Gromacs

LP · #1 (**permalink**) 1st July, 2003, 07:01 PM

I'm trying to find basic info on Gromacs.

While looking at the page of currently running projects, it shows Gromacs as 100 frames, but all the ones I have downloaded show as 500 frames.

Can someone explain? TY

LP · #2 (**permalink**) 1st July, 2003, 07:25 PM

Quote:

Originally Posted by Ladypcer

I'm trying to find basic info on Gromacs.

While looking at the page of currently running projects, it shows Gromacs as 100 frames, but all the ones I have downloaded show as 500 frames.

Can someone explain? TY

Ah, ok. I think I am confusing frames with steps.

Daniel ~ · #3 (**permalink**) 1st July, 2003, 07:35 PM

You see I told you WE would be glad to answer any questions! You've made an honest man of me! ":O}

LP · #4 (**permalink**) 1st July, 2003, 07:39 PM

Quote:

Originally Posted by Daniel ~

You see I told you WE would be glad to answer any questions! You've made an honest man of me! ":O}

I often answer my own questions, given enough time.

Daniel ~ · #5 (**permalink**) 1st July, 2003, 07:44 PM

Given enough time, our questions serve as our answers.":O}

mookydooky · #6 (**permalink**) 1st July, 2003, 07:51 PM

Most of the projects running now use gromacs. To make sure, you can check your task manager to see that you are running FahCore_78.exe. This is the gromacs core. To make sure you're running gromacs all the time along with SSE, you can use the "-advmethods -forceasm" flags. The easiest way to enable these flags is to use a shortcut with the flags to run the client.

LP · #7 (**permalink**) 1st July, 2003, 07:54 PM

Do you recommend putting -local in there too?
(Using the graphical version)

mookydooky · #8 (**permalink**) 1st July, 2003, 08:00 PM

Quote:

Originally Posted by Ladypcer

Do you recommend putting -local in there too?
(Using the graphical version)

You only need to use the -local flag if you are running multiple clients. If you're running only one, you don't need it.

LP · #9 (**permalink**) 1st July, 2003, 08:11 PM

Ok, thank you very much.

LP · #10 (**permalink**) 2nd July, 2003, 04:46 AM

Quote:

Originally Posted by mookydooky

Most of the projects running now use gromacs. To make sure, you can check your task manager to see that you are running FahCore_78.exe. This is the gromacs core. To make sure you're running gromacs all the time along with SSE, you can use the "-advmethods -forceasm" flags. The easiest way to enable these flags is to use a shortcut with the flags to run the client.

I'm running the FaHCore_78, and flagged the shortcut, but it's still using 3DNow.

LP · #11 (**permalink**) 2nd July, 2003, 04:56 AM

I'm also running 3.24 on all of machines. Should I upgrade to the beta 3.25 on my AMD's?

dod · #12 (**permalink**) 2nd July, 2003, 04:57 AM

Quote:

Originally Posted by Ladypcer

I'm running the FaHCore_78, and flagged the shortcut, but it's still using 3DNow.

Are you using the 3.25 client from here?

http://www.stanford.edu/group/pandegroup/beta/beta.html

we got our posts crossed

LP · #13 (**permalink**) 2nd July, 2003, 05:04 AM

Quote:

Originally Posted by dod

Are you using the 3.25 client from here?

http://www.stanford.edu/group/pandegroup/beta/beta.html

we got our posts crossed

Ok. To change over, I need to shut down the client, download the beta, and then what? Do I need to delete the existing core.exe like it says in this thread?
IMPORTANT!!! FahCore_78.exe version and folding speed.

I don't want to lose work in progress.

dod · #14 (**permalink**) 2nd July, 2003, 05:38 AM

Quote:

Originally Posted by Ladypcer

Ok. To change over, I need to shut down the client, download the beta, and then what? Do I need to delete the existing core.exe like it says in this thread?
IMPORTANT!!! FahCore_78.exe version and folding speed.

I don't want to lose work in progress.

So long since I did it I just tried on this machine

Try the new client first and see if you get sse or not. Remember to set the forceasm etc. If not, shut down, delete the FAH_78 core, restart the 3.25 and you should download a new core automatically.

LP · #15 (**permalink**) 2nd July, 2003, 05:52 AM

Quote:

Originally Posted by dod

So long since I did it I just tried on this machine

Try the new client first and see if you get sse or not. Remember to set the forceasm etc. If not, shut down, delete the FAH_78 core, restart the 3.25 and you should download a new core automatically.

Here's what I did, tell me if this is right.
I shut down client. Deleted the core.exe. Dragged the 3.25 core.exe into the folder in Program Files. My flags are all set.
I started the program. It continued from where it left off, but shows SSE instead of 3Dnow. It still shows as 3.24 in log.
Is that right?

dod · #16 (**permalink**) 2nd July, 2003, 07:31 AM

Quote:

Originally Posted by Ladypcer

Here's what I did, tell me if this is right.
I shut down client. Deleted the core.exe. Dragged the 3.25 core.exe into the folder in Program Files. My flags are all set.
I started the program. It continued from where it left off, but shows SSE instead of 3Dnow. It still shows as 3.24 in log.
Is that right?

Hmm, mine shows 3.25. Are you looking at an old log?

turbo dan · #17 (**permalink**) 2nd July, 2003, 07:42 AM

It shows 3.25 in my log. As attached.
You could try moving your work folder to another file then run the 3.25 then replace the work folder. I've slept since I did the 3.25 update so I can't rememeber exactly how I did it.

LP · #18 (**permalink**) 2nd July, 2003, 07:43 AM

Quote:

Originally Posted by dod

Hmm, mine shows 3.25. Are you looking at an old log?

I don't think so. This is the only one in the user log.

Opening Log file [July 3 10:47:44]

# Windows Graphical Edition ################################################## #
################################################## #############################

Folding@home Client Version 3.24

http://foldingathome.stanford.edu

Arguments: -advmethods -forceasm

[10:47:44] - Ask before connecting: No
[10:47:44] - Use IE connection settings: Yes
[10:47:44] - User name: ladypcer (Team 45)
[10:47:44] - User ID
[10:47:44] - Machine ID:
[10:47:44]
[10:47:44] Loaded queue successfully.
[10:47:44] Initialization complete
[10:47:44] + Benchmarking ...
[10:47:47]
[10:47:47] + Processing work unit
[10:47:47] Core required: FahCore_78.exe
[10:47:47] Core not found.
[10:47:47] - Core is not present or corrupted.
[10:47:47] - Attempting to download new core...
[10:47:47] + Downloading new core: FahCore_78.exe
[10:47:48] Verifying core Core_78.fah...
[10:47:48] Signature is VALID
[10:47:48] Created: Wednesday April 10, 2002 00:01:22 UTC
[10:47:48] Signed: Thursday April 3, 2003 00:01:22 UTC
[10:47:48]
[10:47:48] Trying to unzip core FahCore_78.exe
[10:47:48] Decompressed FahCore_78.exe (1728512 bytes) successfully
[10:47:48] + Core successfully engaged
[10:47:53]
[10:47:53] + Processing work unit
[10:47:53] Core required: FahCore_78.exe
[10:47:53] Core found.
[10:47:53] Working on Unit 03 [July 3 10:47:53]
[10:47:53] + Working ...
[10:47:53]
[10:47:53] *------------------------------*
[10:47:53] Folding@home Gromacs Core
[10:47:53] Version 1.48 (May 7, 2003)
[10:47:53]
[10:47:53] Preparing to commence simulation
[10:47:53] - Assembly optimizations manually forced on.
[10:47:53] - Not checking prior termination.
[10:47:54] - Expanded 364122 -> 1777885 (decompressed 488.2 percent)
[10:47:54]
[10:47:54] Project: 340 (Run 15, Clone 23, Gen 13)
[10:47:54]
[10:47:54] Assembly optimizations on if available.
[10:47:54] Entering M.D.
[10:48:14] (Starting from checkpoint)
[10:48:14] Protein: p340_gnra_nat
[10:48:14]
[10:48:14] Writing local files
[10:48:50] Completed 30000 out of 500000 steps (6)
[10:48:50] Extra SSE boost OK.

Edited by LP to remove extra content

dod · #19 (**permalink**) 2nd July, 2003, 07:50 AM

Don't know how you work but try setting up the client as a short cut on the desktop. You should be using Folding@home325graphical.exe. Right click the short cut for properties and in the target line add -forceasm and -advmethods. Restart and that should be you.

LP · #20 (**permalink**) 2nd July, 2003, 07:57 AM

Quote:

Originally Posted by dod

Don't know how you work but try setting up the client as a short cut on the desktop. You should be using Folding@home325graphical.exe. Right click the short cut for properties and in the target line add -forceasm and -advmethods. Restart and that should be you.

Ok, did that and it looks right for now.

Folding@home Client Version 3.25

http://foldingathome.stanford.edu

Arguments: -advmethods -forceasm

[12:57:44] - Ask before connecting: No
[12:57:44] - Use IE connection settings: Yes
[12:57:44] - User name: ladypcer (Team 45)
[12:57:44] - User ID =
[12:57:44] - Machine ID:
[12:57:44]
[12:57:45] Loaded queue successfully.
[12:57:45] Initialization complete
[12:57:45] + Benchmarking ...
[12:57:48]
[12:57:48] + Processing work unit
[12:57:48] Core required: FahCore_78.exe
[12:57:48] Core found.
[12:57:48] Working on Unit 03 [July 3 12:57:48]
[12:57:48] + Working ...
[12:57:48]
[12:57:48] *------------------------------*
[12:57:48] Folding@home Gromacs Core
[12:57:48] Version 1.48 (May 7, 2003)
[12:57:48]
[12:57:48] Preparing to commence simulation
[12:57:48] - Assembly optimizations manually forced on.
[12:57:48] - Not checking prior termination.
[12:57:48] - Expanded 364122 -> 1777885 (decompressed 488.2 percent)
[12:57:48]
[12:57:48] Project: 340 (Run 15, Clone 23, Gen 13)
[12:57:48]
[12:57:48] Assembly optimizations on if available.
[12:57:48] Entering M.D.
[12:58:08] (Starting from checkpoint)
[12:58:08] Protein: p340_gnra_nat
[12:58:08]
[12:58:08] Writing local files
[12:58:44] Completed 80000 out of 500000 steps (16)
[12:58:44] Extra SSE boost OK.