Posts by cenit

1) Message boards : Number crunching : Please disable upload certificates? (Message 71514)
Posted 27 Oct 2011 by Profile cenit
Post:
A quick test reveals Rosetta@home still haven\'t fixed their broken upload-server:

08.10.2011 14:33:09 | rosetta@home | [fxd] starting upload, upload_offset -1
08.10.2011 14:33:09 | rosetta@home | Started upload of place_CwEfDw_20111005_EBOV_GP3_1jl1_ProteinInterfaceDesign_05Oct2011_33944_360_0_0
08.10.2011 14:33:09 | rosetta@home | [file_xfer] URL: http://srv6.bakerlab.org/rosetta_cgi/file_upload_handler
08.10.2011 14:33:18 | rosetta@home | [file_xfer] http op done; retval 0 (Success)
08.10.2011 14:33:18 | rosetta@home | [file_xfer] parsing upload response: <data_server_reply>    <status>0</status>    <file_size>0</file_size></data_server_reply>
08.10.2011 14:33:18 | rosetta@home | [file_xfer] parsing status: 0
08.10.2011 14:33:18 | rosetta@home | [fxd] starting upload, upload_offset 0
08.10.2011 14:33:27 | rosetta@home | [file_xfer] http op done; retval 0 (Success)
08.10.2011 14:33:27 | rosetta@home | [error] Error reported by file upload server: invalid signature
08.10.2011 14:33:27 | rosetta@home | [file_xfer] parsing upload response: <data_server_reply>    <status>-1</status>    <message>invalid signature</message></data_server_reply>
08.10.2011 14:33:27 | rosetta@home | [file_xfer] parsing status: -128
08.10.2011 14:33:27 | rosetta@home | [file_xfer] file transfer status -128 (permanent upload error)
08.10.2011 14:33:27 | rosetta@home | Giving up on upload of place_CwEfDw_20111005_EBOV_GP3_1jl1_ProteinInterfaceDesign_05Oct2011_33944_360_0_0: permanent upload error




unfortunately, I had to put Rosetta to NNT back in the days on my most powerful machine.

When will I be able to resume work?
Boinc 6.13.10 is out now and you\'re still on a really old server code (and you also didn\'t disable signature, too, if you don\'t want to upgrade - why, then?)
2) Message boards : Number crunching : Please disable upload certificates? (Message 71315)
Posted 22 Sep 2011 by Profile cenit
Post:
Can the project administrators please disable the upload certificates on this project as was asked by David Anderson? This helps us who test the newer 6.13 clients as now all work we do for you project will get a validate error stamped on it, while the work is otherwise correct.

\"Upload certificates\" are a mechanism that keeps bad guys from DoS\'ing your upload servers
(note: such an attack has never happened, as far as I know).

We\'re changing the format of upload certificates, and we\'re starting to test a version of the client for which old-format certificates won\'t work. Volunteers testers won\'t be able to upload completed jobs, and they may complain to you.

I suggest that all projects disable upload certificates. To do so, add the following to your config.xml file:

<dont_generate_upload_certificates/>
<ignore_upload_certificates/>

To resume using upload certificates, if you wish:

1) upgrade to the current server source code (from trunk)
2) wait for all jobs with old-format certificates to be dispatched
3) re-enable certificates by removing the above lines.

Let me know if any questions.

-- David


With thanks.



I\'m testing and, in fact, I can tell you that I cannot upload any result:
9/22/2011 4:58:27 PM | rosetta@home | [error] Error reported by file upload server: invalid signature
9/22/2011 4:58:27 PM | rosetta@home | Giving up on upload of 2NR7A_abrelax_ex_31488_290_0_0: permanent upload error
3) Message boards : Rosetta@home Science : CASP9 (Message 66557)
Posted 12 Jun 2010 by Profile cenit
Post:
The team BOINC Synergy has selected Rosetta to be its project of the month for May! I hope the extra computing helps with CASP.

our team (BOINC.Italy) yesterday was the most productive team worldwide relating to BOINC credits...
wooo!
let\'s help Baker team and their great research effort in this CASP challenge!
4) Message boards : Number crunching : Please update boinc server? (Message 65041)
Posted 19 Jan 2010 by Profile cenit
Post:
Could you, please, update the boinc software on your server? In this way, you could stop the manager asking work for GPU.

I know that it\'s only a minor visual annoyance, but it would be REALLY helpful for some of us that everyday have to explain in many forums why the boinc manager keeps asking for GPU work without getting any, and why it takes so much for it to desist.

Yes, I know also that a working configuration is not a configuration you would touch, but keep in mind also this problem when thinking about it. Maybe you won\'t find many of those requests on this forum, but I can assure you that it is asked FREQUENTLY on many other ones.

Thanks a lot for your time and keep going on this great project!
5) Message boards : Number crunching : Discussion on increasing the default run time (Message 63070)
Posted 28 Aug 2009 by Profile cenit
Post:

I have noticed that on my faster machine, the limit of 99 decoys is usually reached before the 12-hour expected runtime I\'ve requested. You might want to check the report visible on the Rosetta@home of how well the workunit succeeded to see if your workunits also often stop at the 99 decoys limit instead of near the requested run time.


The workunits ending before the selected run-time get to a stop at 100 decoys, whereas the one recent workunit which made it to the selected 16 hours stopped at 88 decoys. Is there anything I can do to adjust this or is it a lucky-dip?


I\'ve noticed this too. As far as I can tell, it\'s a \"lucky-dip\" as you so accurately describe it. Also known as a crap-shoot in other parts of the world. ;)

In another thread, I suggested increasing the maximum number of decoys from 100 to something higher, but that idea was rejected. I still find the reason for staying with the 100 decoy max totally counter-intuitive, and in fact I\'m not at all sure the reasoning given is correct.

That said, I\'ll make the suggestion again to increase the max decoys to 200 (or even higher), and see where the suggestion goes. For those of us with fast machines, willing to do long run times it will reduce the load on the servers. I admit it will change the \"shape\" of the uploaded data, but it will not change the amount - this last point is the one where I think people haven\'t thought the problem through correctly.


\"Maximum number of decoys\" at 99 was introduced some months ago when Rosetta@home was in \"debug mode\" (I think around v1.50, no new features only bugs solved). It was used as the easy way to solve some bugs that arose with large uploads (if I remember correctly, they didn\'t even investigate if the problem was in BOINC or somewhere in their code, because this trick solved easily the bug). I don\'t think that, atm, it\'s so important to solve drastically this problem; anyway, it should be interesting to know if they have any problem with server load now...
6) Message boards : Rosetta@home Science : Help a newbie out. Work Unit explained? (Message 60072)
Posted 11 Mar 2009 by Profile cenit
Post:
my first confusion is the name. Wth? Is that just dished out at random, or does the name actually mean something (like does that name somehow equal the Ubiquitin-protein ligase as an example)?


for an explanation of work-units\' name... I\'m not able to explain them. They\'re funny...

Then there is the \"stderr out\" bar that then goes on to list a whole bunch of text that at first glance seems like a whole bunch of blah. Second glance did not change my view:

stderr output has been increased a lot in 1.54 to help discover bugs in Rosetta software. Not interesting from the protein point of view.

Finally (while I am here), I noticed that the homepage of Rosetta@home says that R@home is not for profit. But I then read on Dr David Bakers journal (which I skimmed and some parts are a great read!) and he mentioned something about manuscripts (which I assume means, publishing articles in scientific journals). Dont those articles go on to be published for a profit (correct me if I am wrong here)? Or does the heading mean that all the data is released in the public domain, and then you can use the data however way you wish (i.e. publish the data into results, make money etc etc?)
Cheers!


papers are published on scientific journals NOT for profit (at most, they do it to receive funds). Journals are expensive because they have to pay people for peer-reviewing papers (to ensure they\'re correct), not any $ is given to the author. This is the way that science works: you produce a paper and you try to get it published on a journal, if accepted and peer-reviewed.
7) Message boards : Number crunching : difference between robetta and crunchers (Message 59945)
Posted 3 Mar 2009 by Profile cenit
Post:
Cenit....You are trying to compare apples to oranges with your question.
Using SMP in a multi-core computer would indeed solve a workunit very fast. Much faster than applying a single core to a workunit. SMP is actually the prefered method of crunching a workunit at folding@home. It is thier belif that using muliple cores on just one workunit is more efficent than applying say 4 workunits to 4 cores.

BOINC does not use SMP. BOINC is the middleware that runs rosseta@home. It will apply say the 4 cores to 4 workunits. Rosseta@home has nothing to do with how the proccessors crunch the workunit.


I think you completely missed my question.
SMP is an architecture for multithreading, one of the way to parallelize work on many CPU; it\'s supported on boinc and, most of all, I don\'t know what F@H involves here.

Fundamentally, the Rosetta team has elected to use an architecture and technique where there is no need for the nodes to communicate.


I\'m not a protein expert, but as dcdc says, some time ago there was a post about it. Anyway, as just said, I\'m not an expert but I\'m sure that thread \"interactions\", even if more complex, would benefit rosetta. Isn\'t this (rosetta works manipulating many objects) one of the preferred job for multithreading?
8) Message boards : Number crunching : difference between robetta and crunchers (Message 59910)
Posted 2 Mar 2009 by Profile cenit
Post:
I have one more question, that I asked on another thread unreplied:
how can you optimize Rosetta for supercomputers on BOINC, which by definition doesn\'t permit \"p2p\" communications? In other words, on a supercomputer you can define \"interactions\" between software threads running on different processors, on your BOINC client you can\'t. I\'m sure these \"interactions\" could help really a lot your algoritm, but you\'re unable to test it on BOINC platform unless using local SMP client. Am I right? Are you planning on distributing a SMP client? Or it isn\'t so important at this point of the development?

Thanks
9) Message boards : Cafe Rosetta : S\'tel klat drawkcab! (Message 59712)
Posted 21 Feb 2009 by Profile cenit
Post:
Ma I eht ylno eno ohw tonnac dnatsrednu uoy?
10) Message boards : Rosetta@home Science : What have we accomplished? (Message 59608)
Posted 16 Feb 2009 by Profile cenit
Post:
I pulled up a random pdf file and after skimming thru it didn\'t see any mention of the Distributed Computing contributions to the paper. Is this on purpose or did I just pick a paper that did not have it in there? I am curious because maybe if the DC contributions were acknowledged in official releases to Scientists perhaps they could see the results possible and maybe more would jump on board and encourage others to do the same. Obviously \'getting the word out\' is an important step to getting more and new users over time.

I think one way to do that would be to get more and more Scientists involved and aware causing them to use it in their vocabulary causing their students/whatevers to then do the same. This would then, hopefully, cause other students/whatevers to do the same bring DC into the home from the only people possible, the kids! As kids we all thought we could solve all the problems of the World if we just thought about it enough. As adults we begin to realize the daunting tasks involved. IF we could get the idea of DC being a positive influence and a venue for change maybe we could get it installed on every computer, or at least the Developed World ones! BUT I think if its involvement were acknowledged in official papers, it would start the thought processes flowing.

Very few papers, if any, mention DC. Every BOINC project has this \"problem\" from my point of view! It seems that Distributed Computing is still a \"toy\" to play with, something that \"could\" become important but now is not.
Really, the only project that I know which lives on DC is E@H (in fact you can see that the organization itself behind it is on top of boinc resources donors). Here on this forum, maybe one year ago, I read that rosetta@home lags behind many new features because BOINC is very different from a HPC, first and foremost because each core has to run independently, while many optimizations would require interactions between boinc nodes.

For Dr. Baker, why not update BOINC website page dedicated to papers? It could show your group\'s great papers to a much wider audience!
11) Message boards : Rosetta@home Science : Rosetta vs Minirosetta (Message 59529)
Posted 12 Feb 2009 by Profile cenit
Post:
curiosity: I\'m still seeing many WUs that are using the \"old\" Rosetta Beta 5.98
I thought that Minirosetta was able to do everything Rosetta can plus more; now it seems not!
Can some of you explain why are you still using the fortran codebase and not the c++ one?
Thanks in advance!
12) Message boards : Number crunching : LHC@home gives BOINC a bad name (Message 59433)
Posted 7 Feb 2009 by Profile cenit
Post:
For me it doesn\'t matter whose loss it is because waste is never a good thing. If the waste can be eliminated with minimal effort, as it can be at LHC@home, then to not do so is just lazy and irresponsible.

let me tell you that I think you\'re right.

One thing: what happens if LHC@H admins reduce IR to 3? I think it\'s not something that need a \"beta test\" and everything should work out automatically, the way WE (and maybe everybody should) like, even without optimizing the rest of the server (for example enabling the option to resend the lost WUs to fast&reliable hosts - I don\'t know if there\'s such a quick option in the boinc server, if not it would require unavailable work time).
I don\'t think that a couple of days longer is a matter... as Paul says, \"it is neither indespensable to the LHC project itself nor integral to the success of LHC\", and I can tell you that he\'s right, LHC project doesn\'t need LHC@H in any way, maybe it\'s really there \"just so some IT guy can state on his resume that he ran a BOINC project\". A sad sentence, but maybe (quite sure), a true sentence.
In fact, the GRID (http://lcg.web.cern.ch/LCG/)is a powerful worldwide distributed system I was able to use for my Physics thesis: there they have many times the computing power necessary to these \"working units\" than what is available on boinc (at least until LHC really starts up), with the assurance that results are good. I think that, for them, we are only testing a platform, trying to see if there\'s something interesting.
Maybe I\'m wrong, to the point that I would like to be wrong...
13) Message boards : Number crunching : Problems with Minirosetta v1.54 (Message 59261)
Posted 3 Feb 2009 by Profile cenit
Post:
Just got this error trying to perform an update:

2/2/2009 10:05:58 AM|rosetta@home|Sending scheduler request: Requested by user
2/2/2009 10:05:58 AM|rosetta@home|(not requesting new work or reporting completed tasks)
2/2/2009 10:06:03 AM|rosetta@home|Scheduler RPC succeeded
2/2/2009 10:06:03 AM|rosetta@home|Message from server: Server error: can\'t attach shared memory
2/2/2009 10:06:03 AM|rosetta@home|Deferring communication for 1 hr 0 min 0 sec
2/2/2009 10:06:03 AM|rosetta@home|Reason: project is down

Server is up according to the webpage. One task was updated as complete.


you have to wait and it will correct by itself.
Maybe it is a long time from your last rosetta WU... during this time the project changed its web address and so boinc need to re-fetch master file. Leave it alone and in 24 hour max it will redownload it and resume working!






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