News de Folding@Home

ElectricFox

I folded Myself
10/12/2004

New core: AMBER core 82


We are releasing a new core, based on the AMBER MD code (see http://amber.scripps.edu/ .) The AMBER core will give us functionality not present in either the Tinker or Gromacs cores.

AMBER uses double precision only. AMBER does not currently have SSE2 specific assembly code and so it will likely run closer to Tinker than Gromacs in general performance. We are planning on adding SSE2 support in future revs, but to keep the core as stable as possible in the initial rollout, we've left it out. Keep in mind that since AMBER uses double precision, SSE2 won't help *that* much.

Since this is a new core, there may be unexpected problems. However, this core has been extensively tested in house and has done extremely well in beta testing. Also, since it doesn't use SSE2 as heavily as Gromacs or other issues which push the limits on CPUs, it will likely be less troublesome to release than the Gromacs core was.

We are very excited about the new scientific possibilities that are posssible with the new core. More news on these results as they come in!

Source: Folding@Home News

10/12/2004

-Major Update To EM
-AMBER Core Now Recognized
-New Protein Data File Structure
-New EM Calculator


Even though there have been some major changes to EM internally, I always try and make upgrades as easy and simple as possible. This update is no exception. If you are already using EM, you only need to get the upgrade version. There is no need to reinstall EM using the full install zip file.

The new AMBER core is now recognized. I revamped the protein data file. I am no longer basing the protein value on the protein name. I am now using the project number. This should get rid of a lot of those unknown protein point values because the protein name on the Stanford web site doesn't match the actual protein name in the work unit data file. This is a major update to the program so I have gone from version 2 to version 3. I still have more changes to make, but this converts EM to work with this new protein data file structure and recognize the new AMBER core. The calculator has also been updated to work with this new structure also. I expect that because EM has gotten very complicated internally, there may be something I missed. Please post anything you notice that doesn't act correctly or as expected. Provide the work unit name/project number when you post.

The old protein data file will no longer be supported or updated. The old file has been removed from the site and the new one has been put up in its place. If this new method works out, I may be able to make EM update automatically and the days of posting new protein data files may be over... I hope. Only time will tell.

Thanks very much to those of you who have donated a couple of $$$ to the EM-DC.COM web site. I really appreciate the help.

Source: Electron Microscope Homepage

10 caracteres como é habitual... :002:
 
Actualizei para a nova versão e o EMCIII até agora está a trabalhar na perfeição.
Parece-me que os bugs que tinha aqui e ali foram resolvidos.
Muito porreiro.

ElectricFox. Temos que meter aqui os skins may by you :)
 
17-10-2004
-Update To EM (V3.0.3)
-Unk Points Issue
-Linux Tracking Issue


The AMBER core acts differently than the previous cores and it writes a file I have used for years to signal the finish of a frame every time it saves a checkpoint. I have modified EM to watch a different file for this change. Hopefully this will stay the same from now on.

I'm fairly certain that the unknown points issue has been fixed. It does mean that only a single item will be checked in order to determine a work units value, the project number. No other verification is being done after that. We'll have to wait and see if anything goes wrong.

The problem tracking the Linux installs appears to be fixed. Let me know if there are still problems.

Source: Site da Electron Microscope

Download
 
Última edição:
20-10-2004
The EM Protein Data File


As many of you know I have made a change to the protein data file structure. The information is used in several places inside EM. This change to the file has caused some issues to show up. The main one is not all proteins are represented in the latest file. This does cause issues related to displaying information as it relates to statistics and the web pages EM can create. I am working on a single file with all current and past projects that EM will understand. Please stay tuned and know that I will fix this as soon as possible. Thanks for your patience.

Source: Electron Microscope Homepage

Os 10 caracteres do costume... :x2:
 
10/27/2004
-Electron Microscope Language File


As many of you know EM currently has the ability to display its text in 7 different languages. English, French, Italian, German, Dutch, Portuguese, and Danish are the options so far. I have been waiting for some other promised translations, Spanish and Russian, but they have not been forthcoming. Also, there are several areas where features have been changed or added and the files need a small update to include them. French is the only language selection that is 99% complete. The added text is noted in the language file (language.emd) with an asterisk (*) in front of the text that still needs some translation. These translations can not be properly accomplished by using artificial forms like ‘Babel Fish’ or some of the other 'computer' translators available. They just don't do a good job of it. Maybe one day they will, but at the moment they are severely lacking in quality. This needs a human touch. If you are fluent in one of the languages I have noted above, or would like to add to EM by translating the text to a language EM currently does not have, please contact me, or just make the changes to the section of the file you are competent to translate and send it to me. Each line of text can only be approximately as long as it is in English. Finding just the right words is sometimes not very easy. But, as one can see, several people have managed to to an excellent job so far. This is just another way you can contribute something valuable to the Folding@Home project and help someone who would like to view everything in their native language enjoy it even more. If you have any questions, please feel free to send me an email. Thanks for listening.

A very special thank you to all of the contributions made in support of the EM Web Site. They are appreciated very much. Your support has made a big difference.

Source: Electron Microscope Homepage

10 caracteres... :)
 
11/12/2004

-Rough week for FAH: unplanned power outtage and network problems


It's been a rough week for FAH. There was an unplanned power outtage in the building housing our secondary server room. This outtage had an impact campus wide, including in our primary server room. This appears to have lead to a problem with the cooling in our primary server room and that's being dealt with. Also, we continue to have some issues with the network due to the switchover to the new network (Medical school vs Campus). Both of these issues are being actively worked on, but may take some time to finally resolve. FAH is up and working quite well all things considered and hopefully we'll get the last bits up later next week.

Source: Folding@Home News

11/13/2004

-Nova versão (5.03) do cliente gráfico


5.03 (GUI only):
- Screen saver activation fix
- White text instead of blue
- Revised OpenGL code to handle unusual units better
- Better work unit time/frame estimation
- Fixes a redraw problem found when the main title is turned off
- Fixes issue with p268 and other WUs like it
- Fixes issue with frame time update calculation
- Fixes issues with screen saver activation
- Screen saver redraw and stability fix

5.03 GUI Client (Stanford Folding@Home Site)

Os 10 caracteres do costume! ;)
 
29-11-2004

-The Never-Ending HyperThreading Debate


Folks, for many the HT (HyperThreading) issue is one that they just don't understand. While Stanford allows you to run more than one instance of the Folding@Home client on your computer, you are not really helping them if the number of clients you are running is not equal to the number of REAL CPU's you actually have. While running two instances of the F@H client will return two work units more quickly than doing one at a time, that is not what is important. Returning one work unit 70% faster and starting the next generation of tests on the work unit, is what Stanford wants. Speed in working through each protein generation is very, very important. Sometimes quality is better than quantity. Quality in this case is work being returned more quickly. While it is well known that an HT CPU can run 2 work units because the OS treats it like two CPU's, and you can gain a possible 15-30 percent increase in points for that computer, it also means that each work unit is returned more slowly. In simple terms, if the project has 300 generations needed to test a theory on a protein model, and running two instances at once delays the return of work for 1 day each time, you end up with a 300 day delay. That translates to about a 10 month delay in examining your data for the final result. The bottom line is simply this: Run 1 instance for each CPU you have. An HT CPU is not two CPU's, it is one. Let's work to advance the science and spend a little less time worrying about the number of points you get.

This is a direct quote from Dr. Vijay Pande:
1) If you care primarily about points, running 2 procs on HT is still the best bet. We are grateful for all contributions and if people choose to run 2 procs on HT, our approach is that all contributions are welcome.

2) If you care about the science foremost and are interested in our recommendations, then do not run 2 procs on HT, but please just run one process. That won't be best for points, but is best for the science.

3) If your machine cannot make the deadlines, then one should run the timeless WUs.

I hope that clears these issues up and thanks to all for their contributions.

Thanks for listening and please do the right thing.

Larry

Source: Electron Microscope Homepage

Fica um link do tópico "Hyperthreading vs. Performance Fraction" no fórum do Folding@Home.

Interesante esse debate! Metro e pessoal dos P4 HT digam a vossa opinião.
 
Última edição:
A thread está fantástica.
Bom naõ tinha ainda visto isso mas temos por ali várias respostas que servem para argumentar contra ambas as opiniões.
Pessoalmente poderiamos ver as coisas desta forma. De cada vez que uso o PC para fazer qq coisa além do Folding estou a retirar recursos precisoso e a atrasar os calculos das WUs.
Percebo a parte de a WU demorar menos tempo só com uma a correr mas 3 WUs são completadas mais rapidamente com HT do que se tiver sempre só uma a correr.

Pessoalmente penso que faz mais sentido deixar estar duas WUs a correr e não é pelos pontos que dão.

Eu passo a responsabilidade para o lado do Pande Group para que façam ou WUs mais eficientes ou um programa que tire proveito do HT e que não seja necessário correr ao subterfugio de meter 2 WUs.

Penso que seria bem pior se tivesse o meu CPU sem OC ou se o desliga-se durante a noite.
Por isso.
Keeeeeeepppppp Folding:)
 
11-12-2004

-Electron Microscope III Version 3.0.7 Released


What's New Version 3.0.7?

I have fixed a few things about the display, mostly how the protein name is displayed. Some items were moved around so that the protein name did not overwrite the points. I think the new views are a lot better. All comments are of course welcome.

Some people making skins have been asking for a few enhancements. So, in response to the requests I have made a few changes. There is a new EmptySkin.ini file with a couple of the new features added. The main one was to make the items "flat" so they could blend in better with their background. Doing this changes more than it seems on the surface. The 3D borders of the items take up space. When they are made "flat" they shrink in size automatically. I have compensated for most of the changes, but a few I can't automatically change because I have no way of knowing if it affects a certain skin or not. Sometimes the skin height will need a few pixels added to it. But again, this depends on the skin. The default setting is "True" for this feature. This makes it backward compatible with all current skins. The skin setting is called Object3DBorders.

Second, the labels containing the Box Name and the CPU information can now have their backgrounds set to transparent. This allows you to blend this information into the background. The skin setting is called BoxLabelsTransparent. This is also a True/False setting. In this case the default setting is False. This makes it backward compatible with all current skins.

Third, the center of the scrollbar can change colors, but it didn't have the ability to hold an image. There is now a new image variable for the scrollbar background. The image is called ScrollBarPic and is in the image section. This puts the last of the over-all image view puzzle together for a complete picture.

The last addition involves sounds. You can now have different sounds for minimizing and maximizing the skin. There are also two more sounds, one for Frame Complete and one for Finished Work Unit. Sounds are always played "asynchronously" so they don't interfere with the operation of FAH or EM.

If you run the Serene Screen screensaver program, you can capture it after you put it into the "Window" mode. EM is currently set up to do that in only the single view mode. The others don't look that great so I didn't bother supporting them. Setting the screensaver running all the time does use CPU cycles that could be used for folding. To minimize the amount of cycles used you can do a few things. Disable the column of bubbles and the sound. Next, set the FPS setting to 30-35. The FPS setting makes the biggest difference. If you set it for less than 30 the screensaver doesn't look that good. Generally it will use from 2 to 5 percent of CPU time, and that constantly changes according to what is going on with the tank.

To use this feature, make sure your SereneScreen settings allow you to move the mouse over the screen area without closing it. Start Serene Screen either in the window mode or change it to window mode by pressing the 'F' key. Once you have done that, make sure EM is being viewed with the largest window (Single Work Unit). Right-Click the protein window or the Box name or the CPU info. If SereneScreen is running, you should see the selection "Capture Serene Screen" ... select it. The screensaver should now be embedded in the Protein View area. It will stay there until you close EM or click the screen saver and press the esc key. You can also right click either the Box name or the CPU info and uncheck the "Capture Serene Screen" selection. That's all there is to it.

To use minimal CPU in the screen saver, reduce the FPS setting to about 30 to 35. Turn off the bubbles and the sound. The bubbles and sound don't really make that much difference, but they do take a little CPU time. Enjoy.

If you don't have a copy of Serene Screen you can go to www.serenescreen.com and download a trial version. IMHO it is the best fish tank simulation out there.

Download:
http://home.comcast.net/~wxdude1/emsite/download.html

Source: Electron Microsocope Homepage

10 caracteres do costume ;)
 
31-12-2004
-PHP Worms Attack Forum Software
-Electron Microscope v3.0.8 (update)


The PHP Worms that have been attacking the bulletin boards around the world have given rise to a log on prompt in order to access the Official Folding@Home Forums. The security prompt you will see pop up will have instructions on it. Read them carefully. Currently I think many people just try to add their user name and their password to try and log on. That isn't what the prompt asks you to do. Just add the word forums in the user name field and the word forums in the password field (yepper, they are both the same). This will get you logged on to the forums. This is necessary in order to keep the worms from sucking the life out of the system. I logged on to the F@H forum yesterday and there were over 350 "Guests" logged in. While the system is popular, that's not normal. While checking out other PHP forums I noticed that there were over 850 "Guests" logged in to the Tech Report forums yesterday and this morning there are over 130 logged in there. They not only slow down the forum response time but suck the life out of the bandwidth total people are given each month as a maximum default and after that they have to pay. There are over 6 variants of the worm so far. The Script Kiddies are very busy during the holiday season I guess. Little brainless twits... my social comment the last day of the year.


What's New Electron Microscope v3.0.8

Added -override flag in case Chime refuses to work. This will force EM to try displaying the Chime view anyway. Once added Chime is always forced to work. Starting EM a second time using the flag will remove the flag.

Fixed the problem where EM wouldn't track the so-called "Timeless Tinker" work units. If any further issues are encountered, please drop me an email.

Made some enhancements to the SereneScreen window capture. Also added the ability to capture the Goldfish SS. Widescreen is also supported.

Link

Source News: Electron Microsocope Homepage

Bem isso explica o problema no fórum de Folding@Home (Está sempre a pedir a password cada vez que entro no site do fórum...) :sad:
 
04-01-2005
-Electron Microscope v3.0.9 (update)


While I fixed the tracking of Timeless Tinker work units in the previous version but the fix broke the AMBER core tracking. I have now fixed the AMBER core problem without breaking the Timeless Tinker tracking. I am still looking into other reported issues, but this one needed fixing ASAP.

Link

Source News: Electron Microscope Homepage

10 caracteres ;)
 
Boas pessoal,
desculpem se vou dizer alguma asneira....
a ideia de meter as noticias no forum e muito boa, para o pessoal ir estando atento as novas versoes, mas.... entao e para que serve o site que foi feito Metro? ........
Eu acho que nao seria nada ma ideia meter as noticias no site! E ate fazia com que o site começa-se a circular e a ter visitas a ver se tambm se arranja mais pessoal para a nossa team.

Pelo que vejo o Site tem estado parado, acho que assim nao vale a pena :( se o teu amigo nao tem tempo para te poder actualizar as coisa, ha pessoal na team(tipo eu) disposto a fazer essas mesmas actualizaçoes :) .... acho que assim o dinheiro que foi gasto no registo do site e no seu alojamento esta a ser mal aproveitado.

Bom digam qualquer coisa :)
 
efac disse:
Boas pessoal,
desculpem se vou dizer alguma asneira....
a ideia de meter as noticias no forum e muito boa, para o pessoal ir estando atento as novas versoes, mas.... entao e para que serve o site que foi feito Metro? ........
Eu acho que nao seria nada ma ideia meter as noticias no site! E ate fazia com que o site começa-se a circular e a ter visitas a ver se tambm se arranja mais pessoal para a nossa team.

Pelo que vejo o Site tem estado parado, acho que assim nao vale a pena :( se o teu amigo nao tem tempo para te poder actualizar as coisa, ha pessoal na team(tipo eu) disposto a fazer essas mesmas actualizaçoes :) .... acho que assim o dinheiro que foi gasto no registo do site e no seu alojamento esta a ser mal aproveitado.

Bom digam qualquer coisa :)


efac e restantes:)
Acerca do site é assim. Tambores....... hehe
A questão é que o JGAlmeida ficou de fazer as alterações necessárias para colocar o site facilmente actualizavel. Tipo (como sabem eu não percebo nada de xml, flashs ou afins) alterar ou colocar uma noticia funcionaria tipo o forum. Quem souber explicar isto melhor que avise:)
Mas o JGAlmeida tem andado muito ocupado e não tem conseguido fazer nada.
Basicamente é isto. Eu tb queria que o site estivesse mais bem aproveitado ams é dificil eu fazer tudo como imaginam. Essa parte nem sequer sei fazer. Os tutoriais estou a ver se vou fazendo aos poucos. Queria separa-los a todos de modo a que as actualizações fossem sendo mais faceis. Mas tudo demora tempo.
O ElectricFox tem sido uma grande ajuda. Fez tb uns skins para o EMCIII que estão algures perdidos na thread das duvidas.
Eu tb tenho que começar a estudar para umas coisas:) e tenho perdido algum do meu tempo a ajudar na melhoria do forum como Moderador desta casa. Depois ainda tenho andado a aprender um bocado de Linux. Como podem ver não é facil.
Eu quero que a equipa como sempre disse seja de todos. Não é nada meu. Partilho tudo o que for preciso com todos. Aceito todo o tipo de colaboração.
Estou aberto (escancarado) para melhorar. Se alguem tem alguma sugestão ou afins é favor.

Ahhhh.
Tb pedi ao greven e ao estigma uma maozinha para um logo ou banner, mas imagino que esta época seja dificil. Tb não quero andar sempre a chatear o pessoal.
Portanto meus amigos só não andamos mais depressa porque não consigo mas conto sempre com a ajuda de todos para irmos melhorando:)
Ideias não me faltam estejam descansados:x2:
 
ElectricFox disse:
Fica um link do tópico "Hyperthreading vs. Performance Fraction" no fórum do Folding@Home.

Interesante esse debate! Metro e pessoal dos P4 HT digam a vossa opinião.

BUscar novamente este assunto para pedir a todos para não apagarem WUs.
Quando tiver tempo já coloco uma thread sobre como colocar flags para acabarem e enviarem a WU. Só depois é que mudam de cliente.
Estive a fazer agora issso com o joker:)
Dá um pouco de trabalho mas é importante para não dar cabo do trabalho do pessoal do Folding@Home.

Vamos mas é abrir o champanhe que hoje é dia de festa.
Hoje ninguem trabalha :x2:

[size]Ok. Eu vou trabalhar já daqui a bocado.:([/size]
 
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