Beta 3 available

**Brian the Fist** · 02-28-2003, 05:09 PM

I have completed making the changes to the client from our phase 2 beta test, and the 3rd beta is ready to download. It is the same place as the last (see end of this message). Please see the readme.txt enclosed to see what has been changed, and try to test these features specifically now.

It was also necessary to wipe out the beta 2 database and start clean again for testing purposes, so I hope you didn't get too attached to your structures from the first 2 betas. The first 2 betas will no longer work now, sorry.

For the moment all uploads will be rejected but this will be fixed momentarily. Also, the screensaver is now available too so please test this if you can. Post all bugs in THIS thread now please. This will hopefully be the final beta. Thanks!

To install, download the following package for your OS and overwrite files with the same name in a 'standard' distributed folding client. Download it fresh from the main website or use a recent copy you have. For the windows screensaver, be sure to put Foldtraj.scr wherever it currently is - c:\winnt\system32 or something like that usually.

Files are at:

ftp://ftp.mshri.on.ca/pub/distribfol...ux-i386.tar.gz

for Linux

ftp://ftp.mshri.on.ca/pub/distribfol...beta-win9x.zip

for Windows text client

ftp://ftp.mshri.on.ca/pub/distribfol...beta-win9x.zip

for Windows screensaver

**Brian the Fist** · 02-28-2003, 05:35 PM

An important note is that we are now using our energy function to choose which structure to follow for the next generation. This is more of a 'blind test' since we are pretending we do NOT know the native structure of the protein. Thus it is likely we will not see as low an RMSD as we did for the first betas. However, if the energy function works well (as we hope) we may get structure approaching as good as before. The only way we are still 'cheating' now is in choosing which of the generation 50 structures is best. But how we get to generation 50, unlike before, is now done completely without knowledge of the true structure. (Hope thats clear to everyone).

**Pascal** · 02-28-2003, 06:15 PM

Originally posted by Brian the Fist
An important note is that we are now using our energy function to choose which structure to follow for the next generation. This is more of a 'blind test' since we are pretending we do NOT know the native structure of the protein. Thus it is likely we will not see as low an RMSD as we did for the first betas. However, if the energy function works well (as we hope) we may get structure approaching as good as before. The only way we are still 'cheating' now is in choosing which of the generation 50 structures is best. But how we get to generation 50, unlike before, is now done completely without knowledge of the true structure. (Hope thats clear to everyone).

Looking at the project's plan, we're still in phase Ib - ain't we? so, there won't be any true blind test at all.
I can't tell you anything about, wether the stucutes of the 50th generation will be the nearest to the nature's given or better than them - I don't know.
But for the betatest would it perhaps be possible to decrease the time for actualising the stats? You may have an advantage of this. I've already seen, that the structures of generation 0 are not counted - but that's no problem at all.

Shall we again check every parameter set?
Actually the client has

-it -df -qF -rt

under SuSE Linux version 8.1 - it does work properly.

**Brian the Fist** · 02-28-2003, 06:17 PM

Like I said, if possible please look through the changes in the readme, and especially if you were the one you suggested it or pointed out a bug, check if it's fixed now. It should not be necessary to test this 'from scratch' again, just please check the things that have changed and the bugs that were supposedly fixed.

and hopefully someone will try EVERYTHING on the screensaver...

**mighty** · 02-28-2003, 06:33 PM

Running Windows 2000
Switches: -rt

When I started the new beta3 for the first time, it made a few structures and then changed from "0 gen. buffered" to "1 gen. buferred". How can it buffer a generation when it's doing its very first generation ever?

**Aegion** · 02-28-2003, 06:41 PM

Originally posted by mighty
Running Windows 2000
Switches: -rt

When I started the new beta3 for the first time, it made a few structures and then changed from "0 gen. buffered" to "1 gen. buferred". How can it buffer a generation when it's doing its very first generation ever?

I've noticed the same thing. This 1 group of structures continues to be buffered even when I've completed and uploaded multiple other generations.

Update: After processing some additional structures it apparrently finally got uploaded.

**Guff®** · 02-28-2003, 11:36 PM

Have the text-client BETA running on WinXP and WinME systems, currently all switched as -qf -it -rt.
Nothing to report other than the quick 1 gen. buffer previously noted.
Does the "Data uploaded to server - continuing" dialogue still remain on the screen longer than it needs to, or is it actually taking that long to get all the bits uploaded?

**Brian the Fist** · 03-01-2003, 12:43 AM

Originally posted by Guff®
Have the text-client BETA running on WinXP and WinME systems, currently all switched as -qf -it -rt.
Nothing to report other than the quick 1 gen. buffer previously noted.
Does the "Data uploaded to server - continuing" dialogue still remain on the screen longer than it needs to, or is it actually taking that long to get all the bits uploaded?

The '1 generation buffered' is normal (though evidently confusing to you.. And the message says 'data uploaded', as in past tense. When you see that message, the data is accepted already by our server. It just stays on so you don't blink and miss it...

**AMD_is_logical** · 03-01-2003, 12:46 AM

Originally posted by Brian the Fist
Like I said, if possible please look through the changes in the readme, and especially if you were the one you suggested it or pointed out a bug, check if it's fixed now.

The problem of excessive network trafic to my NFS server has been fixed.

So far, no problems.

**m0ti** · 03-01-2003, 05:00 AM

I see that it also resumes folds exactly where it left off for gens 1-50.

**Michael H.W. Weber** · 03-01-2003, 06:43 AM

I just launched the 3rd DF beta client. First of all I'd like to congratulate Howard for the obvious improvements made (evident in terms of rapidly progressing decrease of RMSD) which also reflects that all our computation efforts were worth the investment of time & money.

Here comes the problem:

1. For the first generation, 500 structures have to be calculated - which I did. After uploading, however, the stats display only 40. How is this possible? I see that this happened for others, too. I am aware that there was a discussion concerning the crediting of the first generation. If it is not credited at all, then why giving a score of 40 structures? Or is there some score weighing formula?
2. dfGUI (in its latest Windos-based version) reports the user's handle as an "invalid integer number".

3. I am a little annoyed that the previous beta stats were lost. I think these should be kept, too, since they indicate which people are really ready to help develop the client and not only run the stable stuff. Of course I won't cry over it the whole day now...

Michael.

P.S.: Hope this is news, since I had not taken the time to read all the stuff above. If not - just forget what I have written.

[edit]: The second generation was scored with EXACTLY 28 structures (20 were calculated as indicated by DF client) - why ever...

**Brian the Roman** · 03-01-2003, 07:19 AM

Is it just my imagination or is there evidence that the luck factor seems to have been largely removed by the betas?
Before, there seemded to me that there were more cases of users who's total # of structures was more out of line with their best result. If luck were completely removed then one would expect that one's rank in # of structures would always match one's rank in terms of RMSD. It looks to me like we're a little closer to that now.

ms

**Pascal** · 03-01-2003, 07:23 AM

At first, I wanna say a big Thank you very much!
Great work is done up to now, Howard

The client didn't make any probs on my system up to now (SuSE Linux 8.1)

I have another idea, which would make the client's behaviour a bit more logical - there is one point, that's not so lgical at all.

In our team, we discussed about the structures, that get stuck and restarted after three minutes.
But - in comparisation of different CPUs and client options - there are huge differencies in the computing speeds, that result in using a barrier of 3 min as a break.
So - if someone has a slower CPU, the client's behaviour maks him a loser.
Also someone is a loser, if his CPU works on another client.

Don't get too shocked - we have thought about a solution:
The client should count the CPU cycles during running the client - or makes a little benchmark, that defines a timestep y.

Now the client stops the stuck structures after x CPU cycles or - after a timestep y.
So - in this way - less CPU cycles are wasted. If you have a faster CPU - you may win with this in comparison with a slower machine a little bit - but in gerenal - it's an enhancement of the client's speed.

**Digital Parasite** · 03-01-2003, 08:42 AM

Originally posted by Michael H.W. Weber
2. dfGUI (in its latest Windos-based version) reports the user's handle as an "invalid integer number".

Michael, I have stated several times that dfGUI doesn't understand the new beta and will produce strange results. dfGUI uses the progress.txt and filelist.txt files to gather information and those have been drastically changed for the beta client.

Software is sometimes backwards compatible but very few can predict the future.

I am working on a new version of dfGUI that will support the beta client.

Jeff.

**Brian the Fist** · 03-01-2003, 11:49 AM

Originally posted by Pascal
In our team, we discussed about the structures, that get stuck and restarted after three minutes.
But - in comparisation of different CPUs and client options - there are huge differencies in the computing speeds, that result in using a barrier of 3 min as a break.
So - if someone has a slower CPU, the client's behaviour maks him a loser.
Also someone is a loser, if his CPU works on another client.

We're a step ahead of you - the 3 minutes is not the limit anymore - it now 'times out' after 3 minutes or about 250000 tries (to place a residue), whichever comes first. On a 2GHz machine, these turn out to be about the same. The 250000 tries was carefully chosen based on previous observations and is not arbitrary. It will not be lowered for any reason as soing so will damage potential results.

Anyways, sounds like it's mostly bug free now (knock on wood) - anyone tried playing with the screensaver yet?? Pretty please?

**IronBits** · 03-01-2003, 12:40 PM

Where are the stats pages for this Beta?

**IronBits** · 03-01-2003, 01:01 PM

Originally posted by Brian the Fist
Anyways, sounds like it's mostly bug free now (knock on wood) - anyone tried playing with the screensaver yet?? Pretty please?

I hate it when you do that.

I started it up and it went right out and got an update. I hope it's still the BETA... maybe update the TEXT on the screen to indicate it's a BETA. So far so good otherwise.
I had to install the regular screensaver, then overwrite it with the BETA client *.scr and the other two files that were in the archive.

**AMD_is_logical** · 03-01-2003, 01:26 PM

Originally posted by IronBits
Where are the stats pages for this Beta?

Go to: http://beta.distributedfolding.org/index.html
Then click on "teams" (to find your team) or the "Stats" button (to get the stats summary).

**IronBits** · 03-01-2003, 01:39 PM

When I double click on the .scr file, it complains about someone messing with the filelist.txt file.
I don't see an easy way to change my options... I hope you don't expect folks to mess with the registry just to make changes.

When I press Q it doesn't upload the results...
next time I start it, it uploads the work and gets more.

**Pascal** · 03-01-2003, 02:16 PM

Originally posted by Brian the Fist
We're a step ahead of you - the 3 minutes is not the limit anymore - it now 'times out' after 3 minutes or about 250000 tries (to place a residue), whichever comes first. On a 2GHz machine, these turn out to be about the same. The 250000 tries was carefully chosen based on previous observations and is not arbitrary. It will not be lowered for any reason as soing so will damage potential results.
..

Hm. Not very pretty, another question:

How big is the part of people with a 2 GHz or faster computer? Throw away these three minutes - how much can you do on a non-optimated 600 MC/s Pentium III within 3 minutes? I think, that's rather a little bit rubbish, if there is no time left.
Or not?

**PinHead** · 03-01-2003, 02:40 PM

2 Part request ---------

1.) What is the current points system? I am having a tough time telling if the dual processor system is duplicating work.

2.) Would it be possible to get a -da switch?

-da -1 would "die after" ( program exit ) the current complete set of folds were finished.

-da -some positive number would "die after" (program exit) the positive number of complete sets of folds were finished.

By complete sets I mean all of the sets involved before starting from scratch to pick new values to drill down into.

p.s. I know it is a personality flaw, but I just hate leaving half completed work when I have to stop the client.

**Mikus** · 03-01-2003, 03:37 PM

There may be a user perception problem once the beta goes live.

With the current software, the user sees the count of structures going up steadily. Stalls are rare and usually last less than three minutes. The user gets a sense of accomplishment from being recognized for all the structures he builds.

With the beta software, the user keeps seeing stalls all the time. Most take the full three minutes. There can even be stall after stall on the same structure. If structures are still counted as the measure of his contribution, the user can get a sense of frustration seeing all those stalls, since the count of structures now increases more slowly.

One possible way to restore the user's sense of steady contribution might be to recognize the user's INPUT to the project, rather than counting the user's OUTPUT (structures built). Suppose the count (suitably scaled) of ASCII characters drawn to the screen were used as a measure of participation. Now, even when looking at the screen during a stall, the user could SEE the contribution he was making.

mikus

**Pascal** · 03-01-2003, 03:50 PM

I think I have found a bug, perhaps it is already found and does not seem to be too serious.
I'm still on my machine listed at the bottom of this posting with SuSE linux 8.1 (KDE 3.1) as OS.

For several hours three or four clients did really well work at the same time (each one started in a bash shell). But several times (perhaps 5-6 times) I got this error message:

...
pascal@athlon:~/Projekte/df/distribfold> ./foldit
[foldtrajlite] FATAL ERROR: [000.000] Unable to find file rod9saoi_0_rod9saoi_protein_1_0000012.val; cannot continue - replace file and start again, or manually delete filelist.txt
Hit Return
...

I had a look at a kind of system monitor - there was no swapping at all. CPU load was on an acceptable level - also the temperatures if die and chipset. So - is there perhaps anyone with a linux system that can reconstruct this bug?

EDIT: This only happened with the -qt parameter.

**Brian the Roman** · 03-01-2003, 04:41 PM

I installed the ss and ran it for a little while. I'll keep going back to it once in a while. seemed to work fine except for a message about a corrupt filelist.txt. I went in and deleted it and everything was fine.

My suggestion is for the screen saver to delete the file itself and restart automatically. I am assuming the SS is intended for completely uninformed users. For example, my wife would have had no idea how to respond to the message. In other words, the SS should be idiot proof.

ms

**Pascal** · 03-01-2003, 05:06 PM

./foldtrajlite -f protein -n native -it -rt

hecking for newer versions...
[foldtrajlite] FATAL ERROR: [000.000] Unable to find file rod9saoi_0_rod9saoi_protein_1_0000012.val; cannot continue - replace file and start again, or manually delete filelist.txt

Client crached. Same situation as above - no swapping.
Temperatures are okay - indeed.

At that time - three clients were running - two with -it -rt, one with -it -rt -qt

**IronBits** · 03-01-2003, 05:40 PM

Originally posted by Brian the Roman
I installed the ss and ran it for a little while. I'll keep going back to it once in a while. seemed to work fine except for a message about a corrupt filelist.txt. I went in and deleted it and everything was fine.
ms

The SS does not upload the work when it quits. By deleting the filelist.txt file, you didn't get credit...
It does upload it the next time you start it tho...
I had the same error message if I double clicked on the .scr file. ;(

**Insidious** · 03-01-2003, 06:12 PM

So I said... OK, let's give the SS version a try.

The install went fine (overwrote the regular files as instructed)

my play time consisted of using 'preview' in display ss settings to see how it worked.

I set it up to buffer more data, use more memory, and connect to the internet at will.

Display settings were the 75% screen size, 1024x768x32 with high detail.

I tried the various renderings and with each, the display was very
"twitchey" There is NO WAY I could have that jumpy thing in the corner of my eye when I'm trying to get some work done. Screensavers need to be very smooth and unobtrusive to be tolerated by me. That thing in the background has about the same effect as one too many cups of coffee....

next, as I used 'p' to pause it and played with the rotate, drag, zoom etc. I eventually came to the time for it to prepare for the next generation. Well The machine decided I no longer needed to be in charge and put up it's little "minimizing....." note and let me sit and wait until IT decided I could use my machine once again. That would NEVER do! You need to make this thing so that when I move my mouse or hit a key it IMMEDIATELY lets me get to work.

"Uh, yes sir... let me pull that information up for you.... yes, I realize you are my boss and in an extreme hurry, but I need to wait until my screen saver decides I can use the computer again"

UH, I DON'T THINK SO

Oh yeah, no lockups or error messages!

-Sid

**PinHead** · 03-01-2003, 06:36 PM

OK I must have done something wrong on the screen saver install.

Downloaded and installed the normal screensaver. Configured it and it kicked off and started folding. Unzipped the beta and let it overwrite the files.

Went to the display properties and set the time down to 1 minute. BTW any change to the ss using display properties looks like it's hung, but you just have to wait a while.

Waited for 1 minute and when it kicked off it downloaded an update. Now I have a black screen with what looks like a DOS box saying that the screensaver was updated successfully. It now filcker about every minute (screensaver timing) blanking the screen and coming back to the same black screen with a dos box.

Claims to have updated protein.trj and native.val.

What did I do wrong? The beta should not have picked up an update and the original was just downloaded so it should not have had an update. I say that even though I am positive I overwrote the original files.

**PinHead** · 03-01-2003, 06:44 PM

Screen Saver

The error log is showing a checksum failure on df_logo.bmp.

The machine above is a PIII-500 with 98SE on it.

**Insidious** · 03-01-2003, 06:50 PM

PinHead,

Be sure you unzipped the .scr file to the correct directory. It goes to a different place than the rest of them.

for my machine:

all files EXCEPT the .scr file go to the distributed folding directory under program files. (sorry already uninstalled and don't remember the exact name...)

the .scr file goes to windows/system32

-Sid

**PinHead** · 03-01-2003, 07:24 PM

Thanks Insidious!

I knew I did something wrong.

It was c:\windows\system for win98se.

Now I have the right engine on the right protein.

**IronBits** · 03-01-2003, 07:37 PM

DOH !!! Thanks for letting me know where to put that .scr file .
\winnt\system32
Now it shows I'm using protein 96aa, and it's faster

It is also in fullscreen, entire screen is black except for the TEXT and the picture of the protein as it moves around...

**IronBits** · 03-01-2003, 07:47 PM

Minimizing Energy of best structure pops up, and so does the task bar at the bottom. (I'm in preview mode)
And the mouse pointer is staying on the screen.

After I drag it around the screen, rotate it, zoom in/out etc. (which causes the mouse to look like a large + and disappears) until that "minimizing energy" box pops up again, then the tray shows up and the mouse pointer shows up again, for awhile before disappearing again.
I can see where you might want to have an option to put it back the to the default view.

**Killerrabbit** · 03-01-2003, 08:03 PM

I am a newbie at Beta and I downloaded the screesaver since it would be best to see how it runs and see if I could break it. I have Windows 98 and my computer and a AMD chip but I can't remeber what it is I think its like a K-6 or something like that.

First off the downlaoding went smooth and that was good. I then unzipped the files wrote down my handle and double clicked on the screen saver icon to start it up. A weird thing with the screen going blank and then seeing my Windows in a small square in the right hand corner and I could still click on things and such. Note please make it possible to go straight to the screen saver and avoid that part, for people not knowing what it is might think the program didn't work.

I then got a thing to put my handle number in and I did thinking it would go striaght on. It almost did until I got an error message and now it won't let me back on. Here is the error message that it says it was: "
========================[ Feb 28, 2003 11:04 PM ]========================
ERROR: [001.008] {trajtools.c, line 95} CheckMD5: File not found .\df_logo.bmp
ERROR: [001.007] {saver.c, line 1452} File failed checksum .\df_logo.bmp

========================[ Feb 28, 2003 11:05 PM ]========================
ERROR: [001.008] {trajtools.c, line 95} CheckMD5: File not found .\df_logo.bmp
ERROR: [001.007] {saver.c, line 1452} File failed checksum .\df_logo.bmp

========================[ Feb 28, 2003 11:06 PM ]========================
ERROR: [001.008] {trajtools.c, line 95} CheckMD5: File not found .\df_logo.bmp
ERROR: [001.007] {saver.c, line 1452} File failed checksum .\df_logo.bmp
ERROR: [001.002] {rotlib.c, line 86} Unable to open input file .\rotlib.bin.bz2
FATAL ERROR: [001.008] {foldtrajlite2.c, line 2160} Cannot open rotamer library"

The bottom one is the one I got and now I can't get into the screen saver it says that I need to go and downlaod it again or seomthing like that. Could someone explain to me using layman terms what to do and what went wrong. Remeber I represent the common user that won't know a lot of computer jargon.

Thanks,
Wabbit

**PinHead** · 03-01-2003, 08:44 PM

I am not sure if I understand the screen saver features!

Drag to rotate:
Well movining the mouse of course turns of the screen saver.
Hold click and drag does nothing.

Rotate:
Shift and move the mouse does nothing.
Shift, hold click and move the mouse causes video memory corruption and a hard lock.

Zoom:
Ctrl and move the mouse does nothing.
Ctrl, hold click and move the mouse causes video memory corruption and a hard lock.

OS is win98se

Oddity that I observed. When attempting the above functions, the cusror shows as an arrow on some parts of the screen and as a text input I-beam on other parts of the screen.

-----------------------------------------------------

As a side note:
Maybe when the screen saver calculates energy and the trajectory, you could do away with the graphic progress bar and just use a text block progress bar. The constant flashing lets you barely make out what the progress % is , but you can't read what it is doing. I guess it is only doing 1 of 2 things.

**Insidious** · 03-01-2003, 08:47 PM

you have to hit 'p' first to pause the screensaver, then you can
do the drag, rotate and zoom stuff.

-Sid

**IronBits** · 03-01-2003, 08:52 PM

I didn't have to pause it before moving around/zooming...
using the BETA... and it blanks out the whole screen (windows 2000)

**Insidious** · 03-01-2003, 09:02 PM

Originally posted by IronBits
I didn't have to pause it before moving around/zooming...
using the BETA... and it blanks out the whole screen (windows 2000)

everytime I hit a key or moved my mouse, it stopped the SS and went to the desktop. How does your computer know if you are moving the mouse to play with the screen saver or moving your mouse to get to the desktop?

(I suspected I was missing something....

)

**PinHead** · 03-01-2003, 09:09 PM

Pausing did the trick in win98se!

Thanks again Insidious

**PinHead** · 03-01-2003, 09:19 PM

Killerrabbit!

You may want to look at Insidious post that is just a few posts back.

The errors you are seeing are similar, all though not exact, to the errors I was receiving when trying to click on the foldtraj.scr file when it was located in c:\ program files\Distributed Folding Project.

Do a search for foldtraj.scr . The one under c:\windows\... or c:\winnt\... should be the corrrect location.

Then copy or unzip just the foldtraj.scr to that location.
(since the other beta files are already installed in the correct location)

You may or may not have to reboot for it to work correctly. On win98se, I always had to reboot after copying over the file.

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