Problems with Rosetta version 5.45

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Profile David E K
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Message 35737 - Posted: 30 Jan 2007, 2:32:48 UTC
Last modified: 30 Jan 2007, 19:46:47 UTC

Please post problems with Rosetta@home 5.45 here. Like the previous version, we're interested in whether graphics-related crashes are reduced with this version. We hope there is a significant improvement in the stability of the graphics, and we've turned back on the display of sidechains and rotation of the protein. There are still issues with graphics on Mac ppc and intel platforms.

Edit: The Mac graphics issues that we are still experiencing on local tests do not affect the main application. Sometimes the graphics thread may stall (the displayed cpu time in the graphics window does not increment) but please keep in mind that the rosetta application is still doing valid work - the work unit will still look like it is running okay in the boinc manager. If you come accross this situation, you may close the window or keep it open, however, once the window is closed, you will not be able to open it again for the particular work unit in progress.
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alexpoon

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Message 35753 - Posted: 30 Jan 2007, 13:32:00 UTC - in response to Message 35737.  
Last modified: 30 Jan 2007, 13:32:57 UTC

Please post problems with Rosetta@home 5.45 here. Like the previous version, we're interested in whether graphics-related crashes are reduced with this version. We hope there is a significant improvement in the stability of the graphics, and we've turned back on the display of sidechains and rotation of the protein. There are still issues with graphics on Mac ppc and intel platforms.

A very small problem, the description txt don't show in the graphic mode:D
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Message 35776 - Posted: 30 Jan 2007, 22:11:45 UTC

Everything is running fine with iMac4,1 Core Duo and Boinc Manager 5.4.9.

Not sure if this is a minor bug as I don't run Rosetta much. If I have the graphics window running and switch to another program, all is well. If I click on the graphics window, the window comes to the front as it should, but the menus stay with the other program, not Boinc. If I am in the other program and switch to Boinc, the graphics window closes.
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Message 35781 - Posted: 31 Jan 2007, 1:07:34 UTC

Seems to be a problem with running a Poweredge 6450 and Centos 4.2. Two of the four process stopped at about 63 percent. I know this is vintage hardware, but I have another Poweredge running Windows 2003 RC2 and it runs fine.

Maybe an OS switch is in order?
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Message 35782 - Posted: 31 Jan 2007, 1:35:12 UTC - in response to Message 35781.  

Your computers are hidden. Please post a link to your error results.
Seems to be a problem with running a Poweredge 6450 and Centos 4.2. Two of the four process stopped at about 63 percent. I know this is vintage hardware, but I have another Poweredge running Windows 2003 RC2 and it runs fine.

Maybe an OS switch is in order?


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Message 35814 - Posted: 31 Jan 2007, 16:02:26 UTC - in response to Message 35782.  

Your computers are hidden. Please post a link to your error results.
Seems to be a problem with running a Poweredge 6450 and Centos 4.2. Two of the four process stopped at about 63 percent. I know this is vintage hardware, but I have another Poweredge running Windows 2003 RC2 and it runs fine.

Maybe an OS switch is in order?



I had to abort two process because they were stuck and way overtime. I believe they were due on Janurary 18th. I can't view WU back that far.
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KuniaKid

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Message 35888 - Posted: 1 Feb 2007, 5:05:35 UTC

version 5.45 won't download

1/31/2007 7:03:37 PM|rosetta@home|Started download of file rosetta_5.45_windows_intelx86.exe
1/31/2007 7:03:38 PM||[http_debug] HTTP error: Transferred a partial file
1/31/2007 7:03:38 PM||Project communication failed: attempting access to reference site
1/31/2007 7:03:38 PM||[http_debug] HTTP_OP::init_get(): http://www.google.com
1/31/2007 7:03:38 PM|rosetta@home|Temporarily failed download of rosetta_5.45_windows_intelx86.exe: http error
1/31/2007 7:03:38 PM|rosetta@home|Backing off 1 minutes and 0 seconds on download of file rosetta_5.45_windows_intelx86.exe
1/31/2007 7:03:39 PM||Access to reference site succeeded - project servers may be temporarily down.



I've been getting this for a day or so.
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Keith Akins

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Message 35889 - Posted: 1 Feb 2007, 5:43:04 UTC
Last modified: 1 Feb 2007, 5:43:22 UTC

Just noticed that I have "Pending" granted credits. Is this new for 5.45? WU's appear to be completed successfully.
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Message 35890 - Posted: 1 Feb 2007, 6:04:20 UTC - in response to Message 35889.  

Just noticed that I have "Pending" granted credits. Is this new for 5.45? WU's appear to be completed successfully.



The validator is not running.

Se this page https://boinc.bakerlab.org/rosetta/rah_status.php

Anders n
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Message 35926 - Posted: 1 Feb 2007, 17:35:54 UTC - in response to Message 35890.  

Thanks. We are aware of that and are looking into it right now.
Just noticed that I have "Pending" granted credits. Is this new for 5.45? WU's appear to be completed successfully.



The validator is not running.

Se this page https://boinc.bakerlab.org/rosetta/rah_status.php

Anders n


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Message 36010 - Posted: 2 Feb 2007, 18:52:38 UTC
Last modified: 2 Feb 2007, 18:55:12 UTC

I still can't get it to download.


2/2/2007 8:49:25 AM||[http_debug] HTTP_OP::init_get(): http://srv4.bakerlab.org/rosetta/download/rosetta_5.45_windows_intelx86.exe
2/2/2007 8:49:25 AM|rosetta@home|[file_xfer] Started download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:49:26 AM||[http_debug] HTTP error: Transferred a partial file
2/2/2007 8:49:26 AM||Project communication failed: attempting access to reference site
2/2/2007 8:49:26 AM||[http_debug] HTTP_OP::init_get(): http://www.google.com
2/2/2007 8:49:26 AM|rosetta@home|[file_xfer] Temporarily failed download of rosetta_5.45_windows_intelx86.exe: http error
2/2/2007 8:49:27 AM||Access to reference site succeeded - project servers may be temporarily down.
2/2/2007 8:49:27 AM||[http_debug] HTTP_OP::init_get(): http://srv3.bakerlab.org/rosetta/download/rosetta_5.45_windows_intelx86.exe
2/2/2007 8:49:27 AM|rosetta@home|[file_xfer] Started download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:49:28 AM||[http_debug] HTTP error: Transferred a partial file
2/2/2007 8:49:28 AM||Project communication failed: attempting access to reference site
2/2/2007 8:49:28 AM||[http_debug] HTTP_OP::init_get(): http://www.google.com
2/2/2007 8:49:28 AM|rosetta@home|[file_xfer] Temporarily failed download of rosetta_5.45_windows_intelx86.exe: http error
2/2/2007 8:49:28 AM|rosetta@home|Backing off 24 min 55 sec on download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:49:29 AM||Access to reference site succeeded - project servers may be temporarily down.


Times are HST

and this from different machine, same network:


2/2/2007 8:53:30 AM|rosetta@home|[file_xfer] Started download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:53:31 AM||Project communication failed: attempting access to reference site
2/2/2007 8:53:31 AM|rosetta@home|[file_xfer] Temporarily failed download of rosetta_5.45_windows_intelx86.exe: http error
2/2/2007 8:53:33 AM|rosetta@home|[file_xfer] Started download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:53:34 AM||Access to reference site succeeded - project servers may be temporarily down.
2/2/2007 8:53:34 AM|rosetta@home|[file_xfer] Temporarily failed download of rosetta_5.45_windows_intelx86.exe: http error
2/2/2007 8:53:35 AM|rosetta@home|[file_xfer] Started download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:53:36 AM||Project communication failed: attempting access to reference site
2/2/2007 8:53:36 AM|rosetta@home|[file_xfer] Temporarily failed download of rosetta_5.45_windows_intelx86.exe: http error
2/2/2007 8:53:37 AM||Access to reference site succeeded - project servers may be temporarily down.
2/2/2007 8:53:37 AM|rosetta@home|[file_xfer] Started download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:53:39 AM||Project communication failed: attempting access to reference site
2/2/2007 8:53:39 AM|rosetta@home|[file_xfer] Temporarily failed download of rosetta_5.45_windows_intelx86.exe: http error
2/2/2007 8:53:39 AM|rosetta@home|Backing off 3 hr 7 min 40 sec on download of file rosetta_5.45_windows_intelx86.exe
2/2/2007 8:53:40 AM||Access to reference site succeeded - project servers may be temporarily down.

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Message 36018 - Posted: 2 Feb 2007, 20:26:17 UTC
Last modified: 2 Feb 2007, 20:27:57 UTC

Yep, me too........

Nevermind............just all went through :)
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Message 36029 - Posted: 3 Feb 2007, 3:11:55 UTC

I've started getting "Computation Error" for every Rosetta wu. the messages all show the same as the few below:

2/2/2007 6:20:28 PM|rosetta@home|Reason: Unrecoverable error for result 1who__BOINC_ABRELAX_NEWRELAXFLAGS_frags83__1521_4110_0 (No main program specified)
2/2/2007 6:20:30 PM|rosetta@home|Reason: Unrecoverable error for result 1louA_BOINC_ABRELAX_NEWRELAXFLAGS_frags83__1522_4982_0 (No main program specified)
2/2/2007 6:20:31 PM|rosetta@home|Reason: Unrecoverable error for result 1hz6A_BOINC_ABRELAX_NEWRELAXFLAGS_frags83__1521_4982_0 (No main program specified)
2/2/2007 6:20:32 PM|rosetta@home|Reason: Unrecoverable error for result 1acf__BOINC_ABRELAX_NEWRELAXFLAGS_frags83__1521_4983_0 (No main program specified)

(No main program specified) ...

Right now I have 37 of them on one system - which does neither you nor I any good at all.
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Message 36031 - Posted: 3 Feb 2007, 7:58:18 UTC

The granted credit is staring to look better. Maybe now I will have a chance to win the golden Chromosome Award. ;-)
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Message 36050 - Posted: 3 Feb 2007, 19:51:14 UTC

Meshmar, which host are you having trouble with? Can you link us to a few of the result pages?
Rosetta Moderator: Mod.Sense
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Message 36060 - Posted: 3 Feb 2007, 20:50:42 UTC

Looks like Meshmar is getting:

Exit status -185 (0xffffff47)
Computer ID 371695
Report deadline 12 Feb 2007 2:57:25 UTC
CPU time 0
stderr out <core_client_version>5.8.8</core_client_version>
<![CDATA[
<message>
No main program specified
</message>
]]>

Such as here: 60144263

Have you tried resetting the project?
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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Message 36075 - Posted: 4 Feb 2007, 2:21:58 UTC

That's the one Feet1st. I tried resetting - and it did the same for a batch more wu ... so now that system is happily working on Malaria and Tampaku. No idea why it suddenly decided it didn't like Rosetta. Every other system is still working on them with no issues ...
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Message 36123 - Posted: 4 Feb 2007, 21:42:10 UTC


Windows Vista, New Boinc 5.8.8 , server errors ????



2/4/2007 4:38:22 PM|rosetta@home|[file_xfer] Throughput 21092 bytes/sec
2/4/2007 4:38:29 PM|rosetta@home|Starting 1b3aA_BOINC_ABRELAX_NEWRELAXFLAGS_frags83__1522_8018_0
2/4/2007 4:38:34 PM|rosetta@home|[error] Can't link projects/boinc.bakerlab.org_rosetta/rosetta_5.45_windows_intelx86.exe to slots/0/rosetta_5.45_windows_intelx86.exe
2/4/2007 4:38:36 PM|rosetta@home|Computation for task 1b3aA_BOINC_ABRELAX_NEWRELAXFLAGS_frags83__1522_8018_0 finished

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Message 36137 - Posted: 5 Feb 2007, 4:10:03 UTC
Last modified: 5 Feb 2007, 4:29:53 UTC

The 'stuck at 100%' bug has returned with this result here.

The prefferred run time had just been cut from 24hrs to 1hr to encourage Rosetta to make way for LHC (which rarely has work and which I therefore give highest priroity when it does have some), but instead this result hung having reached its new completion point.

I don't know if I provoked it, or if it would have happened anyway at the end of the original run length. Either way I'd say it is a bug, tho obviously less serious of it only occurs with a shortened run.

For others who see this, the best fix I have found is to stop BOINC and restart it, which then pushes the stuck task to start uploading.

edit add:

BTW - in response to your question in the first posting in this thread, this box has no graphics (not even an X-server) so it is not a gfx bug (unless the bug is that the windup code goes looking for the gfx...)

edit 2 add

and two more examples here and here, all different boxes, all running Linux, all stopped at 100% after run time shortened.

This is clearly relevant as it caused the watchdog message to appear, but what I still say is a bug is that the watchdog seems to make the result stick instead of ending properly.

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Message 36138 - Posted: 5 Feb 2007, 4:28:42 UTC

What's this mean ?

2/4/2007 11:25:38 PM||[error] Can't create HTTP response output file projects/boinc.bakerlab.org_rosetta/rosetta_5.45_windows_intelx86.exe
2/4/2007 11:25:44 PM||[error] Can't create HTTP response output file projects/boinc.bakerlab.org_rosetta/rosetta_5.45_windows_intelx86.exe
2/4/2007 11:25:50 PM||[error] Can't create HTTP response output file projects/boinc.bakerlab.org_rosetta/rosetta_5.45_windows_intelx86.exe
2/4/2007 11:25:56 PM||[error] Can't create HTTP response output file projects/boinc.bakerlab.org_rosetta/rosetta_5.45_windows_intelx86.exe
2/4/2007 11:25:56 PM|rosetta@home|Backing off 10 min 27 sec on download of file rosetta_5.45_windows_intelx86.exe

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