Posts by Rhiju

1) Message boards : RALPH@home bug list : Bug reports for 5.96 (Message 3835)
Posted 22 Mar 2008 by Rhiju
Post:
A small update, mainly tests of a new mode for modeling RNA structures with experimental constraints. Let us know if you see anything fishy!
2) Message boards : RALPH@home bug list : Bug reports for 5.90/5.91 (Message 3569)
Posted 21 Dec 2007 by Rhiju
Post:
I didn't see the message in, e.g., the stderr -- where is it showing up?

This isn't really a bug, but more of an item that Rosetta@Home users will probably go nuts about. I suspect it has to do with the new BOINC API.

Recent WU's have an interesting line that says ERRORS: CANCELLED.

Any idea what it means? Might be useful to put it in the FAQs if it's always going to say that.

==Mike

3) Message boards : RALPH@home bug list : Bug reports for 5.90/5.91 (Message 3568)
Posted 21 Dec 2007 by Rhiju
Post:
The linux executable should behave better now. Thanks to Conan others for the "front-lines" warning from ralph! Let us know how its working.


It would appear that no matter what time you have in your preferances it will not be adhered to.
I had 4 Ralph WU's running when I went to bed (no idea how long they had been running as nothing was showing), all were at high priority.
They were still running this morning so I stopped BM and restarted, this made the WU's immediatly report and give their stats.
They had run for 19 to 20 hours and probably would of kept running till they were stopped. They produced 11 to 13 decoys.

718960
719023
719030
719087

4) Message boards : RALPH@home bug list : Bug reports for 5.90/5.91 (Message 3558)
Posted 20 Dec 2007 by Rhiju
Post:
Hi Conan: Thanks, this is interesting and unexpected! I forgot to mention in the home page that we also updated the version of the BOINC api that is used to compile Rosetta@home, in anticipation of a new release of the BOINC client software (6.0). We'll look into whether this causes a problem with the reporting of % complete, etc.


I am currently running 3 work units of the "1px8" variety.
They are behaving very weirdly.
I checked my computer and saw that only one WU was progressing in time and percentage done (a CPDN WU) and no other counters were moving.
I have 4 cores and Boinc Manager said that my 3 other cores were all running at High Priority on my 3 Ralph work units.
No CPU Time done, No Percent Done and No Time Left counters were moving.
In fact The CPU Time was on 0.00% as was Percent done.
Suspending and restarting made no difference.
Stopped Boinc and restarted Boinc Manager and I now had the RALPH WU's showing over and hour had been completed and between 18% and 30% had been completed.
But the counters still are not moving, only when you stop and restart the manager do you see what progress has been done.

The WU's are still running at the moment 715097
715153
715237

I checked my system (Linux) and found all 4 cores are running so the WU's have not hung and are actually processing, it is just that I can't see what is happening.

5) Message boards : RALPH@home bug list : Bug reports for 5.90/5.91 (Message 3554)
Posted 20 Dec 2007 by Rhiju
Post:
Update to 5.90! Keep us posted on weirdness.
6) Message boards : RALPH@home bug list : Bug reports for 5.89 (Message 3553)
Posted 20 Dec 2007 by Rhiju
Post:
Thanks for the screenshot -- we're looking into this, but the craziness may not be fixed for a few updates...

Noticed graphic bug in accepted energy bar in this work unit:
http://ralph.bakerlab.org/workunit.php?wuid=632126
It looked like that few minutes but disappeared after while.


Edit: As you can see, it appeared when 43.69% was completed.

7) Message boards : RALPH@home bug list : Bug reports for 5.89 (Message 3536)
Posted 15 Dec 2007 by Rhiju
Post:
Hi: yup, they're going to take a while... when we apply filters (to allow premature exits for unpromising model), they will average 2-3 hours per model. But these are totally worth it!

wowzers, takes a while to run these guys thru. I just finished my first, took almost six hours (21,240 secs)to do one decoy on my p-4 2.8ghz Win-xp box. I'm gonna have to up my preferences if they are all going to run this long!

Resid 709016

8) Message boards : RALPH@home bug list : Bug reports for 5.88 (Message 3531)
Posted 12 Dec 2007 by Rhiju
Post:
Yea, we're flooding ralph with a bunch of test jobs for this workunit -- we can't figure out why its crashing. Yet. Bear with us! We'll probably do another update later today if we can figure out the fix.

Hmmm... another addressing crash.

==Mike

9) Message boards : RALPH@home bug list : Bug reports for 5.87 (Message 3519)
Posted 11 Dec 2007 by Rhiju
Post:
Hi Mike: Please go ahead and let them run!

I suspect the answer is no, but do you want us to abort WU's from a previous version (in this case 5.85) when a new version comes out?

==Mike

10) Message boards : RALPH@home bug list : Bug reports for 5.87 (Message 3517)
Posted 11 Dec 2007 by Rhiju
Post:
Thanks for continuing to post! It helps tremendously.
11) Message boards : RALPH@home bug list : Bug reports for 5.84 (Message 3506)
Posted 6 Dec 2007 by Rhiju
Post:
We're looking into it -- I just contacted Rob, who can probably give you an update on these tests.

5 x the same error as BigMike mentioned ("Incorrect function. (0x1) - exit code 1 (0x1), ERROR:: Exit from: .fragments.cc line: 465"): results 689005, 688961, 688506, 688423, 689759, named "1****_BOINC_ABINITIO_BEST25_VF_SCORE3-1*--1****-vf__2657_*_*".
All wingmen immediately failed too.

Peter

12) Message boards : RALPH@home bug list : Bug reports for 5.84 (Message 3467)
Posted 16 Nov 2007 by Rhiju
Post:
Thanks for posting!
13) Message boards : RALPH@home bug list : bug report for version 5.81 (Message 3466)
Posted 16 Nov 2007 by Rhiju
Post:
fixed! Thanks!
The whole WU 586085 failed, 2 results because of "WU download error: couldn't get input files: calcium_1emn.pdb.gz, error_code -200" (Windows) and res 660290 because of "SIGSEGV: segmentation violation" (Linux).

And what will akismet say to this message?
[edit]It definitely dislikes the message text, probably the links.
We can try to atach few paragraphs from any book? ;-)
I've stripped http: from the beginning, sorry. But this is still not enough.
Now I've found good workaround for local adresses, e.g. this is this thread - :/forum_reply.php?thread=337 - voila!

Peter

14) Message boards : RALPH@home bug list : Bug reports for 5.78 (Message 3345)
Posted 7 Sep 2007 by Rhiju
Post:
Hey everybody, thanks for the support!

This is a particularly crazy time because we are in the midst of the CAPRI competition to predict protein-protein interactions, and we'd really like to run some workunits. There are two "puzzles" that we've been given and they're both pretty cool, related to the interactions of some important signaling proteins (the so-called GTPases and the plexins).

We just got the ability to queue stuff to ralph so you'll start seeing some jobs. By the way, the first round that I sent out had a silly error (which I just fixed); sorry about that. Looking forward to getting ralph and rosetta running smoothly again!

Hi all :)

How about some work on Ralph to take some load off Rosetta when !? it come
back to life;)

Anders n

15) Message boards : RALPH@home bug list : Bug reports for 5.72-5.76 (Message 3319)
Posted 12 Aug 2007 by Rhiju
Post:
Hi: Yea, I was putting up info on new apps when ralph crashed for a few hours -- putting up some updates now.

Also, thanks for the post of a job that's going on too long for the watchdog.


Here is one.

Edit any info on the new apps?

16) Message boards : RALPH@home bug list : Bug reports for 5.72-5.76 (Message 3314)
Posted 11 Aug 2007 by Rhiju
Post:
Hmm, I didn't think about the heartbeart or watchdog issue. Good point. So far I haven't seen any early exit due to that problem, but I'll keep an eye out for it!

In this type of vu "157d__BOINC_MINIMIZE_NOFLAGS_RNA_ABINITIO-157d_-_2295_834_0" the steps, accepted energi and accepted RMSD does not change after about 5500 steps in each model. But you can se the grafics move and the new dots comming in the right corner.

Anders n

Edit I think that can lead to that the wu's error out on heartbeat for slow computers.

17) Message boards : RALPH@home bug list : Bug reports for 5.72-5.76 (Message 3312)
Posted 8 Aug 2007 by Rhiju
Post:
Thanks, we're not going to send those out to Rosetta@home!

Two that have failed with the same error
This one
And this one



> Same fault and again it is the "1vie" type Work Unit, they ALL fail,
600557


Just a 'me too' post :-)
Boinc 5.8.15, Ralph 5.73, Workunit 531614, Result 599889, OS Linux 32-bit.

18) Message boards : RALPH@home bug list : Bug reports for 5.72-5.76 (Message 3306)
Posted 7 Aug 2007 by Rhiju
Post:
Thanks we noted these, and they'll be tested again on ralph with a fix before getting sent out to Rosetta@home.

3 more, these ones on a Windows machine

1i8f type WU

<core_client_version>5.8.15</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 21600
# random seed: 2188650
ERROR:: Exit from: .hbonds.cc line: 651

calbindin_BOINC_MFR type WU
MFR type WU

<core_client_version>5.8.15</core_client_version>
<![CDATA[
<message>
Incorrect function. (0x1) - exit code 1 (0x1)
</message>
<stderr_txt>
# cpu_run_time_pref: 21600
# random seed: 2188650
ERROR:: Exit from: .fragments.cc line: 769




Here is another MFR with same fault
MFR type WU

19) Message boards : RALPH@home bug list : Bug reports for 5.72-5.76 (Message 3290)
Posted 22 Jul 2007 by Rhiju
Post:
Thanks for continuing to post... things have overall been pretty quiet, and ralph has been chugging along great. This might be our last update before we update the real rosetta@home app, so I'm hoping that this looks good!
20) Message boards : RALPH@home bug list : Bug reports for 5.71 (Message 3289)
Posted 22 Jul 2007 by Rhiju
Post:
Sorry about this -- the shaded sphere view is experimental. Glad to hear that the ribbons view still works fine.

When displaying the graphic and pressing "B" three times to display the view with the balls, if you rotate the image 180 degrees to the left, you end up displaying the shaded portion of the sun effect. Seems the orientation of the sun should probably be fixed relative to the viewer of the graphic, so all the windows would always show the sun in the upper right, even if you rotate one of the images.

Also, currently running a Rosetta 5.68 jumping task and the image in the searching and accepted boxes is bouncing all around. i.e. it is not properly centered in the box. However, changing the view back to the ribbons and it is centered normally. Looks like the low energy box is effected the same way.



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