Problems with Minirosetta Version 1.67

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Profile David E K
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Message 61204 - Posted: 15 May 2009, 17:09:15 UTC

I understand everyone's concerns. I think it was only fair to grant credit for those invalid jobs. We try our best to keep things chugging along but inevitably there's some down time and catching up to do.
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Message 61205 - Posted: 15 May 2009, 17:28:38 UTC

In case anyone was wondering, Norton Internet Security 2009 rejects MiniRosetta as a suspect application again. Solution same as before.

Is there any way to get Symantec on board either by submitting the application to them or getting them to whitelist the suspect signature or to sign the application so that is passes through for every new version automatically?

I wonder what happens to those people who don't babysit the application when a new version comes out. Do they sit idle until Rosetta Beta WUs get issued?
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Message 61213 - Posted: 16 May 2009, 3:56:57 UTC
Last modified: 16 May 2009, 4:01:34 UTC

too many to count.
https://boinc.bakerlab.org/rosetta/result.php?resultid=251304400
https://boinc.bakerlab.org/rosetta/result.php?resultid=251138400
https://boinc.bakerlab.org/rosetta/result.php?resultid=251061951
https://boinc.bakerlab.org/rosetta/result.php?resultid=250718136
https://boinc.bakerlab.org/rosetta/result.php?resultid=250703582
https://boinc.bakerlab.org/rosetta/result.php?resultid=250641116
https://boinc.bakerlab.org/rosetta/result.php?resultid=250604999
Also alot of errors seem to be on my mac and not my windows machine so it must be something with to do with apple.
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Message 61216 - Posted: 16 May 2009, 8:48:00 UTC

Got a SIGBUS from https://boinc.bakerlab.org/rosetta/result.php?resultid=250688320 :

Starting watchdog...
Watchdog active.
Continuing computation from checkpoint: chk_S_1AOGA_10_0001_FastRelax__chk1_fa ... success!
Continuing computation from checkpoint: chk_S_1S3QA_2_0001_FastRelax__chk1_fa ... success!
SIGBUS: bus error

Crashed executable name: minirosetta_1.67_i686-apple-darwin
built using BOINC library version 6.5.0
Machine type Intel 80486 (32-bit executable)
System version: Macintosh OS 10.5.6 build 9G55
Sat May 16 04:47:32 2009

atos cannot load symbols for the file minirosetta_1.67_i686-apple-darwin.
0 0x006c0345 SIGPIPE: write on a pipe with no reader
1 0x004a3d8e SIGPIPE: write on a pipe with no reader
...
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nick n
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Message 61218 - Posted: 16 May 2009, 14:28:56 UTC
Last modified: 16 May 2009, 14:31:16 UTC

After an update to Boinc 6.6.29 every single one has crashed. All say something is absent such as this
Sat May 16 03:26:33 2009 rosetta@home Output file threading_lb_test1_hb_t317__IGNORE_THE_REST_11832_2317_0_0 for task threading_lb_test1_hb_t317__IGNORE_THE_REST_11832_2317_0 absent

Wu examples
https://boinc.bakerlab.org/rosetta/result.php?resultid=251397003
https://boinc.bakerlab.org/rosetta/result.php?resultid=251390439
https://boinc.bakerlab.org/rosetta/result.php?resultid=251367304
https://boinc.bakerlab.org/rosetta/result.php?resultid=251358761
Any word when this will be fixed?
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Message 61219 - Posted: 16 May 2009, 15:14:56 UTC - in response to Message 61204.  

I understand everyone's concerns. I think it was only fair to grant credit for those invalid jobs. We try our best to keep things chugging along but inevitably there's some down time and catching up to do.


i have 5 IRP tasks that have validate errors, yet i see no correction for them.

https://boinc.bakerlab.org/rosetta/result.php?resultid=250733786
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733768
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733765
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733753
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733750

I would guess you will be correcting this issue of no credit for me as well as others?
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Snags

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Message 61221 - Posted: 16 May 2009, 17:10:08 UTC - in response to Message 61219.  

I understand everyone's concerns. I think it was only fair to grant credit for those invalid jobs. We try our best to keep things chugging along but inevitably there's some down time and catching up to do.


i have 5 IRP tasks that have validate errors, yet i see no correction for them.

https://boinc.bakerlab.org/rosetta/result.php?resultid=250733786
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733768
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733765
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733753
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733750

I would guess you will be correcting this issue of no credit for me as well as others?


Look again. I made your links clickable to make it easier. Scroll to the bottom of each page and for the first one you will see:

Claimed credit 14.3171326524704
Granted credit 14.3171326524704

Click on the second one, scroll to the bottom and you'll see:

Claimed credit 18.5770681489
Granted credit 18.5770681489

And so on.

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Snags

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Message 61222 - Posted: 16 May 2009, 17:22:35 UTC

Here's a new one:
gen2_direct_frag_cst_hb_t367__IGNORE_THE_REST_1UFBA_4_12133_14

Both attempts ended with validate errors after completing 99 models very quickly (roughly 10 and 20 minutes). One Windows machine, one Mac, no other obvious problems.

Snags
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Alien
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Message 61231 - Posted: 17 May 2009, 9:24:26 UTC - in response to Message 61222.  
Last modified: 17 May 2009, 9:25:50 UTC

Here's a new one:
gen2_direct_frag_cst_hb_t367__IGNORE_THE_REST_1UFBA_4_12133_14

Both attempts ended with validate errors after completing 99 models very quickly (roughly 10 and 20 minutes). One Windows machine, one Mac, no other obvious problems.

Snags


I've got one of those " gen2's " here too:

gen2_seqrelax_100_frag_cst_filt5_hb_t328__IGNORE_THE_REST_2GVKA_2_12252_35_0

Thanks to who ever is responsible for getting the pending credits straightend out again ...........

Alan
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Message 61241 - Posted: 17 May 2009, 20:41:45 UTC

Two more tasks with the:

atos cannot load symbols for the file minirosetta_1.67_i686-apple-darwin.
0 0x006c0345 SIGPIPE: write on a pipe with no reader
1 0x004a3d8e SIGPIPE: write on a pipe with no reader
2 0x91cf02bb SIGPIPE: write on a pipe with no reader
3 0xffffffff SIGPIPE: write on a pipe with no reader
4 0x0002a4a7 SIGPIPE: write on a pipe with no reader
5 0x000910d0 SIGPIPE: write on a pipe with no reader
6 0x00518bdc SIGPIPE: write on a pipe with no reader
7 0x00b59c20 SIGPIPE: write on a pipe with no reader
8 0x0013b068 SIGPIPE: write on a pipe with no reader
9 0x00005db8 SIGPIPE: write on a pipe with no reader
10 0x0000292e SIGPIPE: write on a pipe with no reader
11 0x00002855
Thread 0 crashed with X86 Thread State (32-bit):

Still able to complete most tasks with no issue... THe annoying thing is that the task ran for quite a bit before failing.

threading_lb_test1_hb_t362__IGNORE_THE_REST_11843_3687_0
threading_lb_test1_hb_t328__IGNORE_THE_REST_11837_3300_0

Hmmm, not going to tell you guys your job, but, the tasks seem to have run forever and completed no decoys. Nearly at the 3 hour limit and not a single decoy.

One wingman completed two decoys in 6,457 seconds for one of the tasks on Linux... well, if it were easy anyone could do it.
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Message 61252 - Posted: 18 May 2009, 21:30:15 UTC

I have aborted three WUs from the following batch:

pp_lr6_A_score12_rlbd_1fkj_IGNORE_THE_REST_DECOY_12373_149_0 using minirosetta version 167.

When I go into the graphics these pp_lr6 WUs show you on model 21 (or whatever) but with 0 steps, 0 accepted energy and no graphics.

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Message 61256 - Posted: 19 May 2009, 4:52:30 UTC - in response to Message 61221.  

I understand everyone's concerns. I think it was only fair to grant credit for those invalid jobs. We try our best to keep things chugging along but inevitably there's some down time and catching up to do.


i have 5 IRP tasks that have validate errors, yet i see no correction for them.

https://boinc.bakerlab.org/rosetta/result.php?resultid=250733786
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733768
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733765
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733753
https://boinc.bakerlab.org/rosetta/result.php?resultid=250733750

I would guess you will be correcting this issue of no credit for me as well as others?


Look again. I made your links clickable to make it easier. Scroll to the bottom of each page and for the first one you will see:

Claimed credit 14.3171326524704
Granted credit 14.3171326524704

Click on the second one, scroll to the bottom and you'll see:

Claimed credit 18.5770681489
Granted credit 18.5770681489

And so on.



I see that within each task the credit was corrected, but out on the summary page it was just blank.

BTW...whats up with RAC? I keep pumping out the tasks and get 10-15 pts over claimed but my RAC keeps diving and flat lining. I have no pending credit.
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Message 61259 - Posted: 19 May 2009, 7:31:11 UTC - in response to Message 61216.  

Simliar error at WU https://boinc.bakerlab.org/rosetta/result.php?resultid=251404320

Setting database description ...
Setting up checkpointing ...
Setting up graphics native ...
BOINC:: Worker startup.
Starting watchdog...
Watchdog active.
SIGBUS: bus error

Crashed executable name: minirosetta_1.67_i686-apple-darwin
built using BOINC library version 6.5.0
Machine type Intel 80486 (32-bit executable)
System version: Macintosh OS 10.5.7 build 9J61
Tue May 19 08:42:26 2009

atos cannot load symbols for the file minirosetta_1.67_i686-apple-darwin.
0 0x006c0345 SIGPIPE: write on a pipe with no reader
1 0x004a3d8e SIGPIPE: write on a pipe with no reader
2 0x91e5e2bb SIGPIPE: write on a pipe with no reader
3 0xffffffff SIGPIPE: write on a pipe with no reader
4 0x0002a4a7 SIGPIPE: write on a pipe with no reader
5 0x000910d0 SIGPIPE: write on a pipe with no reader
6 0x00518bdc SIGPIPE: write on a pipe with no reader
7 0x00b59c20 SIGPIPE: write on a pipe with no reader
8 0x0013b068 SIGPIPE: write on a pipe with no reader
9 0x00005db8 SIGPIPE: write on a pipe with no reader
10 0x0000292e SIGPIPE: write on a pipe with no reader
11 0x00002855
Thread 0 crashed with X86 Thread State (32-bit):
eax: 0xffffffe1 ebx: 0x91e268c2 ecx: 0xbfffc25c edx: 0x91df2286
edi: 0x00000000 esi: 0x00000000 ebp: 0xbfffc298 esp: 0xbfffc25c
ss: 0x0000001f efl: 0x00000206 eip: 0x91df2286 cs: 0x00000007
ds: 0x0000001f es: 0x0000001f fs: 0x00000000 gs: 0x00000037

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Snags

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Message 61266 - Posted: 19 May 2009, 12:02:24 UTC - in response to Message 61256.  

greg be said
I see that within each task the credit was corrected, but out on the summary page it was just blank.

As far as I've noticed, it's always worked this way. If a task fails to receive credit when it's first reported (either with a client error or a failed validation) but is subsequently awarded credit that credit will appear on the task details page (and in the user totals) but not on the workunit details page or the tasks for user page.

BTW...whats up with RAC? I keep pumping out the tasks and get 10-15 pts over claimed but my RAC keeps diving and flat lining. I have no pending credit.

Rac has been discussed here.

Snags
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Snags

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Message 61267 - Posted: 19 May 2009, 12:09:34 UTC - in response to Message 61252.  

I have aborted three WUs from the following batch:

pp_lr6_A_score12_rlbd_1fkj_IGNORE_THE_REST_DECOY_12373_149_0 using minirosetta version 167.

When I go into the graphics these pp_lr6 WUs show you on model 21 (or whatever) but with 0 steps, 0 accepted energy and no graphics.



Same on my Mac except I let mine run and it appears to have completed successfully:

pp_lr8_A_score12_rlbd_1cei_IGNORE_THE_REST_DECOY_12312_2808_0

Snags
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P . P . L .

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Message 61274 - Posted: 19 May 2009, 21:53:37 UTC

Hi.

I have this task running that is showing the same problem

with the graphics as the previous app did.

(pp_lr8_A_score12_rlbd_1ayi_IGNORE_THE_REST_DECOY_12312_3908)

quote// The tasks starting with lr8_seq_score12_rlbd_ the graphics

are mostly blank. The only thing working is the time & models count,

stage says: Unknown! Otherwise they run O.K.

end//

pete



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Message 61291 - Posted: 21 May 2009, 4:45:56 UTC

Snags, thanks for the pointer to RAC. I have been all over this RAC credit thing and I think it was modsense that said one should just ignore RAC (as it is not really an accurate measurement of credit). I have to say the Ralph AH RAC is more accurate than Rosetta. I watched my RAC (perhaps due to the credit failures of earlier) plunge and now is slowly building back.

Now on to a computation error message:

Docking_benchmark_natives__2KAI.mppk.pdb.gzdock_score12_hi.xml_11809_336_2
This ran a grand total of 3 seconds and died with: - Unhandled Exception Record -
Reason: Access Violation (0xc0000005) at address 0x004F8B3B read attempt to address 0x00000004

Its been awhile since this happened to me last.
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Message 61295 - Posted: 21 May 2009, 11:54:29 UTC

pp_lr6_A_score12_rlbd_1g4i_IGNORE_THE_REST_DECOY_12373_1941_0
Reason: Access Violation (0xc0000005) at address 0x0064D617 read attempt to address 0x00000000

ev_frb_0_8_mike_chosen_cst_hb.t369_.IGNORE_THE_REST.c.25.0.pdb.c.25.0.loop_12435_20_0
Reason: Access Violation (0xc0000005) at address 0x0058AD29 read attempt to address 0x00000008
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Message 61298 - Posted: 21 May 2009, 14:16:55 UTC

My firewall caught the error report trying to go back on this one. Windows task manager shows it peaked at nearly 750MB of memory during its run.

Unhandled Exception Detected...

- Unhandled Exception Record -
Reason: Out Of Memory (C++ Exception) (0xe06d7363) at address 0x7C812A5B


The dump shows these memory figures:

- Virtual Memory Usage -
VirtualSize: 837242880, PeakVirtualSize: 983842816

- Pagefile Usage -
PagefileUsage: 794591232, PeakPagefileUsage: 941617152

- Working Set Size -
WorkingSetSize: 669687808, PeakWorkingSetSize: 786694144, PageFaultCount: 2711288

WU name is: abinitio_norelax_homfrag_natfrag_129_B_1utg__SAVE_ALL_OUT_6252_9911
and now I see the first to receive it failed with zero CPU time. The other Windows machine failed with "Can't get shared memory segment name: shmget() failed". But they've failed so many tasks with this error, they have a max of 1 per day right now.
Add this signature to your EMail:
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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Evan

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Message 61300 - Posted: 21 May 2009, 17:09:24 UTC

I aborted this one 252913016
(ev_frb_0_8_mike_chosen_cst_hb.t369_.IGNORE_THE_REST.c.50.0.pdb.c.50.0.loop_12435_85_0)

It was going on a long trip to nowhere. It was 2 hours over time, which in itself can be normal, but it wasn't using any cpu's - just sitting there marking time and the graphics window kept on failing to respond.
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Message boards : Number crunching : Problems with Minirosetta Version 1.67



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