Posts by Dimitris Hatzopoulos

61) Message boards : Cafe Rosetta : About the price of oil (Message 18515)
Posted 12 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
I think we need to abandon oil and move on to something else like Hydrogen as oil fields get depleted and it is bad for CO2 emmissions.


My point was that until we move to hydrogen or antigravity or whatever, we shouldn't be accepting prices to be set by a broken oil pricing mechanism (as long as one agrees with the facts I've documented in previous posts - and the summary here)

Btw, substitutes currently used instead of oil (for economic reasons) are even more damaging to the environment, e.g. photos of Shanghai air pollution from Pearl Tower. You would think it was dusk, but not the case, 14:00 in the afternoon.


62) Message boards : Cafe Rosetta : About the price of oil (Message 18346)
Posted 10 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
Today I had some time to clean up the draft article parts posted here earlier and post it in my blog (in english):

http://dhatz.blogspot.com/2006/06/oil-to-38657-per-barrel.html

PS: I had to cut down some of the info I sent here in this thread, as the article otherwise would get too long. Feel free to copy it to people who might be interested.

PPS: In my blog, I also have commentary about outlook and my trades on various other markets (metals, stock indices etc), and ofcourse articles on inviting people to join humanitarian DC projects like Rosetta@home, but most articles are written in greek...
63) Message boards : Number crunching : Overall Progress Report (Message 18240)
Posted 9 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
Start with PROJECT INFORMATION AND HELP INDEX

and reading the material in the "Science" forum.

But to give you an rough idea, until May-06, the project has been running "protein 3D structure prediction" calculations upon already known proteins, in order to improve its methods (about once a week, results were posted in Top predictions link)

From May-06 until about late Aug-06, we're running protein structure prediction calcs upon yet UNKNOWN proteins, as part of the CASP7 bi-annual international experiment (these are the Txyz workunits you'll see, e.g. right now I'm running T307, i.e. crunching target 307 protein).

Right after CASP7 after Aug-06, project has said they'll run WUs on vaccines (e.g. for AIDS) and on gene therapies (for cancer).
64) Message boards : Cafe Rosetta : Moderator contact thread archive (Message 18234)
Posted 9 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
Hi,

in thread

PROJECT INFORMATION AND HELP INDEX!!!
http://boinc.bakerlab.org/rosetta/forum_thread.php?id=1769

the last item (17) seems to be about Wikipedia, but it points to BakerLab papers.

You probably need two links, one to the publications and another to wikipedia.

Keep up the good work, Dimitris

65) Message boards : Cafe Rosetta : Public Radio Journalist Looking for Participants in Seattle area (Message 18233)
Posted 9 Jun 2006 by Profile Dimitris Hatzopoulos
Post:

Actually it has been read by almost 180.


Page views doesn't equal unique persons.

Everytime we click a thread, re-read what was said, or we post in it and reload etc, the "page views" counter gets incremented.

In this particular thread, I must have contributed at least 10 "views" from the current 180+ page views myself.
66) Message boards : Number crunching : Connectivity is bad (Message 18185)
Posted 8 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
I think it must be due to the spike of 60k users trying to download ~10MB each (new Rosetta executable etc) within a relatively short period of a few hours.

Handling 1000s-10,000s of concurrently open HTTP connections is non-trivial and requires some work on Apache sw (and sometimes Linux) config.
67) Message boards : Rosetta@home Science : What is the difference between all these protein related projects? (Message 18147)
Posted 8 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
I just read your very nice "How-To: Join Distributed Computing projects that benefit humanity" page http://www.hyper.net/dc-howto.html. I noticed that it mentioned "Comments about F@H in Wikipedia suggest that due to recent developments, "Folding@Home approach has become somewhat obsolete"(?). My own measure of useful results would be citations (see later)."
I saw that Wikipedia was adjusted to correct(?) that statement (that was restated in the discussion page). I'm not sure where that statement originated from (no sources listed) and it seemed to be more of a random opinion (I did a quick google search and didn't find anything like that)...


Tarx, I'm glad you found the HowTo page useful (it's been viewed about 48k times sofar and I get quite a few emails about it everyday). I have neglected it a bit, since in recent months I've focused my DC-related contributions on Rosetta (writing the Rosetta page in Wikipedia etc)

About my F@H comment, I referred to the then-current info on F@H in Wikipedia (you can read about it in W's "discussion" page, with some references, which was wiped out). As I wrote, my personal benchmark would be citations.

Anyway, I've posted all relevant info I've collected (e.g. the discussion with mshen in F's forums) in earlier posts in this very thread -here- (and btw I know I should copy it into my HowTo page too).

Basically, (having crunched F@H for a couple of years via GoogleToolBar) my current position is the same with Hoelder1in's: "over the years I never really understood how the science done at Folding@home would eventually lead to treatments or cures. With Rosetta@home the connection to identifying drug targets and to drug design seemed much more obvious."
68) Message boards : Cafe Rosetta : Public Radio Journalist Looking for Participants in Seattle area (Message 18142)
Posted 8 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
It's just that from the 60-70.000 Rosetta participants, very few actually check these bulletin board regularly, e.g. my esitmate is that this topic has been read by ~30 people.

We could make it sticky for a while, in the hope more people will see it.
69) Message boards : Cafe Rosetta : About the price of oil (Message 18027)
Posted 7 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
Forbes seemed to think oil is a financial bubble too, back in Aug-05 (although Forbes talks about China, whereas looking closer you'll find that physical oil imports from Asia/China are flat/down in 2005 and 2006 sofar, as e.g. China has been developing domestic energy sources and transitioned to alternatives like coal):

Forbes: Oil Bust Will Dwarf Dot-Com; $35 Oil
Steve Forbes, editor-in-chief of Forbes magazine, predicts that skyrocketing oil prices are just temporary -- and a massive price collapse will dwarf the Dot-Com crash that began in 2000.

In Sydney, Australia this week for a global conference of CEOs, the respected financial editor said the that the price of oil has inflated into an unsustainable and speculative market bubble - and he says that when this bursts, it will make the Dot-Com crash "look like a picnic."

The paper quotes Forbes as saying that the price of oil (which rose above $70 this week) had been inflated by speculators and would soon begin a rapid slide.

"While there is a lot of talk in my country, the U.S., about the housing bubble, I think the real bubble, to be blunt, is in the price of oil," he said.

"It's a huge bubble. I don't know what's going to pop it, but eventually it will pop. The price has to be bought down to earth, and when it does there's going to be a lot of yelping from the hedge fund managers."

Forbes said that speculation on oil hitting $100 a barrel was misplaced.

"(But) if it does, the crash is going to be even more spectacular and will make the tech bubble look like a picnic," he said.

He also believes that the price of oil will decline significantly in 2006.

"I'll make a bold prediction: I think in 12 months, you're going to see oil down to $35, $40 a barrel," Forbes said. "In the meantime, it's a huge drain, more a psychological drain (on the economy), but it's not forever. This thing is not going to last."

Forbes blames the oil price spike on rising inflation and aggressive buying on the part of burgeoning Pacific Rim countries.

"China and India are buying more of the stuff. As the global economy expands, more energy will be consumed," he said.

"But if you look at the price of oil three years ago, it was $20 or $25 a barrel. Supply and demand might have shot it up to $30, $35 a barrel. The rest of it is inflation."

Forbes spoke to The Australian just as news was drifting in regarding the damage sustained to the oil-rich Gulf of Mexico in the wake of Hurricane Katrina. Industry observers say that energy companies such as BP, Chevron and Shell have been forced to shut down offshore platforms, which account for 25% of U.S. domestic oil and gas output.
70) Message boards : Cafe Rosetta : About the price of oil (Message 18018)
Posted 7 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
71) Message boards : Cafe Rosetta : About the price of oil (Message 18017)
Posted 7 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
72) Message boards : Rosetta@home Science : Dial-up (Message 18006)
Posted 7 Jun 2006 by Profile Dimitris Hatzopoulos
Post:

If your PC's hardware is stable, it's a good idea to increase default WU runtime even if you have fast Internet, to use longer WU runtimes (I use 8hr WU runtimes, i.e. each 24/7 PC would finish 3 WUs per day).


If I understand this correct, the longer WU runtimes, the better it is for the project?

If this is the case, I will adapt this setting to the max. But why isn't it like this then by default?


Rosetta@home used to run 8hr WUs by default initially, but longer runtimes led to a larger % of errorneous/aborted WUs (that was before the improvement in the executable and the watchdog thread was implemented).

So I guess the current 3hr/WU is a reasonable compromise to accomodate the average cruncher, who doesn't have his PC running 24/7, minimize errorneous WUs and still ensure rapid (~1day) WU turn-around times.

The project has said recently that if you have a stable and/or 24/7 PC, the recommendation was to put 8hr/WU.
73) Message boards : Cafe Rosetta : Installing Rosetta in high school computer lab (Message 17877)
Posted 7 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
Also, any special settings as far as when it turns on that you would recommend for a school environment? because the pcs stay on the login screen most of the day.


If PCs stay on login prompt, you should install BOINC as a service (it's an checkbox option during 1st install), so it runs even when nobody is logged on.

Note: If you run BOINC as a service and still want to see the Rosetta graphics on occasion, you can go to Services -> BOINC -> "Logon as system accout" and then check the "allow this service to interact with desktop" (this is from WinXP, I guess Win2K is close/same)
74) Message boards : Number crunching : Linux 2.6.12-10-386 client (Message 17872)
Posted 7 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
On the subject of BOINC benchmarks lower under Linux than Win, have a look here

Basically the "standard" BOINC v5.2.13 binary for Linux from Berkeley University is compiled in a way that its benchmark reports roughly HALF the speed (in FLOPS), than the BOINC v5.2.13 binary for Windows, running on the very same hardware.

The science apps (Rosetta, SETI, simap etc) doing the "real" work, might actually be doing MORE work per hour on the same PC under Linux than under Windows, since the OS itself is more efficient.

The solution to get similar credits using Linux, is to use an alternate BOINC client.

Recent progress in the BOINC world is towards awarding credits based on real work done (which I expect to upset some people accustomed to ultra-high benchmarks fitting in L2 cache, as in the case of real science apps accessing memory, often 3GHz and 2GHz PCs might actually doing roughly the same amount of real work per unit of time).
75) Message boards : Cafe Rosetta : 2800 new hosts!! R@H gains more hosts than SETI! (Message 17813)
Posted 6 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
Yes, it's awesome!

And what's more important, is the "word of mouth" and the multiplier effect (people telling friends, family etc) of this publicity.

I hope Rosetta's servers hardware and network link handles the spike in load, I've been noticing delays recently.

Perhaps the project could increase WU runtime (from 3 to 4-5 hr) and/or put specific instructions for dialup users on how to do so.
76) Message boards : Rosetta@home Science : Dial-up (Message 17802)
Posted 6 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
It requires a very dedicated person to run Rosetta@home over dialup IMHO.

Nevertheless, the "variable WU runtime option" (see http://boinc.bakerlab.org/rosetta/forum_thread.php?id=669#10377) was designed SPECIFICALLY for dialup users and people with capped Internet traffic and can reduce traffic requirement to 1/10th or better.

This way you can run a single WU for several CPU hours (default is 3hr, used to be 8hr), up to 4 CPU days.

If your PC's hardware is stable, it's a good idea to increase default WU runtime even if you have fast Internet, to use longer WU runtimes (I use 8hr WU runtimes, i.e. each 24/7 PC would finish 3 WUs per day).
77) Message boards : Number crunching : not sending workunits to multiple users (Message 17689)
Posted 5 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
In thread Validation it is explained why Rosetta runs with "initial replication"=1, quorum=1

Basically, when testing a protein, we all get the same raw protein (aminoacid) data (same WU), the difference being the random seed (i.e. the initial instructions to our "virtual explorer" looking for the lowest elevation point).
78) Message boards : Rosetta@home Science : Rosetta AP article! (Message 17677)
Posted 5 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
Big help over at CNN, atleast a couple hundred thousand pass thru's a day...


Yes, it's great for publicity, but if you look closer you'll see that many media (republishing Donna's article for AP), incl. CNN's version quoted above, DON'T INCLUDE THE ROSETTA URL :-(

Which explains why my DC-page keeps getting hits from Google from people looking for "baker" "idle" etc:

xx.xx.xx.15 - - [05/Jun/2006:15:51:40 +0300] "GET /dc-howto.html HTTP/1.1" 200 27716 "http://www.google.be/search?hl=nl&q=baker+protein+idle&meta=" "Mozilla/4.0
79) Message boards : Number crunching : Removed from Memory.... (Message 17671)
Posted 5 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
BOINC client uses the global preferences (e.g. leave-in-mem setting etc) from the project profile which has the most recent date-stamp (i.e. the profile from the project that you modified for last, in your case Rosetta).

It can be quite confusing (eventually people will use a "BOINC Account Manager" to manage all their projects from a single location).
80) Message boards : Rosetta@home Science : Rosetta screen saver modification request (Message 17660)
Posted 5 Jun 2006 by Profile Dimitris Hatzopoulos
Post:
This is certainly a good idea.

IBM's WCG (IBM is great in marketing its products) has the concept of "Partners" for corporations and institutions.

Read more

List of partners
http://www.worldcommunitygrid.org/about_us/viewOurPartners.do

Presentation (for "decision makers" :-)
http://www.worldcommunitygrid.org/about_us/viewBecomePartner.do


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