minirosetta 2.05

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Sid Celery

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Message 65578 - Posted: 17 Mar 2010, 21:03:05 UTC - in response to Message 65575.  

I also had a lot of errors in tasks such as *__boinc_filtered_loopbuild_threading_*. In fact, every second job terminated by an error. And violating the target CPU time in each of the first (ie all tasks of this type) + strange looking things in graphics part (such as RMSD from 20 to 50 and odd-looking models)
So now I am canceling all jobs of this type, if I see them in the job queue.

It's the only error I've had in the last week on that W7 laptop, and credit was granted in the clean-up job, so I'm not worried by it - I don't understand any of these validate errors but while I was reporting the other one I thought I'd just mention it. I don't think my errors are the same as yours in that case.

I'm more surprised by the disk-usage issue on the Vista desktop which is otherwise very well behaved. I did suspect the task type, but others have gone through now with no problem at all, so maybe it just went a bit 'rogue' on me. I just thought it was worth describing seeing as I noticed it was a bit odd while running for 10 hours, yet the task details didn't indicate anything more than it failed on startup, which wasn't actually the case.

One for the backroom team to ponder.
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svincent

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Message 65655 - Posted: 28 Mar 2010, 0:24:31 UTC

Miscellaneous computation errors:

----

327069193 (v2FcInnerW_1dAl_3GM3_ProteinInterfaceDesign_15Mar2010_18672_254_0) failed on Mac OS X. Similar failure from wingman.

ERROR: f.check_fold_tree()
ERROR:: Exit from: src/protocols/docking/DockingProtocol.cc line: 405
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

----

326722657 (placestub_alt_denovo_1zvy_1z2m_ProteinInterfaceDesign_21Mar2010_18705_22_0) failed on W7

ERROR: in::file::zip minirosetta_database.zip does not exist!
ERROR:: Exit from: ....srcappspublicboincminirosetta.cc line: 137
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>

----

326721814 (tedor-cs_-tdonly-1-calbindin__18708_33_1) failed on W7. Similar failure from wingman.


ERROR: rsd_type_list.size()
ERROR:: Exit from: ....srccorefragmentFrame.cc line: 62
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>
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Evan

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Message 65658 - Posted: 28 Mar 2010, 8:01:15 UTC
Last modified: 28 Mar 2010, 8:09:45 UTC

326722657 (placestub_alt_denovo_1zvy_1z2m_ProteinInterfaceDesign_21Mar2010_18705_22_0) failed on W7

ERROR: in::file::zip minirosetta_database.zip does not exist!
ERROR:: Exit from: ....srcappspublicboincminirosetta.cc line: 137
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish


Add me to the list with

tedor-cs_-tdonly-1-gb3__18708_4647
ERROR: rsd_type_list.size()
ERROR:: Exit from: ....srccorefragmentFrame.cc line: 62
BOINC:: Error reading and gzipping output datafile: default.out
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allenandholmes

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Message 65659 - Posted: 28 Mar 2010, 8:17:07 UTC

I have been processing my current minirosetta task for 4 or 5 days now and have had a suspicion about its checkpointing capabilities. I shut my PC down each night and restart it the next morning for BOINC processing. However the elapsed time displayed resets to 0, the time to completion continues to increase all day long (and between sessions) and the processed percentage is dramatically different from a ratio of elapsed/completion times. Am I wasting my time?
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Sid Celery

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Message 65663 - Posted: 28 Mar 2010, 15:14:17 UTC

One unusual error I haven't seen before - W7-64bit laptop:

Rossmann3x3_abinitio_SAVE_ALL_OUT_design_k031_001_18698_1551_0
Outcome Client error
Client state Compute error
Exit status 1 (0x1)
[...]
<core_client_version>6.10.36</core_client_version>
[...]
# cpu_run_time_pref: 28800
Starting work on structure: _00018
Continuing computation from checkpoint: chk_S_00000018_ClassicAbinitio__stage_3_iter1_10 ... success!
Continuing computation from checkpoint: chk_S_00000018_ClassicAbinitio__stage4_kk_1 ... success!
Continuing computation from checkpoint: chk_S_00000018_ClassicAbinitio__stage4_kk_2 ... success!
std::cerr: Exception was thrown:
no success reading silent file chk_S_00000018_ClassicAbinitio__stage4_kk_3.out

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Mod.Sense
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Message 65666 - Posted: 28 Mar 2010, 21:21:41 UTC - in response to Message 65659.  

I have been processing my current minirosetta task for 4 or 5 days now and have had a suspicion about its checkpointing capabilities. I shut my PC down each night and restart it the next morning for BOINC processing. However the elapsed time displayed resets to 0, the time to completion continues to increase all day long (and between sessions) and the processed percentage is dramatically different from a ratio of elapsed/completion times. Am I wasting my time?


If you would like to see detail on when checkpoints are being taken, you can create or modify the cc_config.xml file. Add the tag for:
<checkpoint_debug>1</checkpoint_debug>
to the log_flags section.

The frequency of checkpoints varies with the various types of tasks.
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marc

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Message 65668 - Posted: 28 Mar 2010, 22:50:33 UTC - in response to Message 64951.  

Hi , guys ;
I sometimes have a trouble with the images ;
well , the trouble is that there are no images at all ;
and when I try to open it , Windows 7 is trying to open it ,
and trying , and trying , then telling me that the program can't be open ,
and so I have to stop the program .
There are no tasks problems , it's running , but the images are not availible .
Marc Denis




This app update includes a fix for checkpointing.

Please report issues and bugs here!

thanks,

DK

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Message 65675 - Posted: 29 Mar 2010, 16:24:01 UTC

Marc, I'm not clear on what you are saying you are doing. You should open the BOINC Manager, go to the advanced view, go to the tasks tab, select a task with status of "running", and then click the show graphics button at the left. Then you should expect to see something like is shown here.

...or are you talking about the screensaver? ...or are you trying to "open it" from Windows explorer? (don't)
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Mad_Max

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Message 65679 - Posted: 30 Mar 2010, 12:30:23 UTC

I think he means that hangs graphical part of the application. (like (Minirosetta_graphics_1.92)
Yesterday I watched 2 times the same bug on my computer - the calculation of the tasks goes good (it seems), but when I try to click "show graphics" graphical application does not show anything, and after some time hangs.
After killing proces "minirosetta_graphics_1.92_windows_intelx86.exe" all seems good, but if click "show graphics" again, its hangs again too.
Job Type was tedor-cs*. Unfortunately no link to a specific WU, because I have them not recorded, and in the log of tasks, they all appear to be successful.
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Evan

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Message 65680 - Posted: 30 Mar 2010, 13:39:28 UTC

I have four of the tedor-cs... programs running at the moment on this computer. They all are working perfectly but only three graphs can be activated. The fourth does not respond.
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Sid Celery

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Message 65681 - Posted: 30 Mar 2010, 17:36:37 UTC

Ditto here. I've had several long-running WUs recently and a click on the "Show graphics" button to see how or if it's progressing at all results in no display.

I have one now: tedor-cs_-csonly-1-Alg13__18706_6784_0

Cpu_run_time_pref: 28800 = 8 hours
Elapsed time 10h 6m 20s
CPU time 9h 45m 47s
Last Checkpoint 9h 44m 41s

No graphics. But I have an LR5_cus8 job that displays just fine.
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svincent

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Message 65703 - Posted: 6 Apr 2010, 5:21:31 UTC

A couple of recent failures with an error message I haven't seen before. Mac OS X

329517823 t308__boinc_corebuild_round2_rerun_cstrun2_sel_core_1.5.broker_corebuild_mtyka_IGNORE_THE_REST_19026_913_0

ERROR: Could not find disulfide partner for residue 6
ERROR:: Exit from: src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc line: 566
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>

329552087 t322__boinc_corebuild_round2_rerun_cstrun2_withcst_sel_core_1.5.broker_corebuild_mtyka_IGNORE_THE_REST_19063_575_0

ERROR: Could not find disulfide partner for residue 49
ERROR:: Exit from: src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc line: 566
BOINC:: Error reading and gzipping output datafile: default.out
called boinc_finish

</stderr_txt>
]]>
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Evan

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Message 65704 - Posted: 6 Apr 2010, 20:53:47 UTC

Another disulphide error
t293__boinc_corebuild_round2_rerun_cstrun2_withcst_sel_core_1.5.broker_corebuild_mtyka_IGNORE_THE_REST_19053_181_0
ERROR: Could not find disulfide partner for residue 97
ERROR:: Exit from: ....srccorescoringdisulfidesFullatomDisulfideEnergyContainer.cc line: 566

A validation error:
t303__boinc_corebuild_round2_rerun_cstrun2_sel_core_1.5.broker_corebuild_mtyka_IGNORE_THE_REST_19023_811_1
The prvious run ended in an error


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.clair.

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Message 65706 - Posted: 7 Apr 2010, 21:00:58 UTC
Last modified: 7 Apr 2010, 21:04:19 UTC

It is unusual that i get any errors,
I dont know if it was a fault at my end or not,
here are my two :-

t322__boinc_corebuild_round2_rerun_cstrun2_withcst_sel_core_1.5.broker_corebuild_mtyka_IGNORE_THE_REST_19063_460_0
ERROR: Could not find disulfide partner for residue 49
ERROR:: Exit from: src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc line: 566


Ross3X3_SAVE_ALL_OUT_relax_t012_18981_82_0
SIGSEGV: segmentation violation
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damon

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Message 65718 - Posted: 9 Apr 2010, 23:31:28 UTC

Has anyone run Rosetta on a netbook (Acer AspireONE AOA150-1777)? My specs:

--
CPU type GenuineIntel
Intel(R) Atom(TM) CPU N270 @ 1.60GHz [x86 Family 6 Model 28 Stepping 2]
Number of CPUs 2
Operating System Microsoft Windows XP
Home x86 Edition, Service Pack 3, (05.01.2600.00)
Memory 1523.88 MB
Cache 512 KB
Swap space 4401.18 MB
Total disk space 144.17 GB
Free Disk Space 120.95 GB
Measured floating point speed 689.15 million ops/sec
Measured integer speed 1752.15 million ops/sec
Maximum daily WU quota per CPU 89/day
--
I've been seeing the following Windows error for a few months:
--
Event Type: Information
Event Source: Application Popup
Event Category: None
Event ID: 26
Date: 4/9/2010
Time: 1:19:22 AM
User: N/A
Computer: ULTRAPORT
Description:
Application popup: Microsoft Visual C++ Runtime Library : Runtime Error!

Program: ...kerlab.org_rosettaminirosetta_2.05_windows_intelx86.exe


This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.


For more information, see Help and Support Center at http://go.microsoft.com/fwlink/events.asp.
--
Unfortunately, I can't locate the text file that keeps a track of what the project was doing at the time of the error. Initially, I thought that the amount of RAM was the problem, so I increased the amount from 1 GB to 1.5 GB. No go.

One of the other symptoms of a problem is the gradual filling of my swapfile with multiple instances of the Rosetta executable shown above. (Windows keeps announcing the resizing of the swapfile. Answering "OK" to each error pop-up doesn't appear to free the space allocated in RAM and the swapfile taken by the problem Rosetta executable instance.)

I have a larger Dell Inspiron B130 that has 2088316K (2 GB) of RAM, is at least three years older than the Netbook, runs only one work unit at a time, but functions smoothly without filling up the swapfile.

Am I asking too much of my Netbook by running Rosetta on it?

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Profile Greg_BE
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Message 65746 - Posted: 15 Apr 2010, 13:38:07 UTC

t293__boinc_corebuild_round2_rerun_cstrun2_sel_core_1.5.broker_corebuild_mtyka_IGNORE_THE_REST_19020_211_0

# cpu_run_time_pref: 14400
ERROR: Could not find disulfide partner for residue 97
ERROR:: Exit from: ....srccorescoringdisulfidesFullatomDisulfideEnergyContainer.cc line: 566
BOINC:: Error reading and gzipping output datafile: default.out


rosetta2_relax_cst_0.1_cm.loopbuild_threading_hb_t297__IGNORE_THE_REST_19126_320_0

disk space error (i have 23.4gb free so no way do i not have enough space)
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Message boards : Number crunching : minirosetta 2.05



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