Bug reports for Ralph 5.09 and 5.10

Message boards : RALPH@home bug list : Bug reports for Ralph 5.09 and 5.10

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Rhiju
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Message 1481 - Posted: 5 May 2006, 2:36:29 UTC
Last modified: 6 May 2006, 6:51:06 UTC

See news page for a description of improvements in 5.09.

Also, by the way, if you\'re seeing problems with workunits of the following type, please abort them: HOMO_XXXX... They have a known problem. We\'re glad we tried these on ralph before on rosetta@home!
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FluffyChicken

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Message 1486 - Posted: 5 May 2006, 12:30:50 UTC - in response to Message 1481.  

See news page for a description of improvements in 5.09.

Also, by the way, if you\'re seeing problems with workunits of the following type, please abort them: HOMO_XXXX... They have a known problem. We\'re glad we tried these on ralph before on rosetta@home!



Hi, although I\'m unable to do actual application test on Ralph :-( do the the file size nature ....

May an idea for future version of Ralph tests (after the many others ;-) would be to try a terminate commend to remove these \'bad\' units. I would assume a way similar to how ClimatePrediction terminates it\'s task over there.

I something like this.
- Select tasks that need terminating (server end)
- When client connects to server, instruct it to stop the task.
- Send a little message along with it (I think others have managed to do this) to say sorry... etc..

Mainly useful for members that use larger caches, so you can pull them out and they don\'t waste time (at the best) or have big problems (at the worst). since the clients will contact to send a result back, update or just becuase it scheduled to.

I know CPDN.net do that because there it wastes lots of time if a model isn\'t working.

Though I\'m tempted to see the new screensaver changes...

Right, of out to a cafe with a good Wi-fi connection with my laptop to have some fun :-)




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Message 1488 - Posted: 5 May 2006, 15:19:17 UTC

Though having some work to test would help ;-)

Unless of course you have all you need sent out.
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Message 1493 - Posted: 5 May 2006, 21:08:14 UTC
Last modified: 5 May 2006, 21:22:26 UTC

Exit status 1 (0x1)
http://ralph.bakerlab.org/result.php?resultid=102884

May 4, 2006
Update to ralph 5.09. Now allows us to post descriptions of workunit on your screensaver (so you know what\'s going on!), graphics is rescaled for large proteins, and some fixes for the jumping mode. Please post bugs in this thread.


I dont use screesaver, but occasinally I click \"show graphics\"

I would like to see how the new graphics looks like ,,, but no WUs to test ?
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Neal

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Message 1496 - Posted: 5 May 2006, 22:34:27 UTC

Anyone else having trouble with the system locking while running tha Ralph 5.09 beta version? My preferences specify to suspend on activity, but system stays locked. Anything I should try??

Neal. (No fancy images)
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Message 1499 - Posted: 5 May 2006, 23:38:28 UTC - in response to Message 1496.  
Last modified: 5 May 2006, 23:40:52 UTC

Anyone else having trouble with the system locking while running tha Ralph 5.09 beta version? My preferences specify to suspend on activity, but system stays locked. Anything I should try??

Neal. (No fancy images)

I\'ve been wondering too, if the ralph app is fully releasing (i.e closing down) immediately or if it takes some time to get to a point where it can checkpoint, before releasing. Sorry, I have no further info on this.

P.S if you click \"reply to this post\" you can just copy and paste the bbcode into your \"forum preferences\", so you CAN have a \"fancy image\". Unless you meant the avatar on the left



tony
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Dimitris Hatzopoulos

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Message 1500 - Posted: 5 May 2006, 23:41:30 UTC

One bug I see with 5.09 is that the \"text description area\" contains multiple occurances of the same text info, so e.g. right now running in front of me I see the same text repeated FOUR (4) times:

\"Testing jumping/strand break protocol on BOINC with 1tul_ and 7 jumps
Sampling a comprehensive list of about 200,000 topologies and strand pairings\"

Perhaps it\'s an oversight where it outputs the text once for every model (now processing model 4)?
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Message 1503 - Posted: 6 May 2006, 0:35:19 UTC
Last modified: 6 May 2006, 1:00:16 UTC

not sure if this is a bug, more a cosmetic thing probably.
got a 5.09 running here right now, opened the graphics (not using the BOINC screensaver), maximized the window and i got a area on the right side, wider than the rmsd area, thats completely black without anything in it. (my screen resolution is 1024*768)
the description of what its doing right now looks like a nice new feature, it just looks a little dark on my sreen if you ask me. i can not verify what dimitris is seeing though, i only got the description once, and i am in model 3 right now.
edit: now at model 4 i got the description twice.
pic:
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doc :)

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Message 1504 - Posted: 6 May 2006, 1:43:30 UTC
Last modified: 6 May 2006, 1:44:50 UTC

too late to edit :)
model 8, description there 3 times now.
edit: still model 8, description appeared a 4th time while i was typing this.
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Message 1505 - Posted: 6 May 2006, 1:47:46 UTC

Every time the Graphical User Interface is restarted, the text area contains one more copy of the description! The graphics area shrinks accordingly!
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Message 1506 - Posted: 6 May 2006, 1:48:39 UTC - in response to Message 1503.  
Last modified: 6 May 2006, 1:51:25 UTC

not sure if this is a bug, more a cosmetic thing probably.
got a 5.09 running here right now, opened the graphics (not using the BOINC screensaver), maximized the window and i got a area on the right side, wider than the rmsd area, thats completely black without anything in it. (my screen resolution is 1024*768)
the description of what its doing right now looks like a nice new feature, it just looks a little dark on my sreen if you ask me. i can not verify what dimitris is seeing though, i only got the description once, and i am in model 3 right now.
edit: now at model 4 i got the description twice.
pic:


The large blank area is the result of the resizing to fit the proteins inside the right box. That blank area looks bigger on 16:9 aspect ratio than it does on normal monitors.
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Message 1508 - Posted: 6 May 2006, 2:54:19 UTC

Here\'s my first 5.09 failure. I don\'t know if it was running at the time, but I did a restart, then went to watch TV while it booted. When I returned, I saw the screensaver with a \"fatal error\" box. It\'s wu 90424.

Result ID 103370
Name JUMP_ALLBARCODES_1tul__SAVE_ALL_OUT_478_262_0
Workunit 90424
Created 5 May 2006 22:18:37 UTC
Sent 5 May 2006 22:26:28 UTC
Received 6 May 2006 3:08:30 UTC
Server state Over
Outcome Client error
Client state Computing
Exit status -1073741811 (0xffffffffc000000d)
Computer ID 2172
Report deadline 9 May 2006 22:26:28 UTC
CPU time 14071.640625
stderr out <core_client_version>5.4.9</core_client_version>
<message>
- exit code -1073741811 (0xc000000d)
</message>
<stderr_txt>
# random seed: 3078577
# cpu_run_time_pref: 14400
# cpu_run_time_pref: 14400
# cpu_run_time_pref: 14400
# cpu_run_time_pref: 14400
WARNING! error deleting file .\\xx1tul.out
# DONE :: 1 starting structures built 36 (nstruct) times
# This process generated 36 decoys from 36 attempts

</stderr_txt>


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Message 1509 - Posted: 6 May 2006, 4:04:08 UTC
Last modified: 6 May 2006, 4:04:49 UTC

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Message 1510 - Posted: 6 May 2006, 4:51:34 UTC
Last modified: 6 May 2006, 4:54:25 UTC

Rhiju,

There is no doubt about it. The Display of the \"JUMPING/STRAND Break Protocol\" is a real cat pleaser. The thing looks like a well baited fish hook. But there does seem to be a problem with the new text display repeating for at least the first three models. With each repeat the overall graphic seems to stretch vertically distorting the display slightly each time the lines are repeated. It is as if a file or variable that should be overwritten is not being cleared correctly. But you have solved the problem of the graphics not fitting in the boxes. That part looks real good. One thing you might consider for the graphic is to keep the count of steps for the first model and display that as the project step count for subsequent models. Also if the RMSD and ENERGY of the target is known, that would be good to include so people can see if they are getting close as the models are running. Obviously this would only for known structures.

So far the only errors I have seen for Mac or Windows on any of these machines has been on the HOMO Work Units, which seem to just be recycles from other systems.

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Message 1511 - Posted: 6 May 2006, 6:54:09 UTC - in response to Message 1510.  

Cool! I saw the same problem with the workunit description, and its pretty annoying. I think I put in the fix in 5.10; let\'s see.

Its great to see that fatal errors are being reported below! I hope Rom is able to use this feedback to pinpoint where in the code things are going wrong...

Rhiju,

There is no doubt about it. The Display of the \"JUMPING/STRAND Break Protocol\" is a real cat pleaser. The thing looks like a well baited fish hook. But there does seem to be a problem with the new text display repeating for at least the first three models. With each repeat the overall graphic seems to stretch vertically distorting the display slightly each time the lines are repeated. It is as if a file or variable that should be overwritten is not being cleared correctly. But you have solved the problem of the graphics not fitting in the boxes. That part looks real good. One thing you might consider for the graphic is to keep the count of steps for the first model and display that as the project step count for subsequent models. Also if the RMSD and ENERGY of the target is known, that would be good to include so people can see if they are getting close as the models are running. Obviously this would only for known structures.

So far the only errors I have seen for Mac or Windows on any of these machines has been on the HOMO Work Units, which seem to just be recycles from other systems.


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Message 1512 - Posted: 6 May 2006, 9:58:18 UTC
Last modified: 6 May 2006, 9:59:25 UTC

And another 5.09 fatal error on the same puter. This time I woke to the screen saver with the fatal error box in the middle of the screen. WU 90425

Result ID 103371
Name JUMP_ALLBARCODES_1tul__SAVE_ALL_OUT_478_263_0
Workunit 90425
Created 5 May 2006 22:18:37 UTC
Sent 5 May 2006 22:26:28 UTC
Received 6 May 2006 10:10:56 UTC
Server state Over
Outcome Client error
Client state Computing
Exit status -1073741811 (0xffffffffc000000d)
Computer ID 2172
Report deadline 9 May 2006 22:26:28 UTC
CPU time 14116.328125
stderr out <core_client_version>5.4.9</core_client_version>
<message>
- exit code -1073741811 (0xc000000d)
</message>
<stderr_txt>
# random seed: 3078576
# cpu_run_time_pref: 14400
# DONE :: 1 starting structures built 50 (nstruct) times
# This process generated 50 decoys from 50 attempts

</stderr_txt>


Validate state Invalid
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Message 1513 - Posted: 6 May 2006, 11:47:44 UTC

This WU (5.10) crashed on my laptop, while I had the graphics activ to display.

http://ralph.bakerlab.org/result.php?resultid=104651

Unusual is, that a windows-crash is reported, windows asked me, if I want to report it to micorsoft



Supporting BOINC, a great concept !
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Message 1514 - Posted: 6 May 2006, 13:13:12 UTC

Odd watchdog behavior on this unit: resid 103076. So far it has run for 7:04 cpu time and still at 1.030 pct complete, but watchdog hasn\'t killed it, it just swapped it out and let another ralph 5.09 run instead?
It\'s on ny laptop, hostid, not a hyperthreaded machine, running BM 5.4.7, and
it doesn\'t seem to be hurting anything att, just sitting there in \'preempted\' status so I haven\'t aborted it or anything (yet).
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Message 1515 - Posted: 6 May 2006, 13:48:51 UTC
Last modified: 6 May 2006, 14:04:02 UTC

This WU (5.09) Windows is being currently run
http://ralph.bakerlab.org/result.php?resultid=104408

The grapics is showing:

Testing jump protocol for an alpha/beta taken from

---- a blank line ----


a previus blind trial experiment (LiveBench)


This is no bug, but above message would fit into *one* line into
the space used by graphics (there is a fine line delimiting)

And this space used by rosetta graphics I guess is about 800x600 Pixels -:(
-> (wich is less than my screen) -
That is 1024x768 32 bit Colour
and has *all* space used by boinc \"show graphics\"

but Rosetta grapics is on a square/rectangle delimited by a fine line
*below off this line
there are other informations
34.4% complete
CPU Time ....
....
.... and on bottom
Roseta@home v5.09 http://boinc.bakerlab.org/rosetta .... accepted energy:-36.21......
*Notice that this is the URL of rosetta *not* of ralph

Wich initially confused me into believing that I was looking at another graphics
* other than the one I wanted to look -:(

*notice The graphics thread is running at thread priority 4
while the crunching thread is running at thread priority 1
and the grapics is very fast !!! and is using 20% CPU !
May be the web interface can be changed to allow less than 20% CPU
for graphics ... and allow slow rates than 20 frames/second too ???


*Now , I will resize my screen to 480x600 Pixels 16 bit ...
and then post how graphics swhon on there

*Completing this post first, (may be a system crash, may occurs) I use OpenGL
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Message 1516 - Posted: 6 May 2006, 14:41:25 UTC

The graphics bug hasn\'t quite been fixed yet (in 5.10). Although only one instance of the descriptive text shows up now, when opening the graphics interface a second (and third, and so on) time, there is an extra blank line between the two lines of text, pushing the rest of the WU info off the screen (model, step, time, percentage, etc), no matter how the window is resized.
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