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Newbie Questions

M

Mok

Limp Gawd
Joined
Feb 19, 2002
Messages
222
Howdy all.

I just recently re-started folding. I have a few machines folding currently, and plan on borging more here at the office. Here at my office I have users who like to keep their machines on all night long, even after I "ask" them not too, might as well make use of the electricity for something! I say I "ask" them not too, because I'm the IT/IS Manager here, but try not to be the "IT Nazi" and force them to do things. So, I can borg if I want too, and not get into trouble for doing it to other's machines.

But, have a couple questions.

I have a hyperthreaded p4-2.4. I've done some initial testing and have observed a few things. First thing, boy, it took a while to get the -local to work. Machine ID 1 always received an "old core" and would just hang, never doing anything. MID 2, it worked right away. If I take off the -local and try to run only MID 1, it still only used 50% cpu according to Task-Manager. Is the F@H client CPU aware, even without the -local switch?

So, with -local added in, and both MID 1 and 2 set to use 100% of idle time, Task Manger shows each using 50%. Switching to the Performance tab does show that each "cpu" is working 100%, so I suppose that is working correctly.

But, I have a question about the HT units working.

Log section from MID 1:
[15:56:06] Folding@Home Gromacs Core
[15:56:06] Version 1.81 (April 6, 2005)
[15:56:06]
[15:56:06] Preparing to commence simulation
[15:56:06] - Looking at optimizations...
[15:56:07] - Created dyn
[15:56:07] - Files status OK
[15:56:07] - Expanded 301543 -> 1815257 (decompressed 601.9 percent)
[15:56:07] - Starting from initial work packet
[15:56:07]
[15:56:07] Project: 1416 (Run 77, Clone 54, Gen 0)
[15:56:07]
[15:56:07] Assembly optimizations on if available.
[15:56:07] Entering M.D.
[15:56:14] Protein: p1416_polyQ_beta-helix

Log Section from MID 2:
[15:30:04] Folding@Home Gromacs Core
[15:30:04] Version 1.81 (April 6, 2005)
[15:30:04]
[15:30:04] Preparing to commence simulation
[15:30:04] - Looking at optimizations...
[15:30:04] - Created dyn
[15:30:04] - Files status OK
[15:30:04] - Expanded 301826 -> 1815257 (decompressed 601.4 percent)
[15:30:04] - Starting from initial work packet
[15:30:04]
[15:30:04] Project: 1416 (Run 34, Clone 53, Gen 0)
[15:30:04]
[15:30:04] Assembly optimizations on if available.
[15:30:04] Entering M.D.
[15:30:11] Protein: p1416_polyQ_beta-helix

Now, both "cpu's" are working on the same project number, but diferent "Run" and "Clone". Have I been wasting cycles on the same fold? Or is this really diferent. I couldn't find any concice answers to this. Accoridng to EM-3 this is a 243 point protein, so it really could be a huge waste of time if it is in fact only going to count once. But, if it is going to count twice, that's good.

On to another question... Has anyone established a "database" of sorts, or at least an idea of how long some of these proteins should take to fold, on what size of CPU?

I ask this because here at my desk, I'm setting up a new machine, a Celeron 2.5G. Right now, it is working on a 48.0 point protein, and each "frame" is taking nearly 15 minutes (according to EM-3). BUT, the prevously mentioned P4-2.4 working on the 243 pointer, is taking close to an hour per "frame".

So, is there a place I can go to get an idea on how long certain point proteins should take on diferent speed machines? I know, there are lots of other variables, but still there has to be some general ideas as to how long some should take.

I think that is it for now.
 
They are two separate work units, just working on the same protien, you will get points for both.

Oldbenwa
 
First off... Glad to have you back!

Your HT is working if each says 50% in the processes tab... and 100% on the graph tab...

They are each working on the same protein, but a different run/gen/clone... This is common, and you're not wasting cycles....

As for the length of time, it depends on the type of protein (Tinker, Gromac, Double Gromac, AMBER, QMD)... There are some others that can probably give you a better idea of what to expect from each processor and protein type...

I wish you luck with the office borging! :D


Keep on Folding!!

 
Welcome to the [H]orde.........

Stanford benches at 110 points per day on a 2.8 Ghz Intel.
This works out at 1.63 Point per Hour per Ghz.
So you will find that most protiens will fold at between 1.6 & 2 Points per Hour per Ghz.
Just which one run fast or slow you only find by doing them.
If you set your boxen to accept Big Packets and you get one you will get a 100% boost to your PpDpG.
If you set a HT P4 up with two clients then you get about a 15% increase in output but each work unit takes almost twice as long to finish.
Tinkers run with a 100% boost on AMD boxen.

So as a rough guess at how long it should take devide Points by working Ghz & 1.6.
This should give you the time in hour for the protien.
If your folding faster then you have a good protien.
If very much slower then start checking for errors & lost cycles

Also you are correct in showing different run, clone, gen numbers if you fold the same protien twice.
You only need to worry if all the numbers are the same.

Luck........ :D
 
Thanks, that eases my mind on the wasting cycles. It is a bit hard to understand as a newbie why some of these take so much longer. Especially since the Celeron machine "appears" to be out-performing the HT P4. But, I guess when the P4 gets finished, that will be over 500 points right there. Not too shabby I guess.

Speaking of the Celeron, that is one of two new boxes I'm setting up for the office. Getting ready to "ghost" it to the 2nd one. So, that's another one that will be live in the next couple hours.

And as far as borging the office. Yeah. I'm already going to be installing some other software because we've been having some "abuse" issues here, and I guess the "IT Nazi" really does have to come out and play. I received an ear-full a few months ago when I instituted the new "pass-phrase" policy, I STILL get complaints. So, while I'm doing the software install, I'll just put the F@H client on there as well, as a service. Not that we're a large office, on the order of 12 machines, but each one is 2.0g or higher, so it's all good. :)
 
So 2.4 x 1.15 / 2 = 1.36 Ghz working speed.
243 / 1.36 / 1.6 = 110 hours.
110 / 100 = 1 hour 6 mins per frame. <- Looks right.

48 / 2.5 / 1.6 = 12 hours.
12 / 100 = 7.2 mins per frame. <- I'm running 6 mins a frame at 2.1 Ghz.
You celeron may be running slow.
Check SSE boost is swithed on.

Luck........ :D
 
Hmnn.... SSE Boost is on.

So, must be a hard protein, and is taking longer.

Guess when I get the "ghost" machine working, we'll see as it will start on a diferent one, and the machines are identical.

Thanks a lot for the information, been very helpful.
 
When you do "ghost" the next box you need to do a fresh install of F@H.
Each client is identified by the User ID + Machine ID which needs to be unique otherwise Stanford looses track of what is sent where and you end up folding for zero points.

Luck......... :D
 
^ What he said!
Always do a fresh install of F@H on a new PC, or 1 install from each of the 2 directories on your HT machines.....


Keep on Folding!!

 
Tigerbiten said:
When you do "ghost" the next box you need to do a fresh install of F@H.
Each client is identified by the User ID + Machine ID which needs to be unique otherwise Stanford looses track of what is sent where and you end up folding for zero points.
Click to expand...

If i take the client.cfg off of one computer and place it in the folder I want fah installed then run the setup does this mess with process? This is what I have been doing with my borgs.
 
AcidTone said:
If i take the client.cfg off of one computer and place it in the folder I want fah installed then run the setup does this mess with process? This is what I have been doing with my borgs.
Click to expand...
This is fine, but they'll all end up running the same config (bigpackets, normal, timeless). Just don't copy the "Machinedepenant.dat" or whatever file, that will break things.
 
ah ok had me kinda worried there for a min that I would have to stop them in the middle of a WU and restart.
 
Also, remember that since hyperthreading looks like two physical processors to Windows, it doesn't give the speed boost of two processors. As people have mentioned, you'll probably get around 115% or so of one processor by running two clients. That will explain the longer frame times when running two instances.

I only run one instance on my 2.8 Ghz Hyperthreaded P4 at work. I do run bigpackets, though. I don't like using up any more RAM than what I do now with one on bigpackets since I still need the RAM for office apps. I don't suggest running more than one instance on office machines and only run bigpackets if they have 512 or more RAM. If the machines have more than 512 RAM, it may not be a bad idea to run more than one instance depending on the software being used on the system.

 
The HT machine I'm folding on now is primarily used to remote-admin all the other machines in the office. I do also do some webpage editing with it, and currently I have Guild Wars installed too. You know, "Testing Network Integrity". It also does some duty as a FTP download spot for burning Linux ISO and images for backups of my network. No office apps even installed.

It is a 512m machine, and I'm noticing that with both ID's running, they are only taking up between 28 and 30 meg of ram. So, that's really not affecting it because of ram.

On your HT machine, since you are running it as a single ID, with no -local switch. If you have F@H set to use 100% idle time, does Task Manager show the F@Hcore only using 50% of the CPU, but the Performance tab show it using 100%?

And yep, I knew I had to delete the work from my ghosted machine (the ghostee?). Found that out when I started the HT using -local, by copying the directories. Figured better clear them out to be safe on the copy.
 
Mok said:
...Guild Wars...
Click to expand...
w00t for guild wars! #1 production killer since... um... wednesday.

:p kinda makes me wish they'd waited for ~1.5 weeks, though... (i have an AP test next friday... should be "interesting")

there are network borging scripts [somewhere] that will borg your entire network, or selected subnets, or specific machines, for you. you can even enter your own user info!
 
Mok said:
The HT machine I'm folding on now is primarily used to remote-admin all the other machines in the office. I do also do some webpage editing with it, and currently I have Guild Wars installed too. You know, "Testing Network Integrity". It also does some duty as a FTP download spot for burning Linux ISO and images for backups of my network. No office apps even installed.

It is a 512m machine, and I'm noticing that with both ID's running, they are only taking up between 28 and 30 meg of ram. So, that's really not affecting it because of ram.

On your HT machine, since you are running it as a single ID, with no -local switch. If you have F@H set to use 100% idle time, does Task Manager show the F@Hcore only using 50% of the CPU, but the Performance tab show it using 100%?

And yep, I knew I had to delete the work from my ghosted machine (the ghostee?). Found that out when I started the HT using -local, by copying the directories. Figured better clear them out to be safe on the copy.
Click to expand...


I haven't checked the performance tab, but it does show as only 50% in task manager, It has to do with the way Windows reports the hyperthreading CPU. It is still running the CPU 100% but the hyperthreading "CPU" throws off calculations. The client is still running full speed, Windows just doesn't show it.

I hope that long winded and confusing reply makes some sense.

 
rogue_jedi said:
w00t for guild wars! #1 production killer since... um... wednesday.

:p kinda makes me wish they'd waited for ~1.5 weeks, though... (i have an AP test next friday... should be "interesting")

there are network borging scripts [somewhere] that will borg your entire network, or selected subnets, or specific machines, for you. you can even enter your own user info!
Click to expand...
i need those b0rging scripts. stat.

hey! are you in AP U.S. History too!? :eek: i am! :D

 
Carnival Forces said:
i need those b0rging scripts. stat.

hey! are you in AP U.S. History too!? :eek: i am! :D

Click to expand...
yes, actually. really sucks that guild wars had to come out a week and a half before the test. i just made level 10 with my character, too... bah. i'll probably have to take this week off to get studying done.

scripts - i don't have them, but i wish i'd saved them the last time they came up. i don't remember where they were mentioned, though. i think that there's a thread back in the past somewhere that mentions them. not sure about that, though.
 
rogue_jedi said:
yes, actually. really sucks that guild wars had to come out a week and a half before the test. i just made level 10 with my character, too... bah. i'll probably have to take this week off to get studying done.

scripts - i don't have them, but i wish i'd saved them the last time they came up. i don't remember where they were mentioned, though. i think that there's a thread back in the past somewhere that mentions them. not sure about that, though.
Click to expand...
heh yeah this exam is gonna *Suck*

especially since someone stole my notes 1/2 way through the year :(

too bad about the scripts :(

 
lessee... i got some tips for the test from my teacher...

read the textbook (picture captions, etc) to get more random info for the test.
there's definitely an essay on the period from 1600s-1800s or something like that (forgot to write it down :eek: but that's the general area)
you don't have to concentrate much on wars... they aren't really emphasized

have you done any DBQs yet? (document based question) cause there's one on there. you shouldn't say the source is "document A" (or 1, depending how they're labeled) you should also inlcude about 50/50 documents/outside info. organize thoughts before you begin.

anyway, good luck... i should probably be studying it now. (but i'm not... stupid internet:p)

really sucks you lost your notes. you get them back? or you gonna have to borrow someone else's?
 
rogue_jedi said:
lessee... i got some tips for the test from my teacher...

read the textbook (picture captions, etc) to get more random info for the test.
there's definitely an essay on the period from 1600s-1800s or something like that (forgot to write it down :eek: but that's the general area)
you don't have to concentrate much on wars... they aren't really emphasized

have you done any DBQs yet? (document based question) cause there's one on there. you shouldn't say the source is "document A" (or 1, depending how they're labeled) you should also inlcude about 50/50 documents/outside info. organize thoughts before you begin.

anyway, good luck... i should probably be studying it now. (but i'm not... stupid internet:p)

really sucks you lost your notes. you get them back? or you gonna have to borrow someone else's?
Click to expand...

yeah those are the same tips i got.
and to divide up your time for the essays: DBQ first, then one essay, then last essay (so the last will be teh weakest)

i guess i'll use someone else's notes :(

yeah we've done like, 3 or 4 practice DBQ's, howabout you?


 
Heh, I remember the AP History exam. That seems like a long time ago now. Heh, DBQ's...those were fun...sorta. I ended up with a 4 on that test. I think most people in the 2 classes at my HS passed (yeah, we had 2 AP History classes cause so many people wanted to take it). We had a great teacher for it and she really prepared us.

Just remember, for those essays, be sure and follow the prompt!

 
Schmave said:
Heh, I remember the AP History exam. That seems like a long time ago now. Heh, DBQ's...those were fun...sorta. I ended up with a 4 on that test. I think most people in the 2 classes at my HS passed (yeah, we had 2 AP History classes cause so many people wanted to take it). We had a great teacher for it and she really prepared us.

Just remember, for those essays, be sure and follow the prompt!

Click to expand...
heh yeah, that would suck; after 30 minutes of writing you proofread your essay and you're like "shit, i didn't answer the question :eek:!!!!"

 
i've done that... i'm glad that the multiple choice is 50% of the test. i generally do really well on the multiple choice, and the best i've done on a essay test is a... um... i think i got a 92 on a DBQ, and a 88 on an essay test. (i suck at answering the questions, apparently... tangents++)

also, the multiple choice works like the SAT. if you don't answer it, it doesn't add anything. if you get it right, it adds one (or something) if you get it wrong, it takes away a fourth (or something) so if you have no clue whatsoever, don't answer. if you can take an educated guess or know it, answer.

he also told us today that we shouldn't really study on thursday (test is friday) - just relax. at that point, it isn't really gonna help anyways. i'm probably gonna go through my notes or something thursday, but i hope to have the majority of my studying done before then.

i get to take the SAT on saturday, too... should be interesting.

we have two classes too. my teacher has told us that he wouldn't have taken the course in high school... i kinda went o_O at that one.

DBQs - two 1st quarter, two 2nd quarter, two 3rd quarter, one this quarter. heh. we're up to civil rights (1965) now... how bout you? we haven't done vietnam yet, but we covered the cold war. wonder how far we're gonna get this week (3 days left... hmm...)
 
*cringing at the memory of my AP Calc classes* ewww....

teacher on pot + Calc = some VERY interesting theories/dreams/thoughts


Keep on Folding!!

 
OSUguy98 said:
*cringing at the memory of my AP Calc classes* ewww....

teacher on pot + Calc = some VERY interesting theories/dreams/thoughts


Keep on Folding!!

Click to expand...
Heh, my favorite memory of AP Calc was the 45-minute argument I had (and won) with my teacher. It took him an entire period to convince him that sqrt(3x) should be graphed higher than sqrt(x). The whole class was agreeing with him, too. It was hilarious. :p
 
rogue_jedi said:
i've done that... i'm glad that the multiple choice is 50% of the test. i generally do really well on the multiple choice, and the best i've done on a essay test is a... um... i think i got a 92 on a DBQ, and a 88 on an essay test. (i suck at answering the questions, apparently... tangents++)

also, the multiple choice works like the SAT. if you don't answer it, it doesn't add anything. if you get it right, it adds one (or something) if you get it wrong, it takes away a fourth (or something) so if you have no clue whatsoever, don't answer. if you can take an educated guess or know it, answer.

he also told us today that we shouldn't really study on thursday (test is friday) - just relax. at that point, it isn't really gonna help anyways. i'm probably gonna go through my notes or something thursday, but i hope to have the majority of my studying done before then.

i get to take the SAT on saturday, too... should be interesting.

we have two classes too. my teacher has told us that he wouldn't have taken the course in high school... i kinda went o_O at that one.

DBQs - two 1st quarter, two 2nd quarter, two 3rd quarter, one this quarter. heh. we're up to civil rights (1965) now... how bout you? we haven't done vietnam yet, but we covered the cold war. wonder how far we're gonna get this week (3 days left... hmm...)
Click to expand...
yeah, i just took my AP french exam (eww, i think i did well on everything but the speaking part, nerves++)

:eek: you guys are slow! we finished through Clinton Wednesday of last week!

yeah, i'm doing a Barron's book and a Princeton Review book, i'm just gonna outline their essay questions and write notes for each chapter in my book (30 of them :(, i'll just do it from the summaries)...how are you planning to study?
 
Carnival Forces said:
yeah, i just took my AP french exam (eww, i think i did well on everything but the speaking part, nerves++)

:eek: you guys are slow! we finished through Clinton Wednesday of last week!

yeah, i'm doing a Barron's book and a Princeton Review book, i'm just gonna outline their essay questions and write notes for each chapter in my book (30 of them :(, i'll just do it from the summaries)...how are you planning to study?
Click to expand...
we missed a few days this year... and... some other stuff (i dunno, i guess we do more detail or something?)

i'm basically going through my notes right now. i'm gonna go through the "terms" (important stuff from each unit) so i know that, and go through the book. that portion will probably be a "look at the pretty picture!" method. then, i'm gonna wing it.


















j/k, i hope. i wanna do well on this (one less course in college, looks good) but i really suck at studying for history.

oh well... we'll see what happens. speaking of studying, i should probably be doing that (or my other homework) instead of posting here. w/e... i'll probably get to work (again) in a while.
 
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