Has Predictor's time come? [Archive] - AMD Users.com

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07-05-2004, 07:44 PM

To All:

With the sharp fall of Seti and constant revamping of their database, and results 'offline / unavailable time to both Seti-BOINC and Seti-1, because it was never designed for large volume, some 200+ teams have just made the transition to Predictor because:

The Charms application is now online and running. This is the next step toward D2OL than Mfold alone was. Mfold and Charms work as a team... The only piece left is the actual porting of D2OL (or the final protease inhibitor wrapper / evaluator) to the BOINC arctecture under the 'Predictor' umbrella.

Predictor is very very quickly gaining popularity as they have a database that was built, avoiding the Seti's mistakes and designed to work in the multi-phasic environment required of an 'mfold-charms-d2ol' composite world.

I know the program is still labeled "Alpha test" and the "Charms" application still technically is. The "D2OL equivalent" application is not officially out..... but everyone we are competing against in other DC tasks is showing up and making their presence known. I believe Predictor will skip the 'beta' test phase officially and simply go 'live'.

I, with a few others, was able to keep us at a stable / holding position until the past few days, but we are no longer able to do so. This is, in my opinion, because AMDs outrun Intels 3:1 or 3:2 on average.

May I ask for an AMD Users team decision as to whether we wish to pursue Predictor as a whole group? Before deciding, I ask each to look at both the the 'mfold' and 'charms' applications as well as how the 'D2OL' module would fit onto the back end of this architecture.

I have the feeling that with the lack of new development on D2OL (as it currrently stands), being the old architecture, we are going to see it (or equivalent) under the BOINC architecture .

So, I ask we as a team, re-evaluate our position of the overall 'BOINC' architecture and projects which use it (with emphasis on Predictor, knowing it is much more up & coming and stable, than most other "alpha" projects) versus 1:1 projects like D2OL and the old Seti Classic (which is now officially dead/winding down). I personally believe that we will see the end of D2OL as we know it in the very near future.

Any, and all opinions and responses would be greatly appreciated.

Thanks,
BC

chaz

07-06-2004, 12:00 AM

Im having lots of problems so far. If I shutdown a client and restart it(suspend then exit), the host ID sometimes changes. Pretty much i'll have 1 machine listed twice, which might not matter but something seems funny.

Also i am getting lots of errors :

209738 60997 4 Jul 2004 0:40:57 UTC 4 Jul 2004 16:44:09 UTC Over Success Done 5286.078125 21.83 0.00
209662 60972 4 Jul 2004 0:43:48 UTC --- In Progress unknown New 0 0.00 0.00
209582 60945 3 Jul 2004 20:57:33 UTC 4 Jul 2004 0:40:51 UTC Over Client error Downloaded 0 0.00 -!-
209504 60919 3 Jul 2004 20:57:33 UTC 4 Jul 2004 0:40:51 UTC Over Client error Downloaded 0 0.00 -!-
208980 60752 4 Jul 2004 0:41:07 UTC 5 Jul 2004 11:49:38 UTC Over Success Done 3745.984375 15.47 17.39
208865 60713 4 Jul 2004 0:40:51 UTC 4 Jul 2004 0:43:47 UTC Over Client error Downloaded 0 0.00 -!-

Result ID 209504
Name t0204C_1_7045_2
Workunit 60919
Created 3 Jul 2004 18:19:20 UTC
Sent 3 Jul 2004 20:57:33 UTC
Received 4 Jul 2004 0:40:51 UTC
Server state Over
Outcome Client error
Client state Downloaded
Exit status 0 (0x0)
Host ID 5442
Report deadline 17 Jul 2004 18:17:33 UTC
CPU time 0
stderr out <core_client_version>3.19</core_client_version>
<message>Couldn't start the app for this result: error -110
</message>
<active_task_state>7</active_task_state>
<signal>0</signal>
<couldnt_start>-110</couldnt_start>

Validate state Invalid
claimed credit 0
Granted credit 0
Client version ---

Any one else having this problem?

Yes this particular machine is overclocked, but Im getting the same on stockers, for example host 5493 is not oc'ed one bit. http://predictor.scripps.edu/results.php?hostid=5493&offset=40

gamer007

07-06-2004, 03:19 AM

Did you try detaching and reattaching P@H? Something like that happen to me on the BOINC Beta Test and everything went back to normal after a detach.

chaz

07-06-2004, 05:07 AM

I guess i'm not the only one :D http://predictor.scripps.edu/forum_thread.php?id=89
Problem is I dont have multiple accounts on my machines....
Maybe I'll try 3.07 again

I have tried detaching and reattaching, but then either i get a mirror host, or a different host id. I'm trying to track their production now, so different id's and having to merge on a daily basis is really screwing up the works,lol

07-06-2004, 06:21 AM

those happen when the app failed to download, but is listed in your
install..

save your keys.. (in email ) unstall...

delete the directory (including client_state.xml)

reinstall 3.19 only...

attach to each project, giving URL and code.
it will hand out new WUs ... the others will recycle quick... so don't worry.

make sure you have full permission to the directory where predictor is running.... some files will show up as r-only... this is normal.

there is no longer a need to (nor a good idea) to suspend before exit.

just exit.

hitting the 'x' in the window is MUCH different (it closes the window), the 'exit' from the file menu shuts down boinc prematurely.

if you have more problems, notify them immediately via their board.

I have ZERO problems here... been at it since Seti 3.05.

after detach, reattach.. yes you must merge hosts... it keeps the database sane.... also do the same 'merge' after uninstal-reinstall-cleanup of all files.... and then attaching to the URL of hte project.

If you want to be 100% safe.... you can use their 3.07... it's ok to use...
then, after running ok...... with boinc down... install just the 3.19 CC....
(upgrade over top of) all will be fine... benchmarks will run.

if i had to guess... i would say dangling files not matching the XML file is the key problem... it is also something they want to know about right away..... 3.19 eliminated this.....so if you still ahve -110... i a) question if you have the real 3.19 -or- b) if your slots & projects folders (exe & pdb reside) match the client_state.xml file.

hope this helps.

BC

chaz

07-06-2004, 01:10 PM

Ok, will give it a whirl, hopefully that'll straighten things out. :D

07-06-2004, 01:25 PM

Ok, will give it a whirl, hopefully that'll straighten things out. :D

also... i just checked... i ws out of sync a bit too...

did an 'update', exit, and restart..

boinc 3.19 picked up with saved window settings, correct params,
and the disk utilization for boinc software was back under 6 mb.

the data was a bit more (about 20 mb)

KEY IS THE UPDATE after attach
with the exit and restart.... it comes back to where it belongs.. complete
with column widths in each window.

BC

also put a copy of boinc_3.19.xxxxxxxxx.exe in the boinc/predictor main directory...

Once you can exit and restart.... with it picking up where you left off.... THEN merge your hosts.....

http://www.tumoeng.com/boinc_319.zip is a pure boinc (from my site).

it is a good copy inside the zip.. (extracting/installing exe within a zip)

*EDIT* ... the most critical file (Client_State.xml) is NOT backed up.... and it will be in next rev..... until then.. only an update can write to it.

07-06-2004, 02:01 PM

I found this on the Predictor boards.... thought it would help explain where predictor is..... it does raise a GREAT deal of merit to D2OL....

I would like to discuss this as a team.

=================== Post ==================

Message boards : Number crunching : Will full Predictor (mfold and charmms) replace all of d2ol ?

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Author Message
Hermes
Joined: Jun 11, 2004
Posts: 6
Posted: 2 Jul 2004 14:43:03 UTC

I would say that Predictor@home is even closer to Distributed Folding (DF) than to Folding@home. Both try to calculate the final folded protein structure. While Predictor uses similar proteins, Distributed Folding is using more or less randomly generated structures and selects the "best looking" one. DF seems more useful for proteins for which no similar proteins are available.

ID: 738 / Rating: 0 [Reply to this post]

Shaktai
Joined: Jun 12, 2004
Posts: 40
Posted: 2 Jul 2004 2:09:25 UTC

D2OL is a completely different type of project from predictor.

Predictor is closer to folding@home in basic concept, and complements F@H well. Predictor looks at predicting how proteins fold, which is about learning the core concepts of how proteins work, and being able to see how they impact health.

D2OL is a drug docking project and sister project to TSC at http://www.childhooddiseases.org/ Its purpose is to help develop effective drug treatments for various diseases and bioterrorism agents. D2OL is still under development and an updated client is planned, but for now, the Rothberg Institute which hosts both projects is undergoing renovation and expansion and renegotiating with Sengent whose software they use. Their resources are stretched and so D2OL development is moving at a slower pace for the time being.

Both projects serve good purposes, but Predictor is focused more on the core or fundemental science that will help future scientists and medical researchers develp more effective treatments for a wider variety of ailments.

(and will one of the "real" scientists please correct me if I have misstated anything).

The best Macintosh team ever assembled.

ID: 720 / Rating: 0 [Reply to this post]

BCCL
Joined: Jun 24, 2004
Posts: 5
Posted: 2 Jul 2004 0:42:25 UTC [Edit this post]

I have been running ddol (d2ol) and it looks like no future development.

will predictor (mfold and charms) be it's replacement?

ID: 715 / Rating: 0 [Reply to this post]

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BC

vaughan

07-06-2004, 02:55 PM

07-06-2004, 07:35 PM

Shaktai seems correct to me. Predictor is more like DF and F@H than D2OL or TSC. I lost faith in DF when they had the debacle with the latest upgrade. I think they lost many contributors then.
I prefer D2OL and TSC to either BOINC application I've tried so far (Seti & P@H). I still haven't been awarded any stats points for my BOINC Seti contributions. At least D2OL / TSC stats work (most of the time).
vaughan

I know why seti/boinc hasn't awarded... it's an ugly answer... first, it takes a quorum of 3 answers, all correct... and if 1 is late... then it whole thing is in pending.... total your current score and take about 1/2 your pending... that is where you will be.

Also w/ seti... because of the 3+ week timeout for work units... (which is too long) it takes too long to see feedback... predictor is at least shorter (2 weeks max).. and will jump shorter if feedback from clients indicates otherwise... remember d2ol and seti 1 both went on single contributors... Now a quorum of 3 identicals is required to validate.... the quality of the DC work is greatly improved and no cheating....

we win some, we lose some....

Please do remember, Seti is up to its eyeballs in issues. I would prefer not to say them here.... as I would be considered slandering them... but they have some bad ones... Predictor, so far, has nearly as many users and still has the fastest database of them all...... so the skill level of the DBA means a lot ...

hope that helps.

07-07-2004, 11:42 PM

FYI guys: I have an inside track and 3.20 is about to be available... BIGTIME fixes, LONG LONG LONG overdue are in.

Remember I have pure boinc_319.zip at my web site for those who want it as it is....

3.20 will fix the bulk of the zero-credit / bad credit problems and (if I am reading correctly) put it as a service instead of a regular application... this will aid in its stability and will 100% stop the -110 errors that so many got with Seti AND Predictor... the GUI will be 'just a gui' (one of the Alpha team guys helped with that a lot).

Once 3.20 is proven ok, and if desired, I will post it up for us to grab. Please let me know.

Anyone needing/wanting 3.19 as it stands (it beats 3.07 by a mile) is welcome to it.. it is the official, released version. Simply PM me and I'll give the URL if you haven't found it here already.

BC.

WienerDog

07-08-2004, 03:37 AM

BC make sure you let us know when 3.20 comes out.......think ill run predictor as it looks from our dropping numbers in D2OL that enthusiasm for that project seems to be drying up

07-08-2004, 04:37 AM

Weiner, et al.

3.19 is usable.... but you must 'update' and 'exit' before shutting down the system....

if you were getting -110 errors.. the simple solution is to detach and reattach to the project... that resets the conditions... prior to doing so, I would go set your prefs for .5 days to 1 days work. it minimizes any loss in the event of an error.

Right now, there are a bunch of WU's set to expire in 2-3 days that need processing... they would completely get bounced/ lost by all who worked on them... if you don't mind doing small chunks, it would be appreciated,
NOT TO MENTION WE WOULD GAIN A TON OF POINTS!!!!!!!!!

http://www.tumoeng.com/boinc_319.zip is the only way to get 3.19 .... Seti is down hard... all of SSL is down.

BC.

WienerDog

07-08-2004, 10:42 AM

got my boxes updated and goin ...we'll seee what happens

07-08-2004, 11:51 AM

got my boxes updated and goin ...we'll seee what happens

Kick butt!!!!

we have some catching up to do.... 7th place will be easy with you and chaz on board. It will be better when I get some juice flowing here too.

what should we have as a goal? suggestions???

BC

Ototero

07-08-2004, 11:57 AM

Are we moving away from D2OL? I've just moved my machines over :cry:

What DCs are people running? Where would you like me to stick my 9gig :shock:

WienerDog

07-08-2004, 11:57 AM

07-08-2004, 12:16 PM

my goal is top 5.............but thaTs just my goal lol
and ill have a 6th box online sometime this week.....for fixing my friends computer,he will run predictor for a month for us.
And hopefully ill have a sixth box of my own by that time :cool:
tho the wife may kick my @$$ :oops:

I'm divorced..... That probably says it all!!!! I should start charging CPU time for fixing PC's as well... You have a good idea there.

My friend loves fishing... His wife has threatened to leave if he keeps going fishing so often. He said he would miss her... . LOL

BC

PS: Forgot to post: May have 3.20 BOINC (which runs as a service and not an application) Thurs 8-Jul.. I hope we all can be using it by weekend.

em99010pepe

07-08-2004, 08:46 PM

Are we moving away from D2OL? I've just moved my machines over :cry:

What DCs are people running? Where would you like me to stick my 9gig :shock:

You could help me in lifemapper. PLEASE.