Posts by milw0rm

1) Message boards : Number crunching : RALPH down a couple of days (Message 62877)
Posted 11 Aug 2009 by milw0rm
Post:
Now even the web server is down, and it does not respond to pings either. As it should now be Monday morning in west coast USA I hope they will be able to fix this soon.

Keith


Im currently receiving errors in my submissions.

The error i am getting is

Temporarily failed upload of XXXXXX: HTTP error.

i upgraded boinc in the hopes it would fix it but it is still errored.

Are the servers on their arse?
2) Message boards : Cafe Rosetta : I love irony (Message 46146)
Posted 13 Sep 2007 by milw0rm
Post:
I was looking at the TOP 10 REASONS WHY I CRUNCH ROSETTA and this was one of the reasons.

8. No outages - work always available!

I love irony!

w00000
3) Message boards : Rosetta@home Science : DISCUSSION of Rosetta@home Journal (3) (Message 44955)
Posted 13 Aug 2007 by milw0rm
Post:
On 6 Jul 2007 David Baker mentioned in his journal (http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1177&nowrap=true#43296) that his manuscripts were nearing completion. Could we all have a status update on this?

Thanks and best to all!
4) Message boards : Number crunching : Failed download (Message 39388)
Posted 15 Apr 2007 by milw0rm
Post:
15/04/2007 12:16:42|rosetta@home|[file_xfer] Started download of file frags83_1bk2_.fasta.gz
15/04/2007 12:17:03||Project communication failed: attempting access to reference site
15/04/2007 12:17:03|rosetta@home|[file_xfer] Temporarily failed download of frags83_1bk2_.fasta.gz: system connect
15/04/2007 12:17:03|rosetta@home|Backing off 1 hr 6 min 12 sec on download of file frags83_1bk2_.fasta.gz
15/04/2007 12:17:06||Access to reference site succeeded - project servers may be temporarily down.

I am glad it is not just me :D

RESTART!
5) Message boards : Rosetta@home Science : Current folds (Message 34878)
Posted 16 Jan 2007 by milw0rm
Post:
I was exited to see that we had a top fold yesterday with s014__BOINC_ABRELAX_SAVE_ALL_OUT_hom018__1406_0.clean.sc. Does anyone know what these proteins are for?

Thanks!
6) Message boards : Cafe Rosetta : Merry Christmas! (Message 33533)
Posted 27 Dec 2006 by milw0rm
Post:
Merry Christmas, Happy Holidays, and Happy New Year to all my fellow BOINCers!

All I want for Christmas is high Rosetta@home stats.. :P
7) Message boards : Rosetta@home Science : CASP 7 Results - T0354 (Message 31821)
Posted 29 Nov 2006 by milw0rm
Post:
Amazing! I am also a top one for T0354. Good to meet you Tiago :)

Good... I'm one of the top predictors of the T354.
I am really expecting some feedback from bakerlab about the meeting.

I hope rosetta made some good results, it is an excellent publicity to the the project and it may help bring more users.

;)


--
Elata
8) Message boards : Rosetta@home Science : CASP 7 Results - T0354 (Message 31795)
Posted 29 Nov 2006 by milw0rm
Post:
Here are the other results from the top predictions page at http://boinc.bakerlab.org/rosetta/rah_top_predictions.php
Congrats to all!

T0327

T0330 domain 2

T0283

T0316, domain 3

--
Elata
9) Message boards : Rosetta@home Science : CASP 7 Results - T0354 (Message 31794)
Posted 29 Nov 2006 by milw0rm
Post:
T0354

I don't have time to go through all of the results at the moment, but to my untrained eye, it looks as though Rosetta@home had the top prediction of the competition in at least T0354!

--
Elata
10) Message boards : Rosetta@home Science : CASP 7 Results (Message 31210)
Posted 16 Nov 2006 by milw0rm
Post:
Thank you James for all of the hard work you are putting into this project! You are quite literally making history with this research.

Hello,

Later this month David Baker and the rest of the CASP team (including myself) will travel to California to attend the CASP meeting (which occurs from November 26-30th). David tells me that a large part of the meeting is spent huddling around laptops, looking at score distributions for the various groups and their various submissions. I think that it will be very interesting to see how many targets each group has submitted, as there were many more targets during this CASP than in any previous.

Also, I'm happy that you noticed Target 0354. I worked on that one quite a lot, and am very proud of our accuracy in that prediction. I also know that we would not have achieved our level of accuracy on so many targets without your help. Thank you very much for your time.


Hello again!

We were excited to see David Baker's post about Target 0354, "This is one of the best ab initio structure predictions we made in the CASP7 experiment", not least because we helped to find it. I see CASP 7 is from November 26th until the 30th. Does anyone know when we will find out the rankings on how well each project did? For instance, when will we know the other group's structure predictions for each protein? I am curious to see how Rosetta@home fared this year. Best wishes to all projects of course!

11) Message boards : Rosetta@home Science : CASP 7 Results (Message 31168)
Posted 15 Nov 2006 by milw0rm
Post:
Hello again!

We were excited to see David Baker's post about Target 0354, "This is one of the best ab initio structure predictions we made in the CASP7 experiment", not least because we helped to find it. I see CASP 7 is from November 26th until the 30th. Does anyone know when we will find out the rankings on how well each project did? For instance, when will we know the other group's structure predictions for each protein? I am curious to see how Rosetta@home fared this year. Best wishes to all projects of course!
12) Message boards : Number crunching : Predictor of the day! (Message 29613)
Posted 19 Oct 2006 by milw0rm
Post:
Thank you to everyone who has replied!

Here is some more data on the protein:

http://predictioncenter.org/casp7/targets/templates/t0354.doc.html
http://www.rcsb.org/pdb/explore.do?structureId=2id1
http://spine.nesg.org:7000/gallery/jsp/ShowStructure.jsp?pdb_id=2id1
http://spine.nesg.org:7000/gallery/reports/CvR5_2id1/reports/fsvr/CvR5.html
13) Message boards : Number crunching : Predictor of the day! (Message 29585)
Posted 18 Oct 2006 by milw0rm
Post:
Does anyone have a time frame on how long it will take to find out how close our simulation is to the real protein? Will we have to wait until CASP 7 to find out? We are very excited to know, so that we can have a celebration party! ;) We recently passed 1 million results which was wonderful and now having a top prediction is like icing on the cake!

Keep folding :)
14) Message boards : Number crunching : Predictor of the day! (Message 29546)
Posted 17 Oct 2006 by milw0rm
Post:
I was absolutely thrilled to see that my team has helped the Rosetta@home project enough to be chosen as the predictor of the day. I was hoping for this for a few months now as our output has gradually increased. This is very exciting!

I am just wondering.. how does the predictor of the day relate to the top predictions, as seen on http://boinc.bakerlab.org/rosetta/rah_top_predictions.php?

Also, where can I see the actual structure which has the top prediction? It is no longer listed on http://boinc.bakerlab.org/rah_results.php?TeamID=1291.

Thanks and best wishes to all!
15) Message boards : Number crunching : Cell Processor (Message 20984)
Posted 23 Jul 2006 by milw0rm
Post:
IBM is also going to be releasing blades which can cluster and use the Cell processor: http://www-03.ibm.com/press/us/en/pressrelease/19198.wss

Imagine running BOINC on one of these if it was optimized to take advantage of it!
16) Message boards : Number crunching : Cell Processor (Message 20941)
Posted 23 Jul 2006 by milw0rm
Post:
Does anyone know if there will be a new version optimized to take advantage of the Cell processor's SPEs or at least the power processor (AltiVec) element?
17) Message boards : Number crunching : Report stuck & aborted 5.01 WU here please - III (Message 14679)
Posted 26 Apr 2006 by milw0rm
Post:
i have just checked two machines here and i too have had 2 units stuck on 116hours and 102 hours!

i stupidly did not record the uni numbers! :(
18) Message boards : Number crunching : WU PRODUCTION_ABINITIO_2acy__239_1514_1 (Message 11706)
Posted 6 Mar 2006 by milw0rm
Post:
Another good idea!!
what i find strange is that sometimes the work units will hang, you will then force boinc to start a new one, it will crunch it happily so you know everything works fine, you force it to go back to the old uni and it hangs again!

That irks me somewhat!
19) Message boards : Number crunching : WUs freeze !!! computer 117981 (Message 11705)
Posted 6 Mar 2006 by milw0rm
Post:
I am with a problem that some WUs
running on subject computer freezes !!!

rosetta 4.80

Initially I just killed boinc
and after ps xu clears
restarted boinc again

note that rosetta is the only project running
on this computer

top
shows 0.0% of use of cpu by rosetta
killing boinc and restarting boinc
only servers to I lost more time doing nothing

the freezes occurs again

Today I lost more the than of 4 hours of cpu IDLE !

Finally I discovered that aborting that WU
via remote gui rpc

that next WU comes to crunch normally !!

A big problem, for my *unmonitored* server

With these freezes I can end with a week of CPU IDLE
Else, to monitor that freezes and abort offending WUs
I have to pay a very costly $$$ diallup connection

*Please, that WUs cannot auto-abort ???

see a example of a returned result
Result ID 10549605
Name BARCODE_30_1ubi__299_25012_0
Workunit 8520285
Created 10 Feb 2006 11:13:57 UTC
Sent 10 Feb 2006 12:50:57 UTC
Received 10 Feb 2006 22:11:01 UTC
Server state Over
Outcome Client error
Client state Computing
Exit status -197 (0xffffff3b)
Computer ID 117981
Report deadline 17 Feb 2006 12:50:57 UTC
CPU time 551.93
stderr out <core_client_version>5.2.14</core_client_version>
<message>aborted by user
</message>
<stderr_txt>

</stderr_txt>


Validate state Invalid
Claimed credit 1.64110392447523
Granted credit 0
application version 4.80



I utterly agree with this.
i have had so many different units spend many hours doing nothing because the rosetta client does not auto cancel a unit that is broken or spends much toolong over the average processing time. this i have to check my computer output stat page every so often, find out who is not submitting and then go to the machine and abort the unit and get it to download a new one, thanks to a small oversight in the rosetta programmer's thought process. "Surely nothing could go wrong, we dont need this", unfortunately, it does! :(

Please fix :D
20) Message boards : Number crunching : No work from project (Message 6004)
Posted 12 Dec 2005 by milw0rm
Post:
Thanks. Is this because I have too many machines on under the same account?


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