Bug reports for Ralph 5.30 and 5.31 and 5.32

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Profile feet1st

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Message 2377 - Posted: 10 Oct 2006, 16:42:42 UTC

V5.31 docking. The graphic doesn't react properly to mouse control when not fully maximized. If I attempt to rotate the Low Energy image, the Native image does the rotating...if any reaction at all. Although I was able to right click and enlarge the low energy image. I could not enlarge the Native structure.

Is there any details on what to expect of a docking WU?? i.e. long running models, and low numbers of steps?
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Profile paul and kirsty yates
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Message 2378 - Posted: 10 Oct 2006, 16:47:50 UTC

not an error as the w/u finished ok but did get this
stderr out <core_client_version>5.4.11</core_client_version>
<stderr_txt>
# random seed: 2896098
# cpu_run_time_pref: 3600
WARNING! error deleting file .aa1IGC.out
WARNING! error deleting file .aa1IGC.out.bonds
WARNING! error deleting file .aa1IGC.out.rot_templates
======================================================
DONE :: 1 starting structures built 1 (nstruct) times
This process generated 1 decoys from 1 attempts
0 starting pdbs were skipped
======================================================


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Message 2379 - Posted: 10 Oct 2006, 19:41:53 UTC - in response to Message 2378.  

not an error as the w/u finished ok but did get this
stderr out <core_client_version>5.4.11</core_client_version>
<stderr_txt>
# random seed: 2896098
# cpu_run_time_pref: 3600
WARNING! error deleting file .aa1IGC.out
WARNING! error deleting file .aa1IGC.out.bonds
WARNING! error deleting file .aa1IGC.out.rot_templates
======================================================
DONE :: 1 starting structures built 1 (nstruct) times
This process generated 1 decoys from 1 attempts
0 starting pdbs were skipped
======================================================



I had the same issue.

Result ID 288375
Name DOC_4HTC_u_pert_mcm_bbmin_1340_20_0
Workunit 254288
Created 10 Oct 2006 11:51:18 UTC
Sent 10 Oct 2006 12:13:39 UTC
Received 10 Oct 2006 16:10:29 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x0)
Computer ID 250
Report deadline 14 Oct 2006 12:13:39 UTC
CPU time 13897.25
stderr out

<core_client_version>5.6.5</core_client_version>
<![CDATA[
<stderr_txt>
# random seed: 2895533
# cpu_run_time_pref: 14400
WARNING! error deleting file .aa4HTC.out
WARNING! error deleting file .aa4HTC.out.bonds
WARNING! error deleting file .aa4HTC.out.rot_templates
======================================================
DONE :: 1 starting structures built 23 (nstruct) times
This process generated 23 decoys from 23 attempts
0 starting pdbs were skipped
======================================================


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

</stderr_txt>
]]>

Validate state Valid
Claimed credit 47.6463856052397
Granted credit 50.3978804981935
application version 5.32
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Message 2380 - Posted: 10 Oct 2006, 21:25:47 UTC - in response to Message 2377.  

Hi, this is a known issue, not just for V5.31. it might be due to the sensitivity of the mouse control setup in the graphics and will be fixed in the futural release.

To answer the second question, for docking WUs, there will be two proteins drawn. One in blue and the other in red. The calculation is, given the structures of two proteins, to search the optimal relatvie orientation between these two "objects" which gives the best anergy according to Rosetta scoring function. The docking protocol mainly comprises two parts. The first step is with low-resolution (only backbone is shown in the graphic) and is meant to find quickly a roughly fit shape complementarity between the two proteins. In the second step, the two proteins are represented by full atoms and the search space is mainly confined locally aiming at refining detailed protein-protein interactions across the interface. This step is relatively time-consuming and a lot of computation is used for optimizing sidechain interactions. Appearing on the graphics, the proteins sometimes do not move at all and that is because we currently have a hard time showing every step of sidechain movement ( we tried that in 5.28, but it resulted in a lot of errors probably due to some graphic issue) But generally users should be able to see in the fullatom docking stage that sidechains wiggle and the relative orientation of the two proteins changes from time to time in a small scale. Compared to ab initio and relax WUs, there are less steps and the run time is about on the same scale. And currently some dianostics on the screen saver such as score and rmsd do not always update timely due to some limitations in Rosetta code and since rmsd is calculated differently in docking, the value might be too large to be shown in the plot area. I will try to put more information explaing scientific aspect of docking soon.

Thanks for everybody's help here.
V5.31 docking. The graphic doesn't react properly to mouse control when not fully maximized. If I attempt to rotate the Low Energy image, the Native image does the rotating...if any reaction at all. Although I was able to right click and enlarge the low energy image. I could not enlarge the Native structure.

Is there any details on what to expect of a docking WU?? i.e. long running models, and low numbers of steps?

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Message 2381 - Posted: 10 Oct 2006, 21:28:51 UTC - in response to Message 2379.  

Your runs are ok, and we have known for a while on Windows platform those output files are gzipped but the original files can not be deleted right away. They will evnentually be after the WU is finished.
not an error as the w/u finished ok but did get this
stderr out 5.4.11

# random seed: 2896098
# cpu_run_time_pref: 3600
WARNING! error deleting file .aa1IGC.out
WARNING! error deleting file .aa1IGC.out.bonds
WARNING! error deleting file .aa1IGC.out.rot_templates
======================================================
DONE :: 1 starting structures built 1 (nstruct) times
This process generated 1 decoys from 1 attempts
0 starting pdbs were skipped
======================================================



I had the same issue.

Result ID 288375
Name DOC_4HTC_u_pert_mcm_bbmin_1340_20_0
Workunit 254288
Created 10 Oct 2006 11:51:18 UTC
Sent 10 Oct 2006 12:13:39 UTC
Received 10 Oct 2006 16:10:29 UTC
Server state Over
Outcome Success
Client state Done
Exit status 0 (0x0)
Computer ID 250
Report deadline 14 Oct 2006 12:13:39 UTC
CPU time 13897.25
stderr out

5.6.5
[CDATA[

# random seed: 2895533
# cpu_run_time_pref: 14400
WARNING! error deleting file .aa4HTC.out
WARNING! error deleting file .aa4HTC.out.bonds
WARNING! error deleting file .aa4HTC.out.rot_templates
======================================================
DONE :: 1 starting structures built 23 (nstruct) times
This process generated 23 decoys from 23 attempts
0 starting pdbs were skipped
======================================================


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


]]

Validate state Valid
Claimed credit 47.6463856052397
Granted credit 50.3978804981935
application version 5.32

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Message 2382 - Posted: 10 Oct 2006, 21:49:08 UTC - in response to Message 2375.  
Last modified: 10 Oct 2006, 21:36:44 UTC

> On my Windows machine, I am still having screensaver lockups. It has carried over from 5.28. The screensaver will be processing and showing data fine but after a long time on (probably greater than 1 hour?) when I move the mouse nothing happens and the screensaver is doing nothing either. Task manager shows the programme is still working fine but not the screensaver. I tried stopping BoincManager.exe and boinc.exe but this did nothing, I can still get the start menu up but unable to get rid of screensaver background. I was about to reboot when I thought to double click on the screensaver and my computer was returned to me.
Has anyone else had this happen?
Not a problem on Linux machines as they don't have the screensaver function. Can it be turned of in Windows?

Yes, I have. On my laptop(never on a desktop). I've seen it predominately with Rosetta dating back to 5.22, but have seen it twice with Setibeta or seti. The screensaver will lock itself on top and will not go away. By clicking on places I can hear that it's actually still interfacing with the IE browser window below and it makes noise. Example, the browser window beneath the screensaver had a box game that if you shot a duck you'd win some fantastic prize. I could hear the gun shots from my clicking the mouse over where that area used to be. Rebooting has been my only option. Not even ctrl/alt/del works. Rom Walton has recieved my message about this many times. It only happens once every week or so, so it's hard to track. If you turn screensaver OFF it doesn't happen.

tony
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Message 2383 - Posted: 10 Oct 2006, 22:31:23 UTC

thanks for the reply chu

thought i should say something in case it was an unknown prob
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Message 2384 - Posted: 10 Oct 2006, 22:34:38 UTC - in response to Message 2383.  

thanks for the reply chu

thought i should say something in case it was an unknown prob

indeed. Perhaps if more report it, it'll become a priority??? LOL
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Message 2385 - Posted: 10 Oct 2006, 22:37:32 UTC

To me it seems like it doesn't happen when the screensaver turns on, but more "maybe" when my power options turns OFF the monitor. Like I said, It doesn't happen often enough for me to even be sure of any efforts to fix it.
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Message 2386 - Posted: 11 Oct 2006, 5:24:38 UTC

I got two WUs which started while Monitor was switched off. One had an error regarding screensaver, it then stopped processing but did not exit (though it said it did) until end of time slot, it then fell over:-

2006-10-11 02:03:43 [ralph@home] rosetta_beta not responding to screensaver, exiting

2006-10-11 05:47:10 [ralph@home] Unrecoverable error for result IDL_RLX_NT_t364_CASP7_hom001_1_1342_3_0 ( - exit code -1 (0xffffffff))

The second WU ran alongside and seems fine so far, having completed one two hour time slot, another 3.5 hours to run, fingers crossed.
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Message 2387 - Posted: 11 Oct 2006, 7:30:14 UTC

Today I get:

2006-10-11 08:05:30|ralph@home|Unrecoverable error for result 1t4o_1_CASPR_1_1t4o_1_xxidid_model_50_core_0001IGNORE_THE_REST_idl_1344_3_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2894240
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: ARG 15 3 2 2 0
chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458

And

2006-10-11 09:23:23|ralph@home|Unrecoverable error for result 1hz6A_BOINC_NATIVEJUMPS_CLOSE_CHAINBREAKS_VARY_BOND_ANGLES_SAVE_ALL_OUT__1343_28_0 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2894605
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: GLU 4 2 0 1 0
chi no 2 nchi 3 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458

One WU went good.

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Message 2388 - Posted: 11 Oct 2006, 11:39:50 UTC

Unrecoverable error for result IDL_RLX_NT_t326_CASP7_hom001_1_1342_3_0 (Incorrect function. (0x1) - exit code 1 (0x1))

resultid=288651
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Message 2389 - Posted: 11 Oct 2006, 12:01:34 UTC
Last modified: 11 Oct 2006, 12:08:36 UTC

and next one:

2006-10-11 14:02:26|ralph@home|Unrecoverable error for result DOC_2VIR_u_pert_mcm_bbmin_1340_17_2 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2895576
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: LYS 9 3 0 2 0
chi no 2 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458


2006-10-11 14:19:44|ralph@home|Unrecoverable error for result IDL_RLX_NT_t291_CASP7_hom001_1_1342_4_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2895459
# cpu_run_time_pref: 3600
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: ARG 15 3 2 1 0
chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458


2006-10-11 14:29:43|ralph@home|Unrecoverable error for result 5croA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_17_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# random seed: 2898706
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: LYS 9 3 2 0 0
chi no 3 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458
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Message 2390 - Posted: 11 Oct 2006, 16:15:44 UTC

What does this text mean?

2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_0
2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1
2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
2006-10-11 09:27:06|ralph@home|Finished upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1


Anders n

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Message 2391 - Posted: 11 Oct 2006, 16:36:02 UTC - in response to Message 2389.  

Hi, it looks like that you may have a corrupted rosetta_database which could be caused by various reasons...
and next one:

2006-10-11 14:02:26|ralph@home|Unrecoverable error for result DOC_2VIR_u_pert_mcm_bbmin_1340_17_2 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)


# random seed: 2895576
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
sin_cos_range ERROR: -1.#IND000 is outside of [-1,+1] range
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: LYS 9 3 0 2 0
chi no 2 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458


2006-10-11 14:19:44|ralph@home|Unrecoverable error for result IDL_RLX_NT_t291_CASP7_hom001_1_1342_4_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)


# random seed: 2895459
# cpu_run_time_pref: 3600
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: ARG 15 3 2 1 0
chi no 4 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458


2006-10-11 14:29:43|ralph@home|Unrecoverable error for result 5croA_BOINC_ABRELAX_SAVE_ALL_OUT_truess__1334_17_1 (Niepoprawna funkcja. (0x1) - exit code 1 (0x1))

Niepoprawna funkcja. (0x1) - exit code 1 (0x1)


# random seed: 2898706
ABORT: bad to aa_rotno_to_packedrotno
aa,rot1/2/3/4: LYS 9 3 2 0 0
chi no 3 nchi 4 aav 1 is_chi_proton_rotamer(aa,aav,i) 0
ERROR:: Exit at: .rotamer_functions.cc line:1458

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Message 2392 - Posted: 11 Oct 2006, 19:47:50 UTC

I just finished what may be a 'problem' unit:
wuid 252995
someone else did it in 5.31 and mine ran 5.32, but we both got 'validate' errors.
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Message 2393 - Posted: 12 Oct 2006, 2:54:43 UTC

there was another error in visual basic (or C++ don't remember for sure) "pure virtual call"

11/10/2006 20:53:30|SETI@home|Deferring task 21au02ab.16275.8016.234634.3.146_2
11/10/2006 20:53:31|ralph@home|Resuming task IDL_RLX_NT_t288_CASP7_hom001_1_1342_5_0 using rosetta_beta version 532
11/10/2006 20:53:32||Using earliest-deadline-first scheduling because computer is overcommitted.
11/10/2006 20:53:32||Suspending work fetch because computer is overcommitted.
12/10/2006 05:49:40|ralph@home|Unrecoverable error for result IDL_RLX_NT_t288_CASP7_hom001_1_1342_5_0 (The system cannot find the path specified. (0x3) - exit code 3 (0x3))
12/10/2006 05:49:40|ralph@home|Deferring scheduler requests for 1 minutes and 0 seconds

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Message 2394 - Posted: 12 Oct 2006, 2:59:09 UTC - in response to Message 2390.  

What does this text mean?

2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_0
2006-10-11 09:26:56|ralph@home|Started upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1
2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
2006-10-11 09:26:59||Curl error: a libcurl function was given a bad argument
2006-10-11 09:27:06|ralph@home|Finished upload of file DOC_2VIR_u_pert_mcm_bbmin_1340_5_0_1


Anders n

If you're using 5.6.5 then Rom has submitted a fix for this to show up in the next version.

tony
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Message 2395 - Posted: 12 Oct 2006, 3:32:15 UTC

We have seen errors (stop in options.cc ) for jobs batch 1349 and will fix that soon. Sorry about this.
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Message 2396 - Posted: 12 Oct 2006, 3:34:10 UTC

This one and this one died before they even got started.

The error is

<core_client_version>5.4.11</core_client_version>
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
ERROR:: Exit at: .options.cc line:453

</stderr_txt>
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