Bug reports for 5.49-5.51


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Rhiju
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Message 2811 - Posted: 3 Mar 2007, 5:49:54 UTC

Let us know what you think with 5.49! We want to really carefully test the new graphics and new RNA modes before going to Rosetta@home. Your feedback will help greatly.
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Christoph

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Message 2812 - Posted: 3 Mar 2007, 10:59:52 UTC

Could someone make a screenshot of the new graphics please, I'm too lazy to attach my computer ;)
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[AF>EDLS>BIOMED] Heyoka

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Message 2813 - Posted: 3 Mar 2007, 11:25:30 UTC - in response to Message 2812.  

Could someone make a screenshot of the new graphics please, I'm too lazy to attach my computer ;)


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alexpoon

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Message 2814 - Posted: 3 Mar 2007, 16:10:32 UTC

I find that the wu cannot come to an end!
When my wu is at the last model.After finished, the cpu time restored to the time that start the last model
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Christoph

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Message 2815 - Posted: 3 Mar 2007, 18:32:37 UTC
Last modified: 3 Mar 2007, 18:33:19 UTC

Wierd

...
03.03.2007 14:59:32|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:08:51|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:08:51|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:08:51|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:20:17|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:20:17|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:20:17|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:25:42|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:25:42|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:25:42|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:31:13|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:31:13|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:31:13|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:31:47|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:31:47|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:31:47|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:32:22|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:32:22|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:32:22|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:33:32|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:33:32|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:33:32|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:34:18|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:34:18|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:34:18|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:35:05|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_518_0 exited with zero status but no 'finished' file
03.03.2007 15:35:05|ralph@home|If this happens repeatedly you may need to reset the project.
03.03.2007 15:35:05|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_518_0 using rosetta_beta version 549
03.03.2007 15:35:11|ralph@home|Computation for task 1l2x_RNA_TEST_SUBMIT_1805_518_0 finished
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Pieface

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Message 2816 - Posted: 3 Mar 2007, 19:52:24 UTC

Hmmm I had one of those like christoph:

((first several restarts deleted))

3/3/2007 1:27:21 PM|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_262_1 exited with zero status but no 'finished' file
3/3/2007 1:27:21 PM|ralph@home|If this happens repeatedly you may need to reset the project.
3/3/2007 1:27:21 PM|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_262_1 using rosetta_beta version 549
3/3/2007 1:27:24 PM|ralph@home|Computation for task 1l2x_RNA_TEST_SUBMIT_1805_262_1 finished
3/3/2007 1:27:24 PM|SETI@home|Resuming task 08dc03ab.11085.22034.379824.3.27_3 using setiathome_enhanced version 515
3/3/2007 1:27:26 PM|ralph@home|[file_xfer] Started upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Finished upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Throughput 31748 bytes/sec

But it looks like it validated alright?

resid 443594


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Rhiju
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Message 2817 - Posted: 3 Mar 2007, 21:33:07 UTC - in response to Message 2816.  

Hi Pieface and Christoph: Thanks for the posts.

I think I know what the problem is -- forgot to put a silly "boinc_finish" call at the end of the new RNA mode. I'll get this fixed in the next update. Despite this problem, the results appear to be coming back fine!


Hmmm I had one of those like christoph:

((first several restarts deleted))

3/3/2007 1:27:21 PM|ralph@home|Task 1l2x_RNA_TEST_SUBMIT_1805_262_1 exited with zero status but no 'finished' file
3/3/2007 1:27:21 PM|ralph@home|If this happens repeatedly you may need to reset the project.
3/3/2007 1:27:21 PM|ralph@home|Restarting task 1l2x_RNA_TEST_SUBMIT_1805_262_1 using rosetta_beta version 549
3/3/2007 1:27:24 PM|ralph@home|Computation for task 1l2x_RNA_TEST_SUBMIT_1805_262_1 finished
3/3/2007 1:27:24 PM|SETI@home|Resuming task 08dc03ab.11085.22034.379824.3.27_3 using setiathome_enhanced version 515
3/3/2007 1:27:26 PM|ralph@home|[file_xfer] Started upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Finished upload of file 1l2x_RNA_TEST_SUBMIT_1805_262_1_0
3/3/2007 1:27:35 PM|ralph@home|[file_xfer] Throughput 31748 bytes/sec

But it looks like it validated alright?

resid 443594



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Profile anders n

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Message 2818 - Posted: 4 Mar 2007, 7:01:13 UTC

Whith 5.50 I get SIGBUS: bus error like this one.

https://ralph.bakerlab.org/result.php?resultid=444448

Anders n
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alexpoon

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Message 2819 - Posted: 4 Mar 2007, 7:27:48 UTC
Last modified: 4 Mar 2007, 7:31:24 UTC

I got this message
4/3/2007|ralph@home|Reason: Unrecoverable error for result 1qwa__BOINC_RNA_ABINITIO__1808_2_1 ( - exit code -1073741819 (0xc0000005))



edit:I see that I received this file
4/3/2007 |ralph@home|[file_xfer] Started download of file casp7.description.shorter.txt

Will it cause to the error?
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gamer007

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Message 2820 - Posted: 4 Mar 2007, 7:33:48 UTC

03/03/2007 10:23:24 PM|ralph@home|Starting 1kka__BOINC_RNA_ABINITIO__1808_5_0
03/03/2007 10:23:24 PM|ralph@home|Starting task 1kka__BOINC_RNA_ABINITIO__1808_5_0 using rosetta_beta version 550
03/03/2007 10:24:19 PM|ralph@home|Computation for task 1kka__BOINC_RNA_ABINITIO__1808_5_0 finished
03/03/2007 10:24:19 PM|ralph@home|Output file 1kka__BOINC_RNA_ABINITIO__1808_5_0_0 for task 1kka__BOINC_RNA_ABINITIO__1808_5_0 absent

Site says it only ran for 2 seconds and got an error.
444237
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Message 2821 - Posted: 4 Mar 2007, 12:14:28 UTC
Last modified: 4 Mar 2007, 12:15:13 UTC

Result

Host



3/4/2007 1:06:14 AM|ralph@home|Starting 1a4d__BOINC_RNA_ABINITIO__1808_2_0
3/4/2007 1:06:14 AM|ralph@home|[cpu_sched] Starting 1a4d__BOINC_RNA_ABINITIO__1808_2_0 (initial)
3/4/2007 1:06:15 AM|ralph@home|[task_debug] task_state=EXECUTING for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from start
3/4/2007 1:06:15 AM|ralph@home|Starting task 1a4d__BOINC_RNA_ABINITIO__1808_2_0 using rosetta_beta version 550
3/4/2007 1:06:56 AM|ralph@home|[task_debug] Process for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 exited
3/4/2007 1:06:56 AM|ralph@home|[task_debug] task_state=EXITED for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from handle_exited_app
3/4/2007 1:06:56 AM|ralph@home|Deferring communication for 1 min 0 sec
3/4/2007 1:06:56 AM|ralph@home|Reason: Unrecoverable error for result 1a4d__BOINC_RNA_ABINITIO__1808_2_0 ( - exit code -1073741819 (0xc0000005))
3/4/2007 1:06:56 AM|ralph@home|[task_debug] result state=COMPUTE_ERROR for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from CS::report_result_error
3/4/2007 1:06:56 AM|ralph@home|[task_debug] Process for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 exited
3/4/2007 1:06:56 AM|ralph@home|[task_debug] exit code -1073741819 (0xc0000005):
3/4/2007 1:06:56 AM|ralph@home|Computation for task 1a4d__BOINC_RNA_ABINITIO__1808_2_0 finished
3/4/2007 1:06:56 AM|ralph@home|Output file 1a4d__BOINC_RNA_ABINITIO__1808_2_0_0 for task 1a4d__BOINC_RNA_ABINITIO__1808_2_0 absent
3/4/2007 1:06:56 AM|ralph@home|[task_debug] result state=COMPUTE_ERROR for 1a4d__BOINC_RNA_ABINITIO__1808_2_0 from CS::app_finished
Kathryn :o)
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genes
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Message 2822 - Posted: 4 Mar 2007, 18:50:27 UTC

Got a bunch of errors with 5.50, but I was away yesterday, so I haven't seen them run yet...

resultid=444352
resultid=444488
resultid=444516
resultid=444519
resultid=444547
resultid=444580
resultid=444591

All of them are access violations, and they only ran for a few seconds.
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Message 2823 - Posted: 4 Mar 2007, 18:56:10 UTC

Another access violation result.
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Rhiju
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Message 2824 - Posted: 4 Mar 2007, 20:40:27 UTC - in response to Message 2823.  

Hi all: I'm looking into these -- basically all the RNA workunits failed with this app, which is actually a good thing, since it should make finding the bug easy. Sorry for the errors!

Another access violation result.

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Message 2825 - Posted: 4 Mar 2007, 22:28:55 UTC - in response to Message 2824.  

I think I found the bug -- its a simple one, and doesn't require a new app, just a fix in my workunit. Sending out some jobs again! Thanks for posting.

Hi all: I'm looking into these -- basically all the RNA workunits failed with this app, which is actually a good thing, since it should make finding the bug easy. Sorry for the errors!

Another access violation result.


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Message 2826 - Posted: 5 Mar 2007, 1:41:19 UTC

Woah, Just had success with my first 5.50 unit!

Not bad seeing as I only gave 192MB memory and a 900MHz celeron.
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Message 2827 - Posted: 5 Mar 2007, 3:15:32 UTC
Last modified: 5 Mar 2007, 3:19:42 UTC

Couple more errors, this time not Access Violations, but code 1 "Incorrect function".

resultid=445073
resultid=445076

I did have two finish successfully, though.

Note: All of these errors occurred on machines that were sitting undisturbed, so no graphics were running. I have graphics enabled, but only for an hour, then blank.
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Message 2828 - Posted: 5 Mar 2007, 5:12:54 UTC
Last modified: 5 Mar 2007, 5:13:27 UTC

Something is strange with these Wu-s.

Look at this text from the result page.

-2931.657911
-stderr out <core_client_version>5.8.15</core_client_version>
-<![CDATA[
-<stderr_txt>
-# random seed: 2725014
-# cpu_run_time_pref: 14400
-======================================================
-DONE :: 1 starting structures built 30 (nstruct) times
-This process generated 0 decoys from 0 attempts


Run time 2931 - pref. time 14400

0 decoys from 0 attempts


https://ralph.bakerlab.org/result.php?resultid=445590
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Message 2830 - Posted: 5 Mar 2007, 9:37:25 UTC
Last modified: 5 Mar 2007, 9:38:37 UTC

Lots of errors, all RNA WU's,

Error code 131. SIGSEGV (Segmetation Violations)

https://ralph.bakerlab.org/result.php?resultid=445159 1esy_BOINC_RNA
https://ralph.bakerlab.org/result.php?resultid=444524 1xjr_BOINC_RNA
https://ralph.bakerlab.org/result.php?resultid=444526 1esy
https://ralph.bakerlab.org/result.php?resultid=444752 1kka

Exit Code:ERROR:Exit at: pose_rna.cc line:868

https://ralph.bakerlab.org/result.php?resultid=445226 1fkaA_BOINC_RNA
https://ralph.bakerlab.org/result.php?resultid=445229 1fkaA
https://ralph.bakerlab.org/result.php?resultid=445239 1fkaA
https://ralph.bakerlab.org/result.php?resultid=445240 1fkaA
https://ralph.bakerlab.org/result.php?resultid=445219 1fkaA
https://ralph.bakerlab.org/result.php?resultid=445221 1fkaA
https://ralph.bakerlab.org/result.php?resultid=445276 1fkaA
https://ralph.bakerlab.org/result.php?resultid=445279 1fkaA

Exit Code:ERROR:Exit at: read_paths.cc line:351

https://ralph.bakerlab.org/result.php?resultid=445304 1ehzA_BOINC_RNA
https://ralph.bakerlab.org/result.php?resultid=445305 1gidA
https://ralph.bakerlab.org/result.php?resultid=445745 1gidA
https://ralph.bakerlab.org/result.php?resultid=444730 1gidA
https://ralph.bakerlab.org/result.php?resultid=444731 1gidA
https://ralph.bakerlab.org/result.php?resultid=445058 1gidA
https://ralph.bakerlab.org/result.php?resultid=445059 1ehzA
https://ralph.bakerlab.org/result.php?resultid=445093 1gidA
https://ralph.bakerlab.org/result.php?resultid=445321 1gidA
https://ralph.bakerlab.org/result.php?resultid=445322 1ehzA
https://ralph.bakerlab.org/result.php?resultid=444312 1gidA
https://ralph.bakerlab.org/result.php?resultid=444437 1ehzA
https://ralph.bakerlab.org/result.php?resultid=444438 1gidA

Validate Errors

https://ralph.bakerlab.org/result.php?resultid=444851 1qwa_BOINC_RNA
https://ralph.bakerlab.org/result.php?resultid=444937 1zih
https://ralph.bakerlab.org/result.php?resultid=445547 1fkaA
https://ralph.bakerlab.org/result.php?resultid=445028 1kka

Exit Code -1073741819 Access Violation

https://ralph.bakerlab.org/result.php?resultid=444313 1a4d_BOINC_RNA
https://ralph.bakerlab.org/result.php?resultid=444341 1q9a
https://ralph.bakerlab.org/result.php?resultid=444394 1zih
https://ralph.bakerlab.org/result.php?resultid=444678 1xjr

Later today a couple of the 1gidA workunits did actually run.
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Message 2831 - Posted: 5 Mar 2007, 16:18:45 UTC

This Wu was atleast at step 1.000.000 when it timed out!

https://ralph.bakerlab.org/result.php?resultid=444991

Anders n
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