were or not. The *MAY* have been. My setting for switiching between tasks is 720 min (12 hours) to try to force most applications to finish before switching ... it is my way of trying to provide best results ... and with 4 plus cores it mostly works. But, I did notice that the several of the Rosetta tasks did get suspended but I did not note which ones ... so more data to ponder if someone is actually going to look at this problem.{/edit} corrected time
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Speedy
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Message 58217 - Posted: 29 Dec 2008, 4:19:26 UTC
Last modified: 29 Dec 2008, 4:55:22 UTC

This task http://www.boinc.bakerlab.org/rosetta/result.php?resultid=217385249 is running on vista home premium & has no graphics, on screen saver & when i click show graphics, when i close the graphics window it comes up with not responding then gives you 3 options
    *Check for a solution & close the program
  • Close the program
    *Wait for the program to respond

i use Close the program. this task has been running with 10 minutes to go for almost an hour with 97.525% done it's moving at roughly .07.5% per minute should i abort it?

it has finished Validate state Initial. i've noticed that my recent task have been going into a pending state but they get credit quite quickly. is this related to the cc2 jobs?


Have a crunching good day!!
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Sid Celery

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Message 58226 - Posted: 29 Dec 2008, 16:47:58 UTC - in response to Message 58093.  

Mike Tyka wrote:
Has anyone seen any new Lockfile problems ? Or are these finally a thing of the past?

I've made a song and dance about this before, so I should report my situation again:

With Mini 1.45 and Boinc 6.2.19 I had 80% success with a 2 hour runtime, dropping to 55% success with a 3 hour runtime over 116 WUs.

Upgrading to Boinc 6.4.5 for a short while before Mini 1.47s came through I thought I noticed less of the lockfile problem, but they've edged out of my history now.

Of the last 103 WUs:
9 were Beta 5.98s - 100% success as usual
94 Mini 1.47 - 93 success, 1 Computation Error here: 217352482
Outcome Client error
Client state Compute error
Exit status 0 (0x0)
<core_client_version>6.4.5</core_client_version>
<![CDATA[
<stderr_txt>
======================================================
DONE :: 1 starting structures 10813.8 cpu seconds
This process generated 1904 decoys from 1904 attempts
======================================================

BOINC :: Watchdog shutting down...
BOINC :: BOINC support services shutting down...
called boinc_finish

</stderr_txt>
<message>
<file_xfer_error>
<file_name>cc_nonideal_3_5_nocst4_hb_t364__IGNORE_THE_REST_2CYEA_4_5826_14_1_0</file_name>
<error_code>-131</error_code>
</file_xfer_error>

</message>
]]>

Claimed credit 52.7338164308948
Granted credit 52.7338164308948

I note some people are still getting problems, but mine seem to have completely gone, whether due to Boinc or the Mini WUs I don't know for sure, but I honestly don't care.

Excellent work, guys. Much appreciated here. Well done. This problem appeared for me along with this new machine in July and this is the first time I'm getting performance anything like this. My RAC has already increased by about 100 a day. I worried it was something I'd done.
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Sid Celery

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Message 58227 - Posted: 29 Dec 2008, 16:59:37 UTC - in response to Message 58180.  

serious credit issue here:
cc2_1_8_mammoth_fa_cst_hb_t303__IGNORE_THE_REST_2AH5A_4_6138_17_0
Claimed credit 106.166115188458
Granted credit 74.8691857584611

That is worse than the other mammoth task I had which had something like a 10 point difference. It also ran over my preferences of time. See long running tasks thread.

In different tasks I've had:
216878857 - CPU time 10076.6
Claimed credit 49.588655190211
Granted credit 100.839750703433

217129212 - CPU time 12904.09
Claimed credit 62.9250827866192
Granted credit 47.1981949319233

It varies. I wouldn't worry about it.
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Sid Celery

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Message 58228 - Posted: 29 Dec 2008, 17:06:43 UTC - in response to Message 58114.  

This makes 10 tasks in a days time that have died with the 0xc error. COME ON!
This ran to within 10 minutes of completion and died. Gees!
Then you insult me with me no credit granted for a 99% completed task.


Later...

dec 24 22.15 UTC - system is stable and RAC is slowly returning to normal.
Chu - thanks for taking the time to look into the average return of the various tasks you sent out. It was definitely a case of too much OC and no way to verify it. Probably would have got to that conclusion after a few more errors.

I must've missed the apology elsewhere in the thread. I'm sure it was there somewhere. But maybe not.

Literally a thankless task.
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Hugh Miller

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Message 58303 - Posted: 31 Dec 2008, 16:01:52 UTC
Last modified: 31 Dec 2008, 16:02:11 UTC

I'm running:

BOINC 6.4.5
Rosetta Mini 1.47

on a machine with:

Win Vista Ultimate 64-bit SP1
Core Duo P8600 2.4GHz
4GB RAM
NVIDIA GEForce 9200M GS chipset, 256MB dedicated graphics memory

The screensaver behaves erratically. Sometimes it presents the familiar screen, other times it just goes white with a spinning cursor; if I hit ESC to exit, I get the errorbox reading:

minirosetta_graphics_1.20_windows_x86_64.exe is not responding

I have to bail manually from the screensaver at that point.
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Sid Celery

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Message 58315 - Posted: 1 Jan 2009, 2:51:47 UTC

Happy New Year from this side of the Atlantic!

Once people sober up can you consider this scenario I've seen:

I glanced at my Boinc Manager earlier this evening and had one long-running WU at nearly 5 hours on a 3 hour run-time. A couple of hours later I noticed it had dropped back massively to just 19 minutes in (still the first model). It's done this again a few times since.

I upgraded to Boinc 6.4.5 a day or two before the Mini 1.47 WUs started coming through (mid-Dec), so I'm not sure which is responsible for this, but since the lockfile errors stopped crashing WUs out there have been several instances of WUs taking a long time with nothing at all reported in the manager's message tab, then finishing relatively early with no error message.

Am I imagining this or are others seeing the same thing? Without error messages I don't really know what to report, nor where to report it, but I'm sure it's happening.

I believe it happened with this completed WU and is currently happening with this in-progress WU. Both are cc2_1_8_mammoth_mix_fa_cst_hb jobs if that makes a difference.

Any ideas?
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Message 58409 - Posted: 3 Jan 2009, 9:07:58 UTC

some compute errors for lr5_score12

resultid=218389174

resultid=218356231
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Message 58411 - Posted: 3 Jan 2009, 9:58:04 UTC

next

resultid=218405620

stopping rosetta for now
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Greenshit

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Message 58413 - Posted: 3 Jan 2009, 12:07:10 UTC

Three Compute errors in a row:
resultid=218358618
resultid=218443805
resultid=218358618

:-(
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Greenshit

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Message 58415 - Posted: 3 Jan 2009, 12:15:48 UTC

sorry for typo, the last one should be:
resultid=218358619
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Message 58425 - Posted: 3 Jan 2009, 17:46:47 UTC
Last modified: 3 Jan 2009, 17:55:23 UTC

I've had a fairly consistent failure rate for the mini-Rosetta app on my 64bit Vista computer for several months now (hence the reason why it is rarely crunching here). I thought I saw some light at the end so I attached again yesterday only to find 3 more tasks that have failed. All have error code:

-1073741819 (0xc0000005)

The workunits are as follows:

218380490
218380489
218380488

I do hope project staff will look into these. I would really like to get back over to ROSETTA on this machine but I can' waste the cycles without the fix. I can run some RALPH WU if this is needed to track it down. Also, all three WU had messages reporting that the "Output file was missing" prior to failure.

Edit Added: Paul Buck mentioned a few posts ago that his tasks that failed were possibly suspended and I know for a fact that the tasks that failed on my computer were indeed suspended and were not left in memory after the suspension.



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Message 58427 - Posted: 3 Jan 2009, 18:19:19 UTC - in response to Message 58425.  

I've had a fairly consistent failure rate for the mini-Rosetta app on my 64bit Vista computer for several months now (hence the reason why it is rarely crunching here). I thought I saw some light at the end so I attached again yesterday only to find 3 more tasks that have failed. All have error code:

-1073741819 (0xc0000005)

The workunits are as follows:

218380490
218380489
218380488

I do hope project staff will look into these. I would really like to get back over to ROSETTA on this machine but I can' waste the cycles without the fix. I can run some RALPH WU if this is needed to track it down. Also, all three WU had messages reporting that the "Output file was missing" prior to failure.

Edit Added: Paul Buck mentioned a few posts ago that his tasks that failed were possibly suspended and I know for a fact that the tasks that failed on my computer were indeed suspended and were not left in memory after the suspension.


quick qustion. are you OC'd at all?
this looks like what I had when my OC speed was to high.
I lowered it and all was ok.

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Message 58428 - Posted: 3 Jan 2009, 18:24:25 UTC

what with this task and its credit?
cc2_1_8_native_cen_cst_hb_t369__IGNORE_THE_REST_1RXQA_14_5863_202_0
https://boinc.bakerlab.org/rosetta/result.php?resultid=218243427
i am running flat out cpu speed and produced 4 decoys in 11679.33 seconds in a setting of 14400 seconds and it grants me UNDER the claimed credit.
Claimed credit 78.1755065660898
Granted credit 32.0937916886001

that's just unbelievable
my frustration is rising again with bad credit granted and problems with downloads on your end as well as the lousy credit for long running tasks.

it is like the project is at the bottom of a sine wave again.
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Message 58429 - Posted: 3 Jan 2009, 18:31:45 UTC

Another lr5_score12 workunit that failed:

1/3/2009 9:34:50 AM|rosetta@home|Computation for task lr5_score12_rlbd_256b_IGNORE_THE_REST_DECOY_5559_1304_0 finished
1/3/2009 9:34:50 AM|rosetta@home|Output file lr5_score12_rlbd_256b_IGNORE_THE_REST_DECOY_5559_1304_0_0 for task lr5_score12_rlbd_256b_IGNORE_THE_REST_DECOY_5559_1304_0 absent


https://boinc.bakerlab.org/rosetta/workunit.php?wuid=199023434
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Message 58445 - Posted: 4 Jan 2009, 4:35:59 UTC - in response to Message 58427.  

@greg_be

No, I am running stock. I lowered my runtime to 1 hour (thus no switching of apps) and of the 4 completed MR that have completed, all look like they will validate. Is there causation here, idk, but I would be interested to know.

It seems like the 4 or 5 times that I have come back to Rosetta with this setup (64bit Vista) everything works well until the runtime is increased to greater than 1 hour. Perhaps I will increase the runtime but switch to "leave app in memory" to see if there is any change...

I've had a fairly consistent failure rate for the mini-Rosetta app on my 64bit Vista computer for several months now (hence the reason why it is rarely crunching here). I thought I saw some light at the end so I attached again yesterday only to find 3 more tasks that have failed. All have error code:

-1073741819 (0xc0000005)

The workunits are as follows:

218380490
218380489
218380488

I do hope project staff will look into these. I would really like to get back over to ROSETTA on this machine but I can' waste the cycles without the fix. I can run some RALPH WU if this is needed to track it down. Also, all three WU had messages reporting that the "Output file was missing" prior to failure.

Edit Added: Paul Buck mentioned a few posts ago that his tasks that failed were possibly suspended and I know for a fact that the tasks that failed on my computer were indeed suspended and were not left in memory after the suspension.


quick qustion. are you OC'd at all?
this looks like what I had when my OC speed was to high.
I lowered it and all was ok.


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Message 58451 - Posted: 4 Jan 2009, 9:30:41 UTC - in response to Message 58445.  

Interesting that Win64 acts up for you. Your only 1 version of boinc manager 'out of date', but that may or may not help. Leaving in memory, thats something the group always recommends. I don't really have any other idea's at the moment. Could someone else look at his tasks and see if they have any idea's why he's crashing?

@greg_be

No, I am running stock. I lowered my runtime to 1 hour (thus no switching of apps) and of the 4 completed MR that have completed, all look like they will validate. Is there causation here, idk, but I would be interested to know.

It seems like the 4 or 5 times that I have come back to Rosetta with this setup (64bit Vista) everything works well until the runtime is increased to greater than 1 hour. Perhaps I will increase the runtime but switch to "leave app in memory" to see if there is any change...

I've had a fairly consistent failure rate for the mini-Rosetta app on my 64bit Vista computer for several months now (hence the reason why it is rarely crunching here). I thought I saw some light at the end so I attached again yesterday only to find 3 more tasks that have failed. All have error code:

-1073741819 (0xc0000005)

The workunits are as follows:

218380490
218380489
218380488

I do hope project staff will look into these. I would really like to get back over to ROSETTA on this machine but I can' waste the cycles without the fix. I can run some RALPH WU if this is needed to track it down. Also, all three WU had messages reporting that the "Output file was missing" prior to failure.

Edit Added: Paul Buck mentioned a few posts ago that his tasks that failed were possibly suspended and I know for a fact that the tasks that failed on my computer were indeed suspended and were not left in memory after the suspension.


quick qustion. are you OC'd at all?
this looks like what I had when my OC speed was to high.
I lowered it and all was ok.



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Path7

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Message 58456 - Posted: 4 Jan 2009, 11:18:26 UTC
Last modified: 4 Jan 2009, 11:27:20 UTC

Exit status: -1073741819 (0xc0000005) unhandled exception detected:

lr5_score12_rlbd_1who_IGNORE_THE_REST_DECOY_5559_986_0
lr5_score12_rlbd_1mjc_IGNORE_THE_REST_DECOY_5559_534_0

AMD Turion Dual-Core RM-70 at stock speed: 2.0 GHz
Windows Vista SP1 32-bit.
Boinc 5.10.45 with throttling 40 %.
Didn't see any errors (before) on this machine after upgrading to minirosetta 1.45.

On their second run these tasks ran:
Successfully on a Mac,
had the same error on Windows Vista.

Have a nice day,
Path7.
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Message 58462 - Posted: 4 Jan 2009, 12:27:15 UTC - in response to Message 58451.  

Interesting that Win64 acts up for you. Your only 1 version of boinc manager 'out of date', but that may or may not help. Leaving in memory, thats something the group always recommends. I don't really have any other idea's at the moment. Could someone else look at his tasks and see if they have any idea's why he's crashing?

@greg_be

No, I am running stock. I lowered my runtime to 1 hour (thus no switching of apps) and of the 4 completed MR that have completed, all look like they will validate. Is there causation here, idk, but I would be interested to know.

It seems like the 4 or 5 times that I have come back to Rosetta with this setup (64bit Vista) everything works well until the runtime is increased to greater than 1 hour. Perhaps I will increase the runtime but switch to "leave app in memory" to see if there is any change...

I've had a fairly consistent failure rate for the mini-Rosetta app on my 64bit Vista computer for several months now (hence the reason why it is rarely crunching here). I thought I saw some light at the end so I attached again yesterday only to find 3 more tasks that have failed. All have error code:

-1073741819 (0xc0000005)

The workunits are as follows:

218380490
218380489
218380488

I do hope project staff will look into these. I would really like to get back over to ROSETTA on this machine but I can' waste the cycles without the fix. I can run some RALPH WU if this is needed to track it down. Also, all three WU had messages reporting that the "Output file was missing" prior to failure.

Edit Added: Paul Buck mentioned a few posts ago that his tasks that failed were possibly suspended and I know for a fact that the tasks that failed on my computer were indeed suspended and were not left in memory after the suspension.


quick qustion. are you OC'd at all?
this looks like what I had when my OC speed was to high.
I lowered it and all was ok.





BOINC 6.4.5 is now available, which suggests that a few people found problems in BOINC 6.4.0 and more recent. I notice that all three of those workunits were the lr5_score12 type, which a few other people have been reporting having problems with. Note that some other threads indicate that Rosetta@home is likely to have problems supplying all the workunits that are requested for at least a few more hours, though.

I've had problems with one of the lr5_score12 workunits lately, but after six workunits in a row that completed successfully but weren't the lr5_score12 type. Choosing the leave in memory option helps, especially if you also raise the upper limit on how much hard drive space BOINC can use, and at least for 32-bit Vista SP1, the upper limit on what fraction of the swap space BOINC can use.

Since then, another non-lr5_score12 workunit has completed on my machine successfully. Another lr5_score12 workunit is still running.

I'm using 14 hour workunits, but with 32-bit Vista, the leave in memory option, and with enough other projects to insure switching to another workunit a few times before these workunits complete.

My lr5_score12 workunit with an error gave an error message similar to yours, so I wouldn't be surprised if it's an error specific to that batch of workunits.

If you'd like to increase the workunit time, I've found that there's a setting for how long workunits can go before deciding whether to switch to another workunit, but I don't remember if Rosetta@home includes this in the settings you're allowed to change. I currently have it set to 2 hours between such decisions, though.
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Sharlee

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Message 58463 - Posted: 4 Jan 2009, 12:31:18 UTC

New error to report:
I am running an i7 CPU at 965 with 6G memory and Kapersky antivirus. Is there anything I can do to fix this problem?


1/4/2009 5:45:01 AM|rosetta@home|Sending scheduler request: To fetch work. Requesting 84480 seconds of work, reporting 0 completed tasks
1/4/2009 5:45:11 AM|rosetta@home|Scheduler request completed: got 7 new tasks
1/4/2009 5:45:13 AM|rosetta@home|Started download of boinc_mfr_aaat01_03_05.200_v1_3.gz
1/4/2009 5:45:13 AM|rosetta@home|Started download of boinc_mfr_aaAT01_03_05.200_v1_3.gz
1/4/2009 5:45:22 AM|rosetta@home|Finished download of boinc_mfr_aaat01_03_05.200_v1_3.gz
1/4/2009 5:45:22 AM|rosetta@home|Finished download of boinc_mfr_aaAT01_03_05.200_v1_3.gz
1/4/2009 5:45:22 AM|rosetta@home|Started download of boinc_mfr_aaat01_09_05.200_v1_3.gz
1/4/2009 5:45:22 AM|rosetta@home|Started download of boinc_mfr_aaAT01_09_05.200_v1_3.gz
1/4/2009 5:45:22 AM|rosetta@home|[error] MD5 check failed for boinc_mfr_aaat01_03_05.200_v1_3.gz
1/4/2009 5:45:22 AM|rosetta@home|[error] expected 9e156df4c561be65533ceb64059254ab, got a500261b0525281e82d9c3166980820c
1/4/2009 5:45:22 AM|rosetta@home|[error] Checksum or signature error for boinc_mfr_aaat01_03_05.200_v1_3.gz
1/4/2009 5:45:44 AM|rosetta@home|Finished download of boinc_mfr_aaat01_09_05.200_v1_3.gz
1/4/2009 5:45:44 AM|rosetta@home|Started download of AT01_.fasta
1/4/2009 5:45:45 AM|rosetta@home|Finished download of AT01_.fasta
1/4/2009 5:45:45 AM|rosetta@home|Started download of boinc_description_file.txt
1/4/2009 5:45:46 AM|rosetta@home|Finished download of boinc_description_file.txt
1/4/2009 5:45:46 AM|rosetta@home|Started download of AT01.pdb
1/4/2009 5:45:49 AM|rosetta@home|Finished download of AT01.pdb
1/4/2009 5:45:49 AM|rosetta@home|Started download of AT012.pdb
1/4/2009 5:45:51 AM|rosetta@home|Finished download of AT012.pdb
1/4/2009 5:45:53 AM|rosetta@home|Finished download of boinc_mfr_aaAT01_09_05.200_v1_3.gz
1/4/2009 5:45:53 AM|rosetta@home|[error] MD5 check failed for boinc_mfr_aaAT01_09_05.200_v1_3.gz
1/4/2009 5:45:53 AM|rosetta@home|[error] expected 01275336f54af3e7ff7d41ae314e4f73, got 7cbad1935a58db3fe90e367e4d2f7daf
1/4/2009 5:45:53 AM|rosetta@home|[error] Checksum or signature error for boinc_mfr_aaAT01_09_05.200_v1_3.gz

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