Folding@Home

[CougTek]

I thought about the Antec Overture II enclosure, but this guy said that the PSU fan is quite loud. Too bad, it would have allow you to fit a full-size ATX mainboard. No go.

I guess the only way to have a really silent box is to buy a mammoth-size Antec P180 and use a Seasonic PSU, but that's quite expensive and it takes a lot of space.

 

[Santilli]

I thought about the Antec Overture II enclosure, but this guy said that the PSU fan is quite loud. Too bad, it would have allow you to fit a full-size ATX mainboard. No go.

I guess the only way to have a really silent box is to buy a mammoth-size Antec P180 and use a Seasonic PSU, but that's quite expensive and it takes a lot of space.

That's what I did with the computer in the other room. Seasonic 400W
on firesale at Frys, 59 dollars, and the case was 120, also on sale due to some new verision coming out, or maybe it was the 160, I don't always remember the stuff after I buy it.



Gigabyte motherboard, 3000+, but, as you've said, there is a big difference in speed between that and a Xeon running @H, as I've noticed already by the stats.

One other detail: Niether computer goes to screen saver with F@H installed. Is it ok to just turn the monitors brightness off, and contrast, to avoid burn in? Is this whole burn in thing bull?

Thanks

Greg

 

[P5-133XL]

P4's are the definative folders but the dual cores have much to forgive. The reason P4's do so well with QMD's is because of memory bandwidth. They do not do well because of absolute computing power. increasing the Ghz does little to improve QMD's performance, but increasing RAM bandwidth does.

Unfortunately, when Intel released the dual processors, they did nothing about increasing the RAM bandwidth. Unfortunately, for folding, two QMD's on a dual does not do signifigently better than on a single core P4.

What that means is that there is no signifigent gain for using a dual core Intel processor over the single core. When, circumstances change and QMD's are no longer avail, then yes the dual core might have benefit (one never knows). So, if you're looking dual core, you might as well look closer at the better one -- the AMD's.

My personal opinion about folding on dual cores.

 

[P5-133XL]

One other detail: Niether computer goes to screen saver with F@H installed. Is it ok to just turn the monitors brightness off, and contrast, to avoid burn in? Is this whole burn in thing bull?

No, it is not total bull. You can still burn out the phospors in a CRT. It is simply much harder to do, that it used to be.

It is totally acceptable to turn down brighness, or even easier, simply turn off the monitor when it is not going to be being used for over 30+ minutes. Like a light bulb monitors wear out both by being continiously on and being turned on/off. There is a trade-off there and I use 20 minutes, but I have nothing to back it up with.

 

[Bozo]

As far as F@H being worth while......

Shortly after 9-11 there was the episode where mail was showing up contaminated with anthtrax powder. Some entire post offices were shutdown.
The F@H community started looking for cures for anthrax. A few months later IIRC, there were 6 posible 'cures' found through F@H. This made the ABC evening news. I'm proud to say I was folding at that time and maybe my PIII helped

After watching family and friends die from cancer, I'll be running F@H as much as I'm able to.

It's worth it

Bozo :mrgrn:

 

[i]

I'm sorry to say that I'm much more skeptical about the scientific value of the Holding @ Foam project.

For me personally, it's wintertime, and as I'm going to be using a certain number of electrons to generate some heat around here anyway, they might as well be doing something else for their trouble.

 

[LiamC]

I thought there was some controversy over the usage of the folding client--being used for something other than cancer or some such. Or was this to do with another distributed computing project?

Would a P!!! 600 be of any use? It's my DOS games box and sits idle. Once I get a cable out to the garage, I can hook up the S754 and I could run an instance on the X2 as it's on 24/7 anyhoo.

 

[P5-133XL]

The X2 would be an excellent addition especially with two instances of F@H running: It is a dual core after all.


On a 600 Mhz P3 I would suggest that you only fold timeless WU's. Everything helps, but there is a point of diminishing returns for the cost of electricity as you go down the cpu performance scale. Only you can judge what you can afford since it is your volunteer effort.

At no point has F@H been limited to cancer. They are trying to deal with diseases related to the mis-folding of proteins regardless of the specific disease. To my knowledge that has been no such controversy for this specific distributed computing project.

 

[Gilbo]

ACK! I rebooted one of my PCs and it stopped folding. I couldn't restart the client either. Even uninstalling, deleting the folders, and reinstalling didn't fix it. There are no error messages in the log. Nothing's happening.

When I run initfolding to configure the client it errors on line 4 of the script, saying:

/opt/foldingathome/client1/foldingathome: no such file or directory

But the file is there! Grrr... Anyone have any ideas. It's an amd64 running Gentoo Linux.

Since I deleted and reinstalled everything I'm confused. It should behave exactly as it did when I first installed it.

 

[P5-133XL]

Santilli,

You don't have to have different usernames for each computer. If you use the same name for all your machines you can accumualte the scores of all your computers into one and become a stat whore like the rest of the team.

However, if you are trying to find out how each of your different machines compare to each other, then using a different username for each works well.

 

[Gilbo]

I think that, maybe, the client is not considered executable. Does this make sense to anyone who knows linux better than I do?

It has execute permissions enabled for it, but perhaps that is not enough.

 

[LiamC]

I think that, maybe, the client is not considered executable. Does this make sense to anyone who knows linux better than I do?

It has execute permissions enabled for it, but perhaps that is not enough.

Does any file require write permissions?

Have you checked case sensitivity--its a common mistake made by primarily Windows users, but easily overlooked.

 

[Gilbo]

I tried downloading the binary from Stanford's site (previously I was using the gentoo package). I encounter the same problem. I cannot run it; I recieve:

gilbo@HarmolodiaServer01 ~ $ FAH504-Linux.exe
-bash: FAH504-Linux.exe: command not found

However, following this link and using ./FAH504-Linux.exe (why would this help, it's exactly equivalent isn't it?) doesn't give the error message. Instead it does nothing at all . ps aux confirms its not running.

Je suis confus...

 

[Gilbo]

Does any file require write permissions?

I don't think any of the additional files appear until you run the client for the first time. At the moment it's just FAH504-Linux.exe so I don't think write permissions would be a problem unless the binary writes to itself.

Have you checked case sensitivity--its a common mistake made by primarily Windows users, but easily overlooked.

Yep. In fact if I use the ./FAH504-Linux.exe method I can use my console's autocomplete (no idea why this works), so I've gotten around that particular problem.

 

[Gilbo]

It's worth mentioning that nothing happens with all the options. -configonly, -help they all produce no output and leave no running processes that I can find. It's all very strange.

All I did when I rebooted was add UDF support to the kernel so I could rip a DVD! Bizarre.

 

[CougTek]

When I was folding on Linux, I always chmod +x the FAH.exe file before executing it. Then I ./FAH.exe and the sky went sunny.

 

[i]

When I run initfolding to configure the client it errors on line 4 of the script, saying:

/opt/foldingathome/client1/foldingathome: no such file or directory

But the file is there!

Are you sure it's expecting that final "/foldingathome" to be a file, and not a folder?

 

[i]

However, following this link and using ./FAH504-Linux.exe (why would this help, it's exactly equivalent isn't it?) doesn't give the error message.

A default shell in Linux is not like DOS -- the current folder you are sitting in is NOT normally included in your $PATH. And you should NOT try to "fix" that.

This is a very basic security consideration. If you were sitting in /tmp/somefolder and issued a "passwd" command, what do you think would happen if some nefarious person had slipped a bogus, key-logging executable called "passwd" into that folder?

If you want to execute something in the current folder -- and it's not by coincidence a folder that's specified in your $PATH -- you must specify the current path. You could input the whole thing (e.g. /mnt/winxp/test/orx/testexe ), but why bother? The single dot (.) indicates the current folder. So to execute a file in the current folder, prefixing the command with "./" should work just fine.

 

[Gilbo]

However, following this link and using ./FAH504-Linux.exe (why would this help, it's exactly equivalent isn't it?) doesn't give the error message.

A default shell in Linux is not like DOS -- the current folder you are sitting in is NOT normally included in your $PATH. And you should NOT try to "fix" that.

This is a very basic security consideration. If you were sitting in /tmp/somefolder and issued a "passwd" command, what do you think would happen if some nefarious person had slipped a bogus, key-logging executable called "passwd" into that folder?

If you want to execute something in the current folder -- and it's not by coincidence a folder that's specified in your $PATH -- you must specify the current path. You could input the whole thing (e.g. /mnt/winxp/test/orx/testexe ), but why bother? The single dot (.) indicates the current folder. So to execute a file in the current folder, prefixing the command with "./" should work just fine.

Thanks i. That's an excellent explanation. And it makes perfect sense.

@Cougtek, that's what I've done, but I'm not getting any love . It just does nothing, leaves no process running, outputs nothing --no matter what config options I've run.

 

[i]

It's worth mentioning that nothing happens with all the options. -configonly, -help they all produce no output and leave no running processes that I can find. It's all very strange.

So what does happen?

Can you copy and paste the prompt, the command you are entering, and the output? Does it provide any output? Does it just drop back to another prompt with no output? Does it just stall and hang there? What?

 

[Gilbo]

There's the command, and the following line i:

gilbo@HarmolodiaServer01 ~/foldingathome $ ./FAH504-Linux.exe
gilbo@HarmolodiaServer01 ~/foldingathome $

There's no delay, no hang, nothing. It instantly returns me to the prompt giving no output. ps aux and top show no processes that I can associate with foldingathome. It seems it just exits immediately, not even giving any errors .

You can see it does this for other options as well:

gilbo@HarmolodiaServer01 ~/foldingathome $ ./FAH504-Linux.exe
gilbo@HarmolodiaServer01 ~/foldingathome $ ./FAH504-Linux.exe -configonly
gilbo@HarmolodiaServer01 ~/foldingathome $ ./FAH504-Linux.exe -help
gilbo@HarmolodiaServer01 ~/foldingathome $

It's kind of hard to solve the problem when there's no error message, no log, nothing :eekers:.

 

[i]

Yah, you're right. That is both weird and frustrating.

I've never used the "strace" command before, as I believe it's meant for a programming when trying to debug an application. But just for the heck of it -- and have your fingers ready to go with CTRL+C (you may have to press it a gazillion times) -- try this:

strace ./FAH504-Linux.exe

Do you see a bunch of gobbledygook (I don't use that word often enough) or nothing at all?

 

[i]

Another thought. You didn't unpack the application as root by any chance, did you? Can you paste in the full output of an "ls -l" command. Here's mine for comparison:

myself@oops:~/temp/Folding$ ls -al
total 11852
drwxr-xr-x  3 myself myself    4096 2005-11-14 01:06 .
drwxr-xr-x  4 myself myself    4096 2005-10-21 22:03 ..
-rwxr-x---  1 myself myself     108 2005-11-10 13:46 client.cfg
-rwxr--r--  1 myself myself  249236 2005-10-21 22:03 FAH502-Linux.exe
-rwxr-x---  1 myself myself 2264152 2005-11-05 20:30 FahCore_65.exe
-rwxr-x---  1 myself myself 3435392 2005-10-31 04:21 FahCore_78.exe
-rwxr-x---  1 myself myself 3486728 2005-10-24 17:26 FahCore_7a.exe
-rwxr-x---  1 myself myself 2542532 2005-10-21 22:14 FahCore_82.exe
-rw-r--r--  1 myself myself   80670 2005-11-13 16:09 FAHlog-Prev.txt
-rw-r--r--  1 myself myself    5508 2005-11-14 23:23 FAHlog.txt
-rw-r--r--  1 myself myself       8 2005-10-21 22:14 machinedependent.dat
-rw-r--r--  1 myself myself    1477 2005-10-21 22:14 MyFolding.html
-rw-r--r--  1 myself myself    7168 2005-11-10 13:48 queue.dat
-rw-r--r--  1 myself myself     170 2005-11-14 23:23 unitinfo.txt
drwxr-x---  2 myself myself    4096 2005-11-14 23:23 work

Note that all files, both user and group, are set to myself.

 

[Gilbo]

Permissions are okay i.

HarmolodiaServer01 foldingathome # ls -l
total 0
-rwxr-xr-x  1 gilbo users 0 Nov 15 08:23 FAH504-Linux.exe

Here's the strace error.

 strace ./FAH504-Linux.exe
execve("./FAH504-Linux.exe", ["./FAH504-Linux.exe"], [/* 26 vars */]) = -1 ENOEXEC (Exec format error)
dup(2)                                  = 3
fcntl(3, F_GETFL)                       = 0x8002 (flags O_RDWR|O_LARGEFILE)
fstat(3, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 2), ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2aaaaaac1000
lseek(3, 0, SEEK_CUR)                   = -1 ESPIPE (Illegal seek)
write(3, "strace: exec: Exec format error\n", 32strace: exec: Exec format error
) = 32
close(3)                                = 0
munmap(0x2aaaaaac1000, 4096)            = 0
exit_group(1)                           = ?

"Exec format error" is repeated a couple times. But it's pretty much gobbledygook to me.

 

[i]

Hmm ... you might like to try an ls -d from within the folder:

myself@oops:~/temp/Folding$ ls -ld
drwxr-xr-x  3 myself myself 4096 2005-11-14 23:35 .
myself@oops:~/temp/Folding$

Other than that, I think you've stumped me for now. I'll keep thinking about it. In the meantime, I just checked the FAH site and it says that version 5.04 is a beta version. Can you try the 5.02 version? That's what I use, and I've never had a problem.

 

[Gilbo]

Thinking it was a bad executable, I redownloaded it. Now I get:

HarmolodiaServer01 foldingathome # ./FAH504-Linux.exe
bash: ./FAH504-Linux.exe: No such file or directory
HarmolodiaServer01 foldingathome # ls -l
total 248
-rwxr-xr-x  1 gilbo users 250964 Oct 18 19:34 FAH504-Linux.exe

As you can see the permissions are correct and I am explicitly stating the path. I don't know if this is better or worse than before :x .

The Gentoo, packaged version, installs a setup script as well as init scripts. The setup script doesn't work either, giving an eerily similar error:

HarmolodiaServer01 foldingathome # /opt/foldingathome/initfolding
/opt/foldingathome/initfolding: line 4: /opt/foldingathome/client1/foldingathome: No such file or directory
HarmolodiaServer01 foldingathome # ls -l /opt/foldingathome/client1/ total 244
-rwxr-xr-x  1 foldingathome nogroup 249236 Nov 15 14:05 foldingathome
HarmolodiaServer01 foldingathome # more /opt/foldingathome/initfolding
#!/bin/sh

cd /opt/foldingathome/client1
/opt/foldingathome/client1/foldingathome -configonly
/bin/chown -R foldingathome:nogroup /opt/foldingathome

You can see that the file called in the script is present and executable. I assume the permisions are set properly. It worked when I set it up a couple days ago. I include the contents of the simple configuration script so you can see it doesn't do anything crazy.

 

[i]

Here's the strace error.

...

"Exec format error" is repeated a couple times. But it's pretty much gobbledygook to me.

Hmm ... well, at least you're getting some output from strace, and it's showing problems. So you know that the application is at least trying to execute. It's clearly not happy about something.

Can you give the old 5.02 a try just to see if it's any better? Try it in a completely new subfolder somewhere off of your home folder.

 

[i]

You know ... with that number sign, it looks like you're trying to do all of this as root. Are you?

 

[i]

Here, look, if you're running this out of a subfolder on /opt, who knows what kind of file permissions are coming into play here.

1. Log in as a normal user.
2. As a normal user, create a 'temp' subfolder from within that user's home directory, e.g. /home/normaluser/temp
3. Download the 5.02 client and save it to /home/normaluser/temp
4. Bring up a command prompt and change to /home/normaluser/temp
5. Launch the client with the old ./FAHblahblahblah command.

What happens if you try that?

 

[Gilbo]

ls -ld:

HarmolodiaServer01 foldingathome # ls
FAH504-Linux.exe
HarmolodiaServer01 foldingathome # ls -ld
drwxr-xr-x  2 gilbo users 3 Nov 15 14:03 .

The Gentoo package is the 5.02 version. The 502 Stanford version gives:

HarmolodiaServer01 foldingathome # ./FAH502-Linux.exe
bash: ./FAH502-Linux.exe: No such file or directory
HarmolodiaServer01 foldingathome # ls -l
total 244
-rwxr-xr-x  1 gilbo users 249236 Aug 20  2004 FAH502-Linux.exe
HarmolodiaServer01 foldingathome # strace ./FAH502-Linux.exe
execve("./FAH502-Linux.exe", ["./FAH502-Linux.exe"], [/* 27 vars */]) = -1 ENOENT (No such file or directory)
dup(2)                                  = 3
fcntl(3, F_GETFL)                       = 0x8002 (flags O_RDWR|O_LARGEFILE)
fstat(3, {st_mode=S_IFCHR|0620, st_rdev=makedev(136, 2), ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x2aaaaaac1000
lseek(3, 0, SEEK_CUR)                   = -1 ESPIPE (Illegal seek)
write(3, "strace: exec: No such file or di"..., 40strace: exec: No such file or directory
) = 40
close(3)                                = 0
munmap(0x2aaaaaac1000, 4096)            = 0
exit_group(1)                           = ?
HarmolodiaServer01 foldingathome # ls -ld
drwxr-xr-x  2 gilbo users 3 Nov 15 14:23 .

 

[i]

Here, look, if you're running this out of a subfolder on /opt, who knows what kind of file permissions are coming into play here.

1. Log in as a normal user.
2. As a normal user, create a 'temp' subfolder from within that user's home directory, e.g. /home/normaluser/temp
3. Download the 5.02 client and save it to /home/normaluser/temp
4. Bring up a command prompt and change to /home/normaluser/temp
5. Launch the client with the old ./FAHblahblahblah command.

What happens if you try that?

 

[Gilbo]

You know ... with that number sign, it looks like you're trying to do all of this as root. Are you?

Ya.

Here's the Stanford executable, installed in a subdirectory in my home folder:

gilbo@HarmolodiaServer01 ~/foldingathome $ ./FAH502-Linux.exe
-/bin/bash: ./FAH502-Linux.exe: No such file or directory

The directory and the file, respectively, have the following permissions:

gilbo@HarmolodiaServer01 ~/foldingathome $ ls -l .. | grep foldingathome
drwxr-xr-x  2 gilbo users 3 Nov 15 14:23 foldingathome
gilbo@HarmolodiaServer01 ~/foldingathome $ ls -l
total 244
-rwxr-xr-x  1 gilbo users 249236 Aug 20  2004 FAH502-Linux.exe

So that shouldn't be a problem either.

Here's the gentoo packaged version run as a normal user:

gilbo@HarmolodiaServer01 ~/foldingathome $ /opt/foldingathome/initfolding
/opt/foldingathome/initfolding: line 4: /opt/foldingathome/client1/foldingathome: No such file or directory

As you can see the problem remains. It's really bizarre eh? Thanks so much for help i. You've been really dedicated . It seems like this machine is out of commission for very strange reasons.

Incidentally does the "total 244" seem odd to you in the ls output in the foldingathome subdirectory? Shouldn't it say "total 1"? Even counting hidden files there are only three files in that directory (. , .. , FAH502-Linux.exe). I don't know if this has anything to do with anything. I hope it's not an indication of FS corruption and only me stupidly interpreting ls' results.

 

[i]

Just for the record, in theory you shouldn't need to do any of this as root. You should able to download, unpack, and execute the client as a normal user. You really only want to do something as root when you need the equivalent of a blowtorch and a sledgehammer. Of course, you might be at that stage at this point. :wink:

As you can see the problem remains. It's really bizarre eh? Thanks so much for help i. You've been really dedicated . It seems like this machine is out of commission for very strange reasons.

Anytime. I'm sorry I can't figure out what's going on there. I'll keep thinking about it. There are some other Linux types around here. Maybe they can come up with some suggestions.

Incidentally does the "total 244" seem odd to you in the ls output in the foldingathome subdirectory? Shouldn't it say "total 1"? Even counting hidden files there are only three files in that directory (. , .. , FAH502-Linux.exe). I don't know if this has anything to do with anything. I hope it's not an indication of FS corruption and only me stupidly interpreting ls' results.

No, when you do an "ls -l" it reports a ballpark total in kilobytes as to how much space is being used within that folder and all subfolders. If you do an "ls -lh" the numbers should be clearer (the "h" is allegedly for "human readable").

 

[Gilbo]

Thanks again i. Have a good night (or day wherever you might be). I must sleep now...

 

[CougTek]

Look at all the teams ahead of us and behind us and you will see that to keep even all we have to do is increase our point count from 9000 per day (56,000 per week) to around 11,000 per day (77,000 per week). If we can exceed 11K then our ranking will actually go up.

We are now doing about 10700 points a day and we will still lose positions in the next six months. We'll just lose positions at a slower pace. Overall, there are 16 teams behind us that are out-producing us and 17 teams in front of us that we are out-producing. But most of the teams behind us are coming on us faster than we are reaching those in front of us.

I think we need to climb at something like 13000 points per day if we want to be part of the top 100 again in a reasonnable future.

But at least we've reached the previous objective (11000 ppd), so congrats everyone.

 

[Buck]

I wish I had some faster machines for the bartender. Currently, he's folding@home on:

P4 3.0 GHz - software & hardware testing
Celeron 2.53GHz - disk cloning & audio recording
PIII 1.2GHz - folding@home

Unfortunately, two of the machines get interrupted from time-to-time for other work (as noted). So, they're not consistently producing results. I just put together a file server for the bartender with an Athlon 1333 CPU. Maybe I should start f@h as a service on that too.

 

[Buck]

What do you think would make a better folding machine, with everything else being equal:

P4 521 2.8E + 915PLWDL

or

ADA3200BP + A8V-MX

 

[CougTek]

Currently, the P4 2.8E would top the Athlon 64 3200+ because of the reasons Mark explained above. My poor little P4 505J (2.66GHz/533MHz FSB) is giving me the edge over Doug and his dual-core X2 3800+, so a 2.8E will certainly defeat a single core Athlon 64 3200+.

 

[Buck]

Hmm . . . I could build a barebones Intel system like that for under $400.00.

 

[LiamC]

I have started folding with my X2 and P!!! for team 10047. I'll bring the S754 online sometime in the next week. Now if I could run the linux client on my SmoothWall box... But maybe I should upgrade it from the P2 400 to the Athlon XP 1600+ I have lying around