Minirosetta v1.40 bug thread

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Message 56944 - Posted: 15 Nov 2008, 3:37:37 UTC

15.11.2008 8:23:48|rosetta@home|Computation for task 1ail__BOINC_ABRELAX_SPLIT_SPLIT2_IGNORE_THE_REST-S25-9-S3-3--1ail_-_4768_650_0 finished
15.11.2008 8:23:48|rosetta@home|Output file 1ail__BOINC_ABRELAX_SPLIT_SPLIT2_IGNORE_THE_REST-S25-9-S3-3--1ail_-_4768_650_0_0 for task 1ail__BOINC_ABRELAX_SPLIT_SPLIT2_IGNORE_THE_REST-S25-9-S3-3--1ail_-_4768_650_0 absent

https://boinc.bakerlab.org/rosetta/result.php?resultid=207358562
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Message 56947 - Posted: 15 Nov 2008, 4:26:54 UTC

Hi.

I just noticed on my Quad that i had six tasks running, now four where

running normailly the two rosetta mini 1.40 where marked as waiting to run

but the time and percentage was going up. I tried suspending them it didn't

work, i don't know if it's Boinc Ver 6.2.14 is the problem or Rosetta.

Any ideas.

pete.


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Message 56956 - Posted: 15 Nov 2008, 13:41:08 UTC

I've found that just increasing the minimum and maximum virtual memory sizes is not enough to make minirosetta v1.40 start using more virtual memory, at least on my Vista SP1 machine. I then increased the maximum amount of disk space BOINC is allowed to use, and the maximum percentage of virtual memory BOINC is allowed to use. Since this, I've been seeing two of the more memory-hungry workunits run at the same time on my dual-core machine more often, such as two minirosetta v1.40 workunits, and have started seeing a higher total size of virtual memory in use. However, I've also stopped seeing workunits with the known tags for use of the new mode of minirosetta v1.40, so it's hard to tell which is responsible for the improvement.
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Message 56959 - Posted: 15 Nov 2008, 15:12:53 UTC - in response to Message 56956.  

...so it's hard to tell which is responsible for the improvement.


Yes, it is always hard to say for certain cause and effect. Keep in mind that CPU time is the main contributor here, not amount of virtual memory utilized. It will actually run faster if it has real memory then virtual. And you cannot force an application to use more memory. It either requires it, or it doesn't.

It is sort of like consuming water as your objective and someone suggests you use a larger glass with the thought that it would help you consume water faster. As long as your prior glass was able to provide water at a rate similar to the rate of consumption, a larger glass will not help.

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Message 56964 - Posted: 15 Nov 2008, 16:10:03 UTC

Aenozer wuan: https://boinc.bakerlab.org/rosetta/result.php?resultid=207358562
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Message 56965 - Posted: 15 Nov 2008, 19:50:30 UTC

1hzh_2exu_fchbonds_20_30sarel_SAVE_ALL_OUT_4704_284_0
Had been running for 25 hours then it was suspended because of time of day. Next day it restarted at 50% (which means 12 hours of computing was lost). Therefore I canceled the unit.
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Message 56967 - Posted: 15 Nov 2008, 20:47:40 UTC - in response to Message 56947.  
Last modified: 15 Nov 2008, 20:56:32 UTC

Hi.

I just noticed on my Quad that i had six tasks running, now four where

running normailly the two rosetta mini 1.40 where marked as waiting to run

but the time and percentage was going up. I tried suspending them it didn't

work, i don't know if it's Boinc Ver 6.2.14 is the problem or Rosetta.

Any ideas.

pete.



Well it looks like it could be the mini app that's the problem as i have got two

Beta 5.98 tasks on now and they are suspending/waiting to run properly, ill

have to keep an eye on it when i get a couple of 1.40's running.

Edit// I forgot, these are the two tasks that where on at the time.

cs_jumping_abrelax_6PNAS_proteins3_homo_bench_cs_jumping_abrelax_cs_ccr19_olange_4727_24570_0
cs_jumping_abrelax_6PNAS_proteins3_homo_bench_cs_jumping_abrelax_cs_ccr19_olange_4727_26842_0

pete.
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Message 56968 - Posted: 15 Nov 2008, 21:44:58 UTC - in response to Message 56959.  

...so it's hard to tell which is responsible for the improvement.


Yes, it is always hard to say for certain cause and effect. Keep in mind that CPU time is the main contributor here, not amount of virtual memory utilized. It will actually run faster if it has real memory then virtual. And you cannot force an application to use more memory. It either requires it, or it doesn't.


I already got all the physical memory my motherboard can use when I saw a slowdown of the programs I normally use a few months ago. At least the greater use of virtual memory to swap out the workunits that aren't running allows me to use the browser and newsreader without the slowdowns I saw recently.

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Message 56969 - Posted: 15 Nov 2008, 21:58:25 UTC - in response to Message 56967.  

Hi.

I just noticed on my Quad that i had six tasks running, now four where

running normailly the two rosetta mini 1.40 where marked as waiting to run

but the time and percentage was going up. I tried suspending them it didn't

work, i don't know if it's Boinc Ver 6.2.14 is the problem or Rosetta.

Any ideas.

pete.



Well it looks like it could be the mini app that's the problem as i have got two

Beta 5.98 tasks on now and they are suspending/waiting to run properly, ill

have to keep an eye on it when i get a couple of 1.40's running.

Edit// I forgot, these are the two tasks that where on at the time.

cs_jumping_abrelax_6PNAS_proteins3_homo_bench_cs_jumping_abrelax_cs_ccr19_olange_4727_24570_0
cs_jumping_abrelax_6PNAS_proteins3_homo_bench_cs_jumping_abrelax_cs_ccr19_olange_4727_26842_0

pete.


Those workunit names look a lot like the names at least one workunit I ran recently, but under 1.40 instead. Under 1.40, they seemed to run OK after I made the changes that let BOINC use more virtual memory to swap out workunits that weren't running.

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=189103816
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Message 56972 - Posted: 16 Nov 2008, 0:24:02 UTC
Last modified: 16 Nov 2008, 0:28:07 UTC

I keep getting compute errors on my minirosetta tasks. The following (from taskID 207659162) is typical:-

stderr out
Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x7C910193 write attempt to address 0x009254E6

Engaging BOINC Windows Runtime Debugger...



Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x7C910193 write attempt to address 0x00408E6E

Engaging BOINC Windows Runtime Debugger...
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Message 56976 - Posted: 16 Nov 2008, 3:10:01 UTC
Last modified: 16 Nov 2008, 4:05:45 UTC

Several errors over the last week or so, which I'm only just catching up with:

These messages (to a greater or lesser degree) appear in the Task IDs listed beneath (note: I've seen this reported in the thread Rosetta Mini with new score terms bug thread too):

<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
too many exit(0)s
</message>
<stderr_txt>
recovering checkpoint of tag S_U9X3X_00000001 with id abrelax_rg_state
recovering checkpoint of tag S_U9X3X_00000001 with id stage_1
recovering checkpoint of tag S_U9X3X_00000001 with id stage_2
# cpu_run_time_pref: 7200
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_1
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_2
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_3
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_4
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_5
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_6
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_7
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_8
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_9
recovering checkpoint of tag S_U9X3X_00000001 with id stage_3_iter1_10
recovering checkpoint of tag S_U9X3X_00000001 with id stage4_kk_1
recovering checkpoint of tag S_U9X3X_00000001 with id stage4_kk_2
recovering checkpoint of tag S_U9X3X_00000001 with id stage4_kk_3
recovering checkpoint of tag S_U9X3X_00000001 with id abrelax_relax
recovering checkpoint of tag S_U9X3X_00000002 with id abrelax_rg_state
recovering checkpoint of tag S_U9X3X_00000002 with id stage_1
recovering checkpoint of tag S_U9X3X_00000002 with id stage_2
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_1
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_2
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_3
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_4
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_5
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_6
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_7
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_8
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_9
recovering checkpoint of tag S_U9X3X_00000002 with id stage_3_iter1_10
recovering checkpoint of tag S_U9X3X_00000002 with id stage4_kk_1
recovering checkpoint of tag S_U9X3X_00000002 with id stage4_kk_2
recovering checkpoint of tag S_U9X3X_00000002 with id stage4_kk_3
recovering checkpoint of tag S_U9X3X_00000002 with id abrelax_relax
recovering checkpoint of tag S_U9X3X_00000003 with id abrelax_rg_state
recovering checkpoint of tag S_U9X3X_00000003 with id stage_1
recovering checkpoint of tag S_U9X3X_00000003 with id stage_2
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_1
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_2
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_3
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_4
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_5
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_6
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_7
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_8
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_9
recovering checkpoint of tag S_U9X3X_00000003 with id stage_3_iter1_10
recovering checkpoint of tag S_U9X3X_00000003 with id stage4_kk_1
recovering checkpoint of tag S_U9X3X_00000003 with id stage4_kk_2
recovering checkpoint of tag S_U9X3X_00000003 with id stage4_kk_3
recovering checkpoint of tag S_U9X3X_00000003 with id abrelax_relax
recovering checkpoint of tag S_U9X3X_00000004 with id abrelax_rg_state
recovering checkpoint of tag S_U9X3X_00000004 with id stage_1
recovering checkpoint of tag S_U9X3X_00000004 with id stage_2
recovering checkpoint of tag S_U9X3X_00000004 with id stage_3_iter1_1
recovering checkpoint of tag S_U9X3X_00000004 with id stage_3_iter1_2
recovering checkpoint of tag S_U9X3X_00000004 with id stage_3_iter1_3
recovering checkpoint of tag S_U9X3X_00000004 with id stage_3_iter1_4


Task ID 205994161
Task ID 206059326
Task ID 206211546
Task ID 206290866
Task ID 206333375
Task ID 206790264
Task ID 206812382
Task ID 206932670
Task ID 207028575
Task ID 207063049
Task ID 207098754
Task ID 207231397
Task ID 207268928
Task ID 207273838
Task ID 207278136
Task ID 207281019
Task ID 207305018
Task ID 207461993
Task ID 207466440
Task ID 207471528
Task ID 207471528


These messages appear in the Task IDs listed beneath:
ERROR: NANs occured in hbonding!
ERROR:: Exit from: ....srccorescoringhbondshbonds_geom.cc line: 763
called boinc_finish
Can't set up shared mem: -1
Will run in standalone mode.


Task ID 206157249
Task ID 207109581

However, these and many more WUs error out with these following details:

Client state Compute error
Exit status -226 (0xffffff1e)
...
<core_client_version>6.2.19</core_client_version>
<![CDATA[
<message>
too many exit(0)s
</message>
...
Can't acquire lockfile - exiting
Can't acquire lockfile - exiting
Can't acquire lockfile - exiting
<repeat many times>


The computer is listed here
AMD Phenom(tm) 9850 Quad-Core, Vista Home Premium x64 Edition, SP1, 8Gb RAM, 330Gb free space, preferences set to 2 hour run time due to constant erroring out with "Can't acquire lockfile - exiting".

This problem never occurs with Rosetta Beta 5.98 (or earlier versions of the Beta) - only with all versions of MiniRosetta since I upgraded to this machine and 64-bit OS.

Of my last 162 WUs:
Beta 5.98 - 58 - 100% success
Mini 1.40 - 104 - 60% success (62) 40% failure (42)

Failure of Mini 1.40 WUs rises rapidly if runtime is increased above 2 hours (60% failure rate)
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Message 56988 - Posted: 16 Nov 2008, 8:30:41 UTC
Last modified: 16 Nov 2008, 8:31:17 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=207486683
https://boinc.bakerlab.org/rosetta/result.php?resultid=207628604
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Message 56991 - Posted: 16 Nov 2008, 13:28:05 UTC

*As far as I can tell from the messages here, people are seeing two major *problems:
*1. long run times with relatively low credit
*2. larger than anticipated memory requirements
*
*Please let me know if you see any other type of problem.

I think I'm seeing something else. I have 2 machines sharing r@h with
seti. I'm seeing that each machine has gotten to a state where BOINC
has suspended a rosetta task in order to restart a seti task. But I see
that the seti task is only getting 50% of the CPU time, according to
boincview/boinc. When I look in Win task manager, I see this is because the
rosetta task is continuing to execute, and thus the rosetta and seti are
trying to share the processor, each getting about 50%. But boincview
has the rosetta task as waiting. But despite that, the cum CPU time reported
in the boincview is increasing, with both the rosetta and seti getting about
30 secs of CPU each minute. In the current case, they've been sharing the
CPU for about 2 hours, so this seems to be a steady state condition.

This rosetta app (or maybe something about the WU) has made it apparently
ignore BOINCs command to suspend and be preempted. The current problem case
is

2008-11-16 04:47:50 [rosetta@home] [cpu_sched] Preempting cs_jumping_abrelax_6PNAS_proteins3_homo_bench_cs_jumping_abrel
ax_cs_ccr19_olange_4727_614_0 (left in memory)

In the first instance, I shut down BOINC and restarted, and it properly
restarted with only the seti wu executing.

Dave
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Message 56997 - Posted: 16 Nov 2008, 14:38:45 UTC

Can't acquire lockfile - exiting

I posted this in another thread, but as it seems to be Mini Rosetta specific I'll copy and paste it here as well. I said...

That's familiar. Go to "Your Account" then "Computing Preferences" check that at the bottom of the first block "Use at most" is set to 100%. That lock file error is common on systems where this is not set to 100% at some projects.



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Message 56999 - Posted: 16 Nov 2008, 15:46:50 UTC
Last modified: 16 Nov 2008, 15:48:01 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=207080587
h013__BOINC_ABRELAX_RANGE_yebf_IGNORE_THE_REST-S25-14-S3-7--h013_-_4675_237_1

it completed ok...but there was alot of messages like this:
stderr out

<core_client_version>6.2.19</core_client_version>
<![CDATA[
<stderr_txt>
recovering checkpoint of tag S_U14X7X_00000001 with id abrelax_rg_state
recovering checkpoint of tag S_U14X7X_00000001 with id stage_1
recovering checkpoint of tag S_U14X7X_00000001 with id stage_2
# cpu_run_time_pref: 21600
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_1
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_2
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_3
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_4
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_5
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_6
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_7
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_8
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_9
recovering checkpoint of tag S_U14X7X_00000001 with id stage_3_iter1_10
recovering checkpoint of tag S_U14X7X_00000001 with id stage4_kk_1

and it goes on and on.....repeating recovering checkpoint of tag S_U14X7X_00000001 as the central theme
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Message 57004 - Posted: 16 Nov 2008, 20:37:57 UTC

Hi.

I got this one overnight it ran for 3hrs, 47min then errored.

h001b_BOINC_ABRELAX_RANGE_yebf_IGNORE_THE_REST-S25-8-S3-3--h001b-_4769_1442_0

https://boinc.bakerlab.org/rosetta/workunit.php?wuid=189422310

<core_client_version>6.2.14</core_client_version>
<![CDATA[
<message>
process exited with code 1 (0x1, -255)
</message>
<stderr_txt

ERROR: NANs occured in hbonding!
ERROR:: Exit from: src/core/scoring/hbonds/hbonds_geom.cc line: 763
called boinc_finish

pete.

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Message 57005 - Posted: 16 Nov 2008, 22:05:46 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=206369194
https://boinc.bakerlab.org/rosetta/result.php?resultid=205975695
=====================
https://boinc.bakerlab.org/rosetta/result.php?resultid=206340374
alidate state Valid
Claimed credit 269.214089450125
Granted credit 81.1915060162041 WTF ??????

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Message 57007 - Posted: 16 Nov 2008, 22:14:47 UTC

https://boinc.bakerlab.org/rosetta/result.php?resultid=207312755
https://boinc.bakerlab.org/rosetta/result.php?resultid=207413491
https://boinc.bakerlab.org/rosetta/result.php?resultid=207413498
https://boinc.bakerlab.org/rosetta/result.php?resultid=207417625
https://boinc.bakerlab.org/rosetta/result.php?resultid=207417646

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Message 57009 - Posted: 16 Nov 2008, 22:39:05 UTC - in response to Message 57005.  

=====================
https://boinc.bakerlab.org/rosetta/result.php?resultid=206340374
alidate state Valid
Claimed credit 269.214089450125
Granted credit 81.1915060162041 WTF ??????


That claimed to granted credit ratio is what typically happens when you return a workunit that had a serious underestimate of the amount of CPU time it needed to run.
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Message 57011 - Posted: 16 Nov 2008, 23:51:25 UTC - in response to Message 56783.  

Hello all,
Just saw an error from this WU:
loopbuild_boinc4_hombench_loopbuild_t308__IGNORE_THE_REST_1UKVY_1_4693_12_0

<core_client_version>6.2.25</core_client_version>
<![CDATA[
<stderr_txt>
# cpu_run_time_pref: 21600
# cpu_run_time_pref: 21600
# cpu_run_time_pref: 21600
# cpu_run_time_pref: 21600
Too many restarts with no progress. Keep application in memory while preempted.
======================================================
DONE :: 1 starting structures 24.3206 cpu seconds
This process generated 0 decoys from 0 attempts
======================================================

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

</stderr_txt>
<message>
<file_xfer_error>
<file_name>loopbuild_boinc4_hombench_loopbuild_t308__IGNORE_THE_REST_1UKVY_1_4693_12_0_0</file_name>
<error_code>-161</error_code>
</file_xfer_error>
</message>

Well, looks like 2 errors: Too many restarts & file_xfer error.

Be aware: I'm running WCG's (beta-)BOINC 6.2.25, which seems to be pretty stable (so far).

Have a nice day,
Path7.


I tried re-running this here locally in the lab and it runs just fine - so not sure what went wrong there i'm afraid :(
Thanks for posting anyway!



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