Problems with Rosetta version 5.43

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genes
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Message 33291 - Posted: 23 Dec 2006, 21:16:34 UTC - in response to Message 33252.  

Thanks, genes; I've reset to 2 CPU, it's still only running 1 WU but it hasn't done a request for work in a while, it just stopped and ran benchmarks, then went back to the single task it was working. Maybe in a while I'll raise it to 4, if it doesn't get another task at the next request for work.


You can click the "projects" tab on the manager, select Rosetta (although it looks like that's all you're running), and click the "update" command. Boinc will then contact the Rosetta website and get your updated info. (It doesn't know you've changed the preferences until you "update".) It will(should) then get more work.

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David

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Message 33299 - Posted: 23 Dec 2006, 21:51:24 UTC - in response to Message 32791.  


I have this problem also with a intel mac running 10.4.8. The problem is surely not limited to the 945 intel video chipset since i have ati video (mbp). I just don't open the graphics and the simulation goes fine


I have just joined, and am also using in Intel iMac running 10.4.8. The first three of my work units also crashed. I saw the last one crash, and I had the Graphics window open at the time. I had it in the background, and when I clicked back on it, I saw that it had frozen a couple of minutes before, but the Boinc application said that it was still running. I couldn't close the graphics window and finally quit Boinc altogether. When I restarted it, it started from zero again (after having been running for 8 minutes) and then crashed after 35 seconds. It then submitted those results and got a new task.

I am now running it with a different screen saver and no graphics window.
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Message 33302 - Posted: 23 Dec 2006, 22:19:33 UTC - in response to Message 33299.  
Last modified: 23 Dec 2006, 22:20:07 UTC

I am now running it with a different screen saver and no graphics window.

That is the current recommendation, until they get back from holiday vacations and resolve the graphics problems. It should clear up the problems you are seeing. If not, that is what this thread is for. Post with what you've got goin' on.
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Running Microsoft's "System Idle Process" will never help cure cancer, AIDS nor Alzheimer's. But running Rosetta@home just might!
https://boinc.bakerlab.org/rosetta/
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Message 33317 - Posted: 24 Dec 2006, 6:16:22 UTC

Suse Linux 10.1 2.6.18.2-jen37-default on Athlon 2400+
Rosetta crash with this WU

cat stderr.txt
Graphics are disabled due to configuration...
# random seed: 3797287
# cpu_run_time_pref: 28800
No heartbeat from core client for 31 sec - exiting
SIGSEGV: segmentation violation
SIGSEGV: segmentation violation
Stack trace (12 frames):
[0x8ab6403]
[0x8ace4bc]
[0xa7f95420]
[0x8b4e786]
[0x8b4ec63]
[0x8b1fdc1]
[0x8b217e9]
[0x80d0581]
[0x8b34fdf]
[0x8ac57f7]
[0x8acf725]
[0x8b60f0a]

Exiting...
Stack trace (13 frames):
[0x8ab6403]
[0x8ace4bc]
[0xa7f95420]
[0x89e17f3]
[0x897a31c]
[0x8a41e94]
[0x83eac95]
[0x80dc119]
[0x84d61db]
[0x85eb303]
[0x85eb3ac]
[0x8b2d9d4]
[0x8048111]

Exiting...

tail stdout.txt
---------------------------------------------------------
score1 done: (best, low) rms (best,low)
 -3.68180609 -8.59113979  0  0
standard     trials:  20000 accepts:   1447 %:   7.24 e/trial:  -0.00333
-----------------------------------------------------
Alternate score2/score5...
kk score2 score5 low_score n_low_accept rms rms_min low_rms
  0  -11.489   -0.333  -11.489   27    0.000    0.000    0.000
  1    1.621   20.123   -8.383   31    0.000    0.000    0.000
  2  -24.474   -2.889  -32.905   34    0.000    0.000    0.000

The bug is same as in this post

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Message 33318 - Posted: 24 Dec 2006, 6:16:42 UTC
Last modified: 24 Dec 2006, 6:17:23 UTC

dublicated
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Joachim
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Message 33416 - Posted: 25 Dec 2006, 16:12:18 UTC - in response to Message 32934.  
Last modified: 25 Dec 2006, 16:14:23 UTC

I've had the same problems with R@H 5.41

S.E.T.I and Einstein@Home are running without problems.

For those of you who have reported the problem of R@H not starting after being paused on linux client, did you see this problem just for 5.43 application?

I am running Linux, with Boinc 5.4.9 and Rosetta 5.43.

Dual CPU AMD 2600MP with 2 Gig RAM.

My graphics button is grayed out thus have no graphic options, which I understand is part of the Linux version. I do find my Rosetta work units "haulting" or saying its running but its not (no cpu activity), whenever I make changes within my Personal settings. Hitting UPDATE makes no difference. Reboot fixes.

I also find the setting found inside your General Preferences of Switch between applications, that when Boinc switches from a one unit to another, the work unit that it left will never get worked on again until computer reboots... When it resumes back to that work unit (before the reboot) it will say "running" but again no CPU activity.

I just stay away from going into my General Preferences to make changes and have set Switch Between Applications to 540 minutes to avoid Boinc from switching between work units. Takes about 5-6 hrs to complete work units so 540min is plenty...



I've the same phenomena. I've running SUSE Linux 10.0 with 512BM RAM on an AMD Athlon 2400+.

If BOINC resumes the rosetta task, rosetta will be shown as aktive, but TOP shows four threads that are doing nothing (no CPU consumption).

If I stop BOINC and then restart it, rosetta will work, since next pausing is required.

On start of BOINC I see some other mistake of rosetta. It ignores my settings for home:


2006-12-19 19:10:40 [---] Starting BOINC client version 5.4.11 for i686-pc-linux-gnu
2006-12-19 19:10:40 [---] libcurl/7.16.0 OpenSSL/0.9.8d zlib/1.2.3
2006-12-19 19:10:40 [---] Data directory: /home/cheffe/BOINC
2006-12-19 19:10:40 [---] Processor: 1 AuthenticAMD AMD Athlon(tm) XP 2400+
2006-12-19 19:10:40 [---] Memory: 503.70 MB physical, 2.72 GB virtual
2006-12-19 19:10:40 [---] Disk: 107.32 GB total, 98.38 GB free
2006-12-19 19:10:40 [Einstein@Home] URL: http://einstein.phys.uwm.edu/; Computer ID: 210695; location: home; project prefs: home
2006-12-19 19:10:40 [SETI@home] URL: http://setiathome.berkeley.edu/; Computer ID: 1909898; location: home; project prefs: home
2006-12-19 19:10:40 [rosetta@home] URL: https://boinc.bakerlab.org/rosetta/; Computer ID: 362206; location: ; project prefs: default
^^ ^^
2006-12-19 19:10:40 [---] General prefs: from SETI@home (last modified 2006-11-28 23:26:41)
2006-12-19 19:10:40 [---] General prefs: using separate prefs for home
2006-12-19 19:10:40 [---] Local control only allowed
2006-12-19 19:10:40 [---] Listening on port 31416

^^ here I missed the data "home", as you can see for Einstein@home and seti@home.




Joachim
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Message 33447 - Posted: 26 Dec 2006, 11:07:04 UTC


:-) Funny i have five machines crunching 5.43 and never had a problem? i have from P2 to P4 Prescott but never ran graphics. :-)If i have had problems then i have usually found a virus or a worm on that machine :-( Now i run anti virus and spy remover as soon as i get an itchy feeling about any thing, first!. :-( Usually the feeling is correct :-( hope that observation helps :-)
:-) As 2 the why the virus effects The WU's :-) LoL:-) it would/ should effect any thing.:-)
Regards
Masud.

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Christoph

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Message 33462 - Posted: 26 Dec 2006, 15:00:05 UTC

This WU got stuck... The screensaver was opened and the cpu time increased and everything worked, except the steps. The protein didn't move and the steps didn't increment. A few days ago I had the same problem. I just had closed and restartet BOINC and it had startet the model again. This time I closed rosetta by the task manager and the WU errored out. :/
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Message 33504 - Posted: 26 Dec 2006, 22:03:52 UTC

I have been having sporadic(sp?) issues with systems setup to run as a service. The service will be stopped, and if I try to start it, it will throw up a generic "can't start service" error. I have to run a repair on BOIC to fix the issue.

So.. I don't think it is a 5.43 error, but it never occured until this version was released.

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RC

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Message 33521 - Posted: 27 Dec 2006, 4:00:23 UTC

These two workunits had errors on my Linux box host 4280:

47741036
47843769

I had noticed that boincmgr was eating up most of my CPU and rosetta was not getting any, so I killed and restarted boinc.

Here's what I saw in the logfile:

2006-12-25 16:40:21 [---] Starting BOINC client version 5.4.9 for i686-pc-linux-
gnu
2006-12-25 16:40:21 [---] libcurl/7.15.3 OpenSSL/0.9.8a zlib/1.2.3
2006-12-25 16:40:21 [---] Data directory: /home/boinc
2006-12-25 16:40:21 [rosetta@home] State file error: missing application file rosetta^?5.43_i686-pc-linux-gnu
2006-12-25 16:40:21 [rosetta@home] Can't handle application version in state file
2006-12-25 16:40:21 [rosetta@home] State file error: no application version rosetta 543
2006-12-25 16:40:21 [rosetta@home] Can't handle workunit in state file
2006-12-25 16:40:21 [rosetta@home] State file error: no application version rosetta 543
2006-12-25 16:40:21 [rosetta@home] Can't handle workunit in state file
2006-12-25 16:40:21 [rosetta@home] State file error: missing task s019__BOINC_ABRELAX_NEWRELAXFLAGS_hom008__1458_16385
2006-12-25 16:40:21 [rosetta@home] Can't link task s019__BOINC_ABRELAX_NEWRELAXFLAGS_hom008__1458_16385_1 in state file
2006-12-25 16:40:21 [rosetta@home] State file error: missing task 1aaa_1_NMRREF_1_1aaa_1_id_model_16IGNORE_THE_REST_idl_1469_1215
2006-12-25 16:40:21 [rosetta@home] Can't link task 1aaa_1_NMRREF_1_1aaa_1_id_model_16IGNORE_THE_REST_idl_1469_1215_0 in state file
2006-12-25 16:40:21 [rosetta@home] State file error: result s019__BOINC_ABRELAX_NEWRELAXFLAGS_hom008__1458_16385_1 not found
[...]
2006-12-25 16:40:21 [---] General prefs: from Einstein@Home (last modified 2006-04-27 09:57:35)
2006-12-25 16:40:21 [---] General prefs: no separate prefs for home; using your defaults
2006-12-25 16:40:21 [---] Remote control allowed
2006-12-25 16:40:21 [---] GUI RPC bind failed: -1
2006-12-25 16:40:22 [---] Remote control allowed
2006-12-25 16:40:22 [---] GUI RPC bind failed: -1
2006-12-25 16:40:23 [---] Remote control allowed

The "GUI RPC bind failed: -1" errors were from boincmgr, which failed to start, so I killed it and restarted boinc again.

Both of these tasks disappeared without a trace...any clues?

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RC

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Message 33537 - Posted: 27 Dec 2006, 11:23:06 UTC - in response to Message 33521.  

These two workunits had errors on my Linux box host 4280:

47741036
47843769

I had noticed that boincmgr was eating up most of my CPU and rosetta was not getting any, so I killed and restarted boinc.


Correction: Rosetta was not running at the time, but malariacontrol was, and boincmgr was taking all of the CPU - so perhaps it's not a Rosetta problem at all, but it's the Rosetta WUs that disappeared...the malariacontrol WU completed without incident.

Thanks
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Profile Eric Ogletree

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Message 33560 - Posted: 27 Dec 2006, 19:09:26 UTC

Got these two errors today:

27/12/2006 8:54:31 AM|rosetta@home|Unrecoverable error for result 2sss_1_NMRREF_1_2sss_1_id_model_09_core_0001IGNORE_THE_REST_idl_1468_9062_0 ( - exit code 1073807364 (0x40010004))
27/12/2006 11:46:12 AM|rosetta@home|Unrecoverable error for result 2sss_1_NMRREF_1_2sss_1_id_model_10_core_0001IGNORE_THE_REST_idl_1468_9062_0 ( - exit code 1073807364 (0x40010004))

Was checking out the graphics at the time these errors occured.

@:^(
There are 10 types of people in the world:
Those who understand binary, and those who don't.
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Alan Roberts

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Message 33619 - Posted: 28 Dec 2006, 14:01:48 UTC

Two recent error results on this machine, a steady performer. Failing results are: 54192172 and 54229941, both 1mmm_1_NMRREF... flavor. BOINC running as a background service, no graphics would have been in play.
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Message 33639 - Posted: 28 Dec 2006, 19:09:08 UTC - in response to Message 33619.  

The error were caused by overflowing the number of hydrogen bonds in a protein that Rosetta can handle. The batch of WUs have been tested on Ralph without seeing such a problem and so far yours is the only case reported here. I think it might just happen randomly with a very low probability. However, if you keep getting this type of error again and again, I would suggest to update some Rosetta database files as the errors could also be due to the corruption of those files.

Two recent error results on this machine, a steady performer. Failing results are: 54192172 and 54229941, both 1mmm_1_NMRREF... flavor. BOINC running as a background service, no graphics would have been in play.


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Renouard

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Message 33653 - Posted: 28 Dec 2006, 23:20:11 UTC

Rosetta v5.43 is regularly "hanging" on me. I'm running the Windows version w/ BOINC screen saver set. Often when I return to my machine I have to kill the rosetta process to get to my desktop.

This isn't new to 5.43. I have another machine running rosetta that does not have this problem but I also use another screen saver on it. This machine is a dual 2.8GHz machine w/ 1GB RAM.



Here's my latest log - the failures are because I killed it twice today.

12/28/2006 2:11:51 PM|rosetta@home|Resuming task s019__BOINC_ABRELAX_NEWRELAXFLAGS_hom010__1458_12966_0 using rosetta version 543
12/28/2006 2:11:51 PM|World Community Grid|Resuming task faah1117_d138n601_x1MEU_00_1 using faah version 528
12/28/2006 2:13:29 PM||Suspending computation - user is active
12/28/2006 2:13:29 PM|rosetta@home|Pausing task s019__BOINC_ABRELAX_NEWRELAXFLAGS_hom010__1458_12966_0 (left in memory)
12/28/2006 2:13:29 PM|World Community Grid|Pausing task faah1117_d138n601_x1MEU_00_1 (left in memory)
12/28/2006 2:13:29 PM||Suspending network activity - user is active
12/28/2006 2:14:01 PM|rosetta@home|Unrecoverable error for result s019__BOINC_ABRELAX_NEWRELAXFLAGS_hom010__1458_12966_0 ( - exit code 1073807364 (0x40010004))
12/28/2006 2:14:01 PM|rosetta@home|Deferring scheduler requests for 1 minutes and 0 seconds
12/28/2006 2:14:01 PM||Rescheduling CPU: application exited
12/28/2006 2:14:01 PM|rosetta@home|Computation for task s019__BOINC_ABRELAX_NEWRELAXFLAGS_hom010__1458_12966_0 finished
12/28/2006 2:23:51 PM||Resuming computation
12/28/2006 2:23:51 PM||Rescheduling CPU: Resuming computation
12/28/2006 2:23:51 PM||Resuming network activity
12/28/2006 2:23:51 PM|Einstein@Home|Started upload of file h1_0343.5_S5R1__5397_S5R1a_0_0
12/28/2006 2:23:51 PM|World Community Grid|Resuming task faah1117_d138n601_x1MEU_00_1 using faah version 528
12/28/2006 2:23:51 PM|rosetta@home|Sending scheduler request to https://boinc.bakerlab.org/rosetta_cgi/cgi
12/28/2006 2:23:51 PM|rosetta@home|Reason: To fetch work
12/28/2006 2:23:51 PM|rosetta@home|Requesting 17280 seconds of new work, and reporting 1 completed tasks
12/28/2006 2:23:52 PM|Einstein@Home|Temporarily failed upload of h1_0343.5_S5R1__5397_S5R1a_0_0: HTTP file not found
12/28/2006 2:23:52 PM|Einstein@Home|Backing off 1 hours, 24 minutes and 57 seconds on upload of file h1_0343.5_S5R1__5397_S5R1a_0_0
12/28/2006 2:23:56 PM|rosetta@home|Scheduler request succeeded
12/28/2006 2:23:58 PM|rosetta@home|Started download of file hom003_s026_.fasta.gz
12/28/2006 2:23:58 PM|rosetta@home|Started download of file hom003_s026_.psipred_ss2.gz
12/28/2006 2:24:00 PM|rosetta@home|Finished download of file hom003_s026_.fasta.gz
12/28/2006 2:24:00 PM|rosetta@home|Throughput 2576 bytes/sec
12/28/2006 2:24:00 PM|rosetta@home|Finished download of file hom003_s026_.psipred_ss2.gz
12/28/2006 2:24:00 PM|rosetta@home|Throughput 14017 bytes/sec
12/28/2006 2:24:00 PM|rosetta@home|Started download of file boinc_hom003_aas026_03_05.200_v1_3.gz
12/28/2006 2:24:00 PM|rosetta@home|Started download of file boinc_hom003_aas026_09_05.200_v1_3.gz
12/28/2006 2:24:04 PM|rosetta@home|Finished download of file boinc_hom003_aas026_03_05.200_v1_3.gz
12/28/2006 2:24:04 PM|rosetta@home|Throughput 500152 bytes/sec
12/28/2006 2:24:04 PM|rosetta@home|Finished download of file boinc_hom003_aas026_09_05.200_v1_3.gz
12/28/2006 2:24:04 PM|rosetta@home|Throughput 730755 bytes/sec
12/28/2006 2:24:05 PM||Rescheduling CPU: files downloaded
12/28/2006 2:24:05 PM|rosetta@home|Starting task s026__BOINC_ABRELAX_NEWRELAXFLAGS_hom003__1462_25667_0 using rosetta version 543
12/28/2006 2:32:27 PM|Einstein@Home|Sending scheduler request to http://einstein.phys.uwm.edu/EinsteinAtHome_cgi/cgi
12/28/2006 2:32:27 PM|Einstein@Home|Reason: To report completed tasks
12/28/2006 2:32:27 PM|Einstein@Home|Requesting 17280 seconds of new work, and reporting 1 completed tasks
12/28/2006 2:32:32 PM|Einstein@Home|Scheduler request failed: HTTP file not found
12/28/2006 2:32:32 PM|Einstein@Home|Deferring scheduler requests for 1 hours, 54 minutes and 57 seconds
12/28/2006 3:12:38 PM||Suspending computation - user is active
12/28/2006 3:12:38 PM|World Community Grid|Pausing task faah1117_d138n601_x1MEU_00_1 (left in memory)
12/28/2006 3:12:38 PM|rosetta@home|Pausing task s026__BOINC_ABRELAX_NEWRELAXFLAGS_hom003__1462_25667_0 (left in memory)
12/28/2006 3:12:38 PM||Suspending network activity - user is active
12/28/2006 3:12:59 PM|rosetta@home|Unrecoverable error for result s026__BOINC_ABRELAX_NEWRELAXFLAGS_hom003__1462_25667_0 ( - exit code 1073807364 (0x40010004))
12/28/2006 3:12:59 PM|rosetta@home|Deferring scheduler requests for 1 minutes and 0 seconds
12/28/2006 3:12:59 PM||Rescheduling CPU: application exited
12/28/2006 3:12:59 PM|rosetta@home|Computation for task s026__BOINC_ABRELAX_NEWRELAXFLAGS_hom003__1462_25667_0 finished

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Profile sslickerson

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Message 33657 - Posted: 28 Dec 2006, 23:32:22 UTC - in response to Message 33653.  

Rosetta v5.43 is regularly "hanging" on me. I'm running the Windows version w/ BOINC screen saver set. Often when I return to my machine I have to kill the rosetta process to get to my desktop.

This isn't new to 5.43. I have another machine running rosetta that does not have this problem but I also use another screen saver on it. This machine is a dual 2.8GHz machine w/ 1GB RAM.


@Renouard

This is a known issue which will be tackled by the Rosetta team after the new year. For now, please do not use the screensaver or view the graphics while running Rosetta. This is only a partial fix but should save you from any "hanging" WU's. Thanks!

Timothy



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Message 33664 - Posted: 29 Dec 2006, 2:11:08 UTC

Problem with this wu

First in a while for Rosetta, normally they happen on RALPH
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Message 33737 - Posted: 30 Dec 2006, 3:13:53 UTC

Spoke too soon, here's another one. Different box, though and different wu.
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Profile Michael Casey

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Message 33807 - Posted: 31 Dec 2006, 2:33:20 UTC

Hi, I didn't view the graphics and found it to be hanging for a while. Here. The boinc client said it was running, but the windows task manager said nothing of the sort. I tried viewing the graphics and nothing happened, so I just aborted it.

-Michael
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Kashyyk

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Message 33813 - Posted: 31 Dec 2006, 8:15:52 UTC

So how about supporting x86_64? I recently went from (32-bit) Windows to 64-bit Linux and would like to help you with my Core2Duo, but I can't :/
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