Posts by Jose

1) Message boards : Number crunching : Talk about Bad Timing (Message 32689)
Posted 15 Dec 2006 by Jose
Post:
Well I was glad to see all of the comments from you in the article. I think it did a good job of expressing to people that this is something they can do, and it's not just for scientists or "computer people" etc. So I just wanted to say thank you Jose for taking the time to participate in the interviews etc. I'm sure it was simply a matter of doubling her work to rewrite the whole article that caused her not to make the changes. Not to mention if she'd already commissioned the artists sketch with the orchids and everything. That's a keeper!


The sad part is that , after the situation, I did ask not to be used. Simply stated, as It stand now, my opinion of the Project leader is not remotely the same as then. So I am quoted, NOW after I asked to be removed saying things that NOW and for reason I cannot say. Major Bummer.
2) Message boards : Number crunching : Talk about Bad Timing (Message 32661)
Posted 14 Dec 2006 by Jose
Post:
Just think of the fame you now have at the HHMI and anyone that has read it :-)

Shame about the Orchid though :(
(probably all the heat from the computers ;)



I asked to be removed. Drat, my request was not respected. That is a major bummer.
3) Message boards : Number crunching : Talk about Bad Timing (Message 32599)
Posted 13 Dec 2006 by Jose
Post:
Bummer

Drat: If memory doesn't fail me I emailed the lady to exclude me from the article. I am trying to search where I placed the emails I sent.

Double Drat: Not only that, the large orchid pictured would not bloom in my house
4) Message boards : Number crunching : Does overclocking adversley affect rosetta? (Message 32361)
Posted 9 Dec 2006 by Jose
Post:
@stevea,

as AMD_is_logical said it was his opinion BUT it was also a YEAR AGO, did you not read the last part of my post ;-)
When it was posted was also not long after the project had been going.


@Jose,
Exactly, nTune that Nvidia provide for its motherboard chipsets, ASUS, ABIT all do similar wrap arounds for their motherboards, even Intel are getting in on the act.

Press a button, it goes through tests altering FSB/HTT/AGP/PCI, RAM timings, graphics cards active overclocking etc.. all at the push of a button or a tick of a box.
the problem comes when people 'trust; this and then go blaming Windows for being crappy for crashing all the time. This is still overclocking, but not in the way enthusiast overclock, They at least understand what the problems are going to be.

Myself, I overclock whatever I can, my Laptops PentiumM is overclocked from 1.7GHz to 1.9GHz. The only computer I have that is not overclocked is my older PentiumIII-m computer since I just cannot find out how to do it. I did use to overclock it's M6 graphcis card though :-D

I had peltiers in my Pentium 75 and K6's ...


I have a nVidia Mobo... I prefer the oldfashion way pf overclocking. As it was taught to me by the OC Deities.. there is OCing an there IS OCing ...lol, lol lol ..what is a fried Mobo among friends. and btw if you dont have the tools to be aware what can happen or to reduce the negative effects ...then you have no right to OC...

But then ...ah the special feeling of taking your hardware to places it was never designed to do....

Xtreme Rules!!!!!!
5) Message boards : Number crunching : Does overclocking adversley affect rosetta? (Message 32345)
Posted 9 Dec 2006 by Jose
Post:
Ah, but but you know how to overclock properly and safely (well unless blowing out watercooling pipes on their new computer Jose ;)

I see it this way,

If you overclock too far your results will fail, crash at some points and so you do not effect the results. Just your own experience and throughput, but hten you'll also find other parts of your computer are unstable.

Don't know what the guy that went off on one is on about, who mentioned banning overclockers?
Most homebuilt computers have software that comes with it to do the overclocking automatically now. Press go and it tries it out for you.

For a start Gil necromanced this thread which is almost a year old!


Overckocking requires a commitment to equipment.(Softeware @#$#$###$$$*&^) To learning and asking questions before doing something that will turn your new and most powerfull CPU into a nie key chain. Overcloclking is nurtured in a community of overclockers....

So, you got those who use opti clients out of here ; Now I see people are going atfter overclockers?

What next?!!!!!

Are they going to prohibit machines whose owners have sex ....

6) Message boards : Number crunching : Does overclocking adversley affect rosetta? (Message 32306)
Posted 9 Dec 2006 by Jose
Post:
To those who are really interested in knowing if overclocking afects the science just look at results of CASP 7, those machines that produced the best fit. The largest proportion of them belonged to people that overclock.



7) Message boards : Number crunching : 1000+ new hosts in past two days & question (Message 30385)
Posted 31 Oct 2006 by Jose
Post:
also, as pointed out, we can't send out many of the design calculations, as they require too much memory (we have to consider all 20 amino acids at all positions in the protein in some cases which involves a lot of precomputation of large interaction tables)
I am sure there would be those who would install whatever memory is required to perform those large calculations on their computers... -H.



There were
8) Message boards : Number crunching : High Scores Anyone? (Message 30288)
Posted 30 Oct 2006 by Jose
Post:
Some of the credit given for these results is slightly high! It's a Celeron 2.8 with a RAC of over 5k:
http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=260872
It looks like the decoys are being considered complete and so are getting full credit even though some are only running for a few seconds.

This one too:
http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=319789


Interesting numbers for his Celerons. In many cases some of the computers identified (recognized by the Rosetta Server) as Celerons are getting more credits than the Pentiums.

¿Could it be a case of a bad id, that the comps are not Celeries?

Or a case of bad validation? A quirk at the validator level?

9) Message boards : Number crunching : 0 credit work unit? (Message 30056)
Posted 26 Oct 2006 by Jose
Post:
Finally Jose am I a mod? Yes I do have a mod a/c. That has nver been a secret.

My views here are as an individual participant -- that is why I am posting as R~~ not on my mod a/c.

As a matter of policy I do not act as a mod on an issue where I have already become emotionally involved as I have here, by Jose & Matt's shared kindergaterten pettiness. When I feel I have got myself sucked in, as here, I leave it to other mods to sort out. Including deleting this post if felt necessary.

When posting as an individual participant my postings are equally subject to moderation as anyone else's. And that is as it should be.

River~~


Woozy Sparky!!!!!!

What caused this reaction? I did not mention you nor your mod status (Although now I am asking myself which one of the mods you are :)] So there is no reason for this angry reaction.

The quoted reaction is flaming too. Worst it was not a reaction to provocation.


Before you point fingers , look yourself in the mirror. BTW all I pointed to Matt before he attacked me is that he got his points. He insulted me, I will not queep quiet when he does.

10) Message boards : Number crunching : 0 credit work unit? (Message 30023)
Posted 26 Oct 2006 by Jose
Post:
I only care about credits because they show me that my computers are continuously turning in valid work. However, I do not like doing work units for no reason. That's a waste of computer time.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=37380301

So, if I'm reading this correctly, the first user had an error. The second user didn't turn it in on time so my computer got the unit. However, the second computer turned it in before I did, and so when I turned mine in a day after I got it I get 0 credits?

That's a waste of 4 hours of computing time! And I don't like crunching work for no reason if the guy who turns it in late still gets credit when I turn it in almost immediately and I get 0 credit! That 4 hours could have been used for a work unit that actually needed crunching.


Your computer claimed 50 credits and was granted 20. So what are you talking about?

Check Again Matt



Maybe it changed between when I originally posted and when you saw it, genius.


So , before you bellyache , you should recheck.
11) Message boards : Number crunching : 0 credit work unit? (Message 30021)
Posted 26 Oct 2006 by Jose
Post:
I only care about credits because they show me that my computers are continuously turning in valid work. However, I do not like doing work units for no reason. That's a waste of computer time.

http://boinc.bakerlab.org/rosetta/workunit.php?wuid=37380301

So, if I'm reading this correctly, the first user had an error. The second user didn't turn it in on time so my computer got the unit. However, the second computer turned it in before I did, and so when I turned mine in a day after I got it I get 0 credits?

That's a waste of 4 hours of computing time! And I don't like crunching work for no reason if the guy who turns it in late still gets credit when I turn it in almost immediately and I get 0 credit! That 4 hours could have been used for a work unit that actually needed crunching.


Your computer claimed 50 credits and was granted 20. So what are you talking about?

Check Again Matt

43616155 302987 24 Oct 2006 0:11:43 UTC 25 Oct 2006 20:56:35 UTC Over Success Done 14,328.41 50.01 20.00

You are the owner of record for computer 302987
12) Message boards : Number crunching : Discussion of the new credit systen (2) (Message 29657)
Posted 19 Oct 2006 by Jose
Post:

...

Well yes, if the new system spoils Jose's fun that might count as a disadvantage... ;)
...

R~~


Can I ask a favor? Do not mention my name.

The way you are stating it: I hunted for cheaters for my temporal enjoyment. I did not. I did so, because I believed that the real cheaters here harming the atmosphere here. Alas those who spouted baseless accusation did more harm than them.

I have never enjoyed hunting for real cheaters.

Every time I documented a cheating episode in my life ( as a Compliance Auditor, a teacher, an uncle and yes, as a volunteer here) a part of me died:

I do believe in the basic honesty of people. I was raised that a person only takes to his grave his reputation for honesty and for his capacity to love so, finding dishonest people affected me a lot and affects me: my belief in the intrinsic good of people and their honesty dies a little and I am worst for it.

That is why I get very angry when a baseless accusation of dishonesty is made. It goes against the basic nature of people.

Oh since I have been here I have noticed that David Baker mentioned he needs about 40 Tera Flops of computing power to process the proteins related with Alzheimer's , and that many of you are basically stating that work units need to be segregated by the computing powers of the machines ....It seems that many of the smaller, less powerful crunchers cannot handle the very large Wu's that are coming down the pipe.

So it seems that the asseveration made by many of you that:
1- The big powerful computers could be substituted by the new people that were going to barge in as soon as the credit systems was fixed was going to be more than enough to continue.
2- That the computing power of certain teams was not needed.

was plain and unadulterated wishful thinking by many of you.

:)



13) Message boards : Number crunching : CPU Upgrade Suggestions Anyone? (Message 29509)
Posted 17 Oct 2006 by Jose
Post:
I'd wait for a CPU upgrade... Intel will come out with the new Core 2 Quad (4 cores... wow!) in november, so probably the Core 2 Duo will be cheaper


I think this is good advice.

And if you want to go all the way, you can probably get a 4-core CPU around Q1 of 2007 (AMD might release their K8L around that time too) and *really* be on the cutting edge :)

I currently have a A64 3000+@1.8ghz, and I think that a Core 2 Quad@2.6ghz would crunch about 10-12 times faster (based on quick math I did based on how many credits people with Conroes get). Wouldn't that be sweet!


There are people crunching DC projects using Kentfields. They are nice.
14) Message boards : Number crunching : New CASP results (Message 29458)
Posted 16 Oct 2006 by Jose
Post:
Jose: actually they haven't contacted the server since Nov2005 and Dec2005 respectively

And to clear something up: I am not accusing anybody of anything, read my second post in this thread, I've said that if it were most other projects, maybe I could quickly jump to some wrong conclusions; but Rosetta seems to be a well set-up and organized project;

If you had questions , you should have contacted the project in private.
IMHO
15) Message boards : Number crunching : New CASP results (Message 29457)
Posted 16 Oct 2006 by Jose
Post:
Jose, rosetta posted a page which has links to their account. It's the top predictions page. It does look a little funny. I didn't know users could opt out of credit. Perhaps they had their accounts zeroed for posting to many flames (giggle, chuckle).


Tony, I was going to say something nasty that started with "Kiss my ...." but decided not to take the bait ( giggle giggle )

My team opted out of close to 4 Million Credits, so yes you can opt out of credits, but the models the people whose credits were zeroed out crunched are not erased. Ditto for the people the project erased their credits.

What that profile shows is that the person has been inactive for more than 30 days, that is past CASP deadline. Maybe he changed his name and merged his computers into the new account.


All I am saying is: Be careful with the accusations and the innuendos. Need I remind you of what happened the last time some of you , yes some of you began using words like cheating in this board?


Why would that whipe out the credit. It would just move the credit around.

P.S. How do you 'opt-out' of credit? I think you're taking some of the comments to heart a little to much. They're just some questions with some sarcastic style answers and speculation ;-) Chill out, let the mods and developers sort out the real answers.

There is one host for maverick in question, last contact was Nov 2005 (just put it to show all hosts.)
Kerr Sweetin again one host but last contact Dec 2005.
Neither has any credit, thought there where some tasks returning 0 credit back then (Win98 ?) but either way that Way before CASP units started...


We asked the developers to erase the credits for a sub-team the same day we past Free DC for the first time. The credits were removed from our team total. We dropped to second again and we then proceeded to crunch our way to the top , again.

Yes I take any insinuation of cheating to heart.
16) Message boards : Number crunching : New CASP results (Message 29452)
Posted 16 Oct 2006 by Jose
Post:
Perhaps they had their accounts zeroed for posting to many flames (giggle, chuckle).


PS Tony: if that were true your Credits would be in the negative side with a RAC of Minus a million .

Giggle,chuckle,chuckle,chuckle,chuckle
17) Message boards : Number crunching : New CASP results (Message 29451)
Posted 16 Oct 2006 by Jose
Post:
Jose, rosetta posted a page which has links to their account. It's the top predictions page. It does look a little funny. I didn't know users could opt out of credit. Perhaps they had their accounts zeroed for posting to many flames (giggle, chuckle).


Tony, I was going to say something nasty that started with "Kiss my ...." but decided not to take the bait ( giggle giggle )

My team opted out of close to 4 Million Credits, so yes you can opt out of credits, but the models the people whose credits were zeroed out crunched are not erased. Ditto for the people the project erased their credits.

What that profile shows is that the person has been inactive for more than 30 days, that is past CASP deadline. Maybe he changed his name and merged his computers into the new account.


All I am saying is: Be careful with the accusations and the innuendos. Need I remind you of what happened the last time some of you , yes some of you began using words like cheating in this board?
18) Message boards : Number crunching : New CASP results (Message 29448)
Posted 16 Oct 2006 by Jose
Post:
I just looked at the new CASP results (CASP7 target T0330 domain2), and two of the four "top predictors" have total credit of 0.00 (maverick and Kerr Sweetin), how is this possible?


Which of the mavericks are you talking about? http://boinc.bakerlab.org/rosetta/user_search_action.php?search_string=maverick
19) Message boards : Number crunching : New CASP results (Message 29447)
Posted 16 Oct 2006 by Jose
Post:
Jose: those two people have TOTAL CREDIT of ZERO. Meaning they did not crunch anything, did not return any results or models!


Probably they had to reset or reattach or simply their credit count is not correct (Since when are credit totals infallible). Look for a glitch in that part of the project : the credit reporting part.

These could be members that have decided for reasons of their own not to have credits assigned/reported

Or could be members that after crunching have decided to detach and have no active computers reported in the last 30 days.

Or Members that have decided to change their profiles and are now participating under another name.

Many reasons that can explain that.
But what you are insinuating is that the model and cruncher were paired in the imagination of a developer/scientist/project manager. You are insinuating fraud.

Despicable , I am willing to grant you that some of the developers/scientists are despicable , jelly-fished spinned beings. That they are dishonest scientists, I wont: specially, on that flimsy evidence.
20) Message boards : Number crunching : New CASP results (Message 29442)
Posted 16 Oct 2006 by Jose
Post:
Seems like they just randomly select "Top Predictors". Really makes you wonder doesn't it? I mean if it was a smaller, less organized project I'd be more suspicious of the project results and overall scientific value, however Rosetta seems to be a project that is "for real"; however I'd still like to hear some explanation for the "Top predictors" glitch.


What glitch?
The people that computed the best models did compute the best models. Rosetta/CASP for one have a very fool proof way of validating and comparing models: they actually have access to the real structures and models.

To be hones, I think your post doesn't do anyone here any good: It belittles small crunchers as well as it calls into question the integrity of the developers.
I may not like some of the developers ( I actually despise some of them) but I cannot fault their science.


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