Double Gromacs = Slow?

B

BakedON

[H]ard|DCer of the Year - 2006
Joined
Nov 27, 2004
Messages
3,449
Yikes.... I have a handfull of 1.8Ghz machines that are just CHOKING on these little 84 pointers. :eek:
They're running like 12m/frame.... which ends up being like 20 hours I guess so I shouldn't complain too much. SOme of them seem to stall though and take a few extra hours at random. My 2.8Ghz P4 got one and kicked it out in under 8 hours so I guess I shouldn't be worried.... I guess that seems right.
Anyone else have problems with these little guys or am I asking too much from my 1.8's?
 
I had a handful of these on my P4 2.66s here at work.... finishing each frame in about 6-8 minutes... which is about 6-8 PPH.....


Keep on Folding!!

 
You might want to check and see that SSE boost is working on these PC's. You can find this information in the following post.

 
Here's a log file of one on my P4 2.66 here at work....

Code: 
[03:05:10] - Preparing to get new work unit...
[03:05:10] + Attempting to get work packet
[03:05:10] - Connecting to assignment server
[03:05:11] - Successful: assigned to (171.64.122.132).
[03:05:11] + News From Folding@Home: Welcome to Folding@Home
[03:05:11] Loaded queue successfully.
[03:05:18] + Closed connections
[03:05:18] 
[03:05:18] + Processing work unit
[03:05:18] Core required: FahCore_79.exe
[03:05:18] Core found.
[03:05:18] Working on Unit 02 [April 27 03:05:18]
[03:05:18] + Working ...
[03:05:18] 
[03:05:18] *------------------------------*
[03:05:18] Folding@Home Double Gromacs Core
[03:05:18] Version 1.72 (February 4, 2005)
[03:05:18] 
[03:05:18] Preparing to commence simulation
[03:05:18] - Looking at optimizations...
[03:05:18] - Created dyn
[03:05:18] - Files status OK
[03:05:19] - Expanded 847611 -> 3365225 (decompressed 397.0 percent)
[03:05:19] - Starting from initial work packet
[03:05:19] 
[03:05:19] Project: 971 (Run 302, Clone 7, Gen 19)
[03:05:19] 
[03:05:19] Assembly optimizations on if available.
[03:05:19] Entering M.D.
[03:05:25] Protein: p971_fkcomp_dock
[03:05:25] 
[03:05:25] Writing local files
[03:05:28] Extra SSE2 boost OK.
[03:05:28] Writing local files
[03:05:28] Completed 0 out of 100000 steps  (0)
[03:11:08] Writing local files
[03:11:08] Completed 1000 out of 100000 steps  (1)
[03:16:48] Writing local files
[03:16:48] Completed 2000 out of 100000 steps  (2)
[03:22:27] Writing local files
[03:22:27] Completed 3000 out of 100000 steps  (3)
[03:28:07] Writing local files
[03:28:08] Completed 4000 out of 100000 steps  (4)
[03:33:48] Writing local files
[03:33:48] Completed 5000 out of 100000 steps  (5)
[03:39:28] Writing local files
[03:39:28] Completed 6000 out of 100000 steps  (6)
[03:45:07] Writing local files
[03:45:07] Completed 7000 out of 100000 steps  (7)
[03:50:47] Writing local files
[03:50:47] Completed 8000 out of 100000 steps  (8)
[03:56:27] Writing local files
[03:56:27] Completed 9000 out of 100000 steps  (9)
[04:02:05] Writing local files
[04:02:05] Completed 10000 out of 100000 steps  (10)
[04:07:45] Writing local files
[04:07:45] Completed 11000 out of 100000 steps  (11)
[04:13:23] Writing local files
[04:13:24] Completed 12000 out of 100000 steps  (12)
[04:19:02] Writing local files
[04:19:02] Completed 13000 out of 100000 steps  (13)
[04:24:41] Writing local files
[04:24:41] Completed 14000 out of 100000 steps  (14)
[04:30:20] Writing local files
[04:30:20] Completed 15000 out of 100000 steps  (15)
[04:35:58] Writing local files
[04:35:59] Completed 16000 out of 100000 steps  (16)
[04:41:38] Writing local files
[04:41:38] Completed 17000 out of 100000 steps  (17)
[04:47:17] Writing local files
[04:47:17] Completed 18000 out of 100000 steps  (18)
[04:52:57] Writing local files
[04:52:57] Completed 19000 out of 100000 steps  (19)
[04:58:36] Writing local files
[04:58:36] Completed 20000 out of 100000 steps  (20)
[05:04:14] Writing local files
[05:04:14] Completed 21000 out of 100000 steps  (21)
[05:09:53] Writing local files
[05:09:54] Completed 22000 out of 100000 steps  (22)
[05:15:31] Writing local files
[05:15:31] Completed 23000 out of 100000 steps  (23)
[05:21:11] Writing local files
[05:21:11] Completed 24000 out of 100000 steps  (24)
[05:26:50] Writing local files
[05:26:50] Completed 25000 out of 100000 steps  (25)
[05:32:29] Writing local files
[05:32:29] Completed 26000 out of 100000 steps  (26)
[05:38:09] Writing local files
[05:38:09] Completed 27000 out of 100000 steps  (27)
[05:43:49] Writing local files
[05:43:49] Completed 28000 out of 100000 steps  (28)
[05:49:29] Writing local files
[05:49:29] Completed 29000 out of 100000 steps  (29)
[05:55:09] Writing local files
[05:55:09] Completed 30000 out of 100000 steps  (30)
[06:00:49] Writing local files
[06:00:49] Completed 31000 out of 100000 steps  (31)
[06:06:29] Writing local files
[06:06:29] Completed 32000 out of 100000 steps  (32)
[06:12:08] Writing local files
[06:12:08] Completed 33000 out of 100000 steps  (33)
[06:17:47] Writing local files
[06:17:47] Completed 34000 out of 100000 steps  (34)
[06:23:26] Writing local files
[06:23:26] Completed 35000 out of 100000 steps  (35)
[06:29:05] Writing local files
[06:29:05] Completed 36000 out of 100000 steps  (36)
[06:34:44] Writing local files
[06:34:44] Completed 37000 out of 100000 steps  (37)
[06:40:22] Writing local files
[06:40:22] Completed 38000 out of 100000 steps  (38)
[06:46:01] Writing local files
[06:46:01] Completed 39000 out of 100000 steps  (39)
[06:51:41] Writing local files
[06:51:41] Completed 40000 out of 100000 steps  (40)
[06:57:20] Writing local files
[06:57:20] Completed 41000 out of 100000 steps  (41)
[07:02:59] Writing local files
[07:02:59] Completed 42000 out of 100000 steps  (42)
[07:08:40] Writing local files
[07:08:40] Completed 43000 out of 100000 steps  (43)
[07:14:20] Writing local files
[07:14:20] Completed 44000 out of 100000 steps  (44)
[07:20:00] Writing local files
[07:20:00] Completed 45000 out of 100000 steps  (45)
[07:25:40] Writing local files
[07:25:40] Completed 46000 out of 100000 steps  (46)
[07:31:19] Writing local files
[07:31:19] Completed 47000 out of 100000 steps  (47)
[07:36:58] Writing local files
[07:36:59] Completed 48000 out of 100000 steps  (48)
[07:42:38] Writing local files
[07:42:38] Completed 49000 out of 100000 steps  (49)
[07:48:19] Writing local files
[07:48:19] Completed 50000 out of 100000 steps  (50)
[07:54:01] Writing local files
[07:54:01] Completed 51000 out of 100000 steps  (51)
[07:59:41] Writing local files
[07:59:41] Completed 52000 out of 100000 steps  (52)
[08:05:22] Writing local files
[08:05:22] Completed 53000 out of 100000 steps  (53)
[08:11:02] Writing local files
[08:11:02] Completed 54000 out of 100000 steps  (54)
[08:16:44] Writing local files
[08:16:44] Completed 55000 out of 100000 steps  (55)
[08:22:28] Writing local files
[08:22:28] Completed 56000 out of 100000 steps  (56)
[08:28:08] Writing local files
[08:28:08] Completed 57000 out of 100000 steps  (57)
[08:33:50] Writing local files
[08:33:50] Completed 58000 out of 100000 steps  (58)
[08:39:31] Writing local files
[08:39:31] Completed 59000 out of 100000 steps  (59)
[08:45:12] Writing local files
[08:45:12] Completed 60000 out of 100000 steps  (60)
[08:50:53] Writing local files
[08:50:53] Completed 61000 out of 100000 steps  (61)
[08:56:34] Writing local files
[08:56:34] Completed 62000 out of 100000 steps  (62)
[09:02:14] Writing local files
[09:02:14] Completed 63000 out of 100000 steps  (63)
[09:07:56] Writing local files
[09:07:56] Completed 64000 out of 100000 steps  (64)
[09:13:37] Writing local files
[09:13:37] Completed 65000 out of 100000 steps  (65)
[09:19:18] Writing local files
[09:19:18] Completed 66000 out of 100000 steps  (66)
[09:24:58] Writing local files
[09:24:58] Completed 67000 out of 100000 steps  (67)
[09:30:40] Writing local files
[09:30:40] Completed 68000 out of 100000 steps  (68)
[09:36:21] Writing local files
[09:36:21] Completed 69000 out of 100000 steps  (69)
[09:42:02] Writing local files
[09:42:02] Completed 70000 out of 100000 steps  (70)
[09:47:42] Writing local files
[09:47:42] Completed 71000 out of 100000 steps  (71)
[09:53:23] Writing local files
[09:53:23] Completed 72000 out of 100000 steps  (72)
[09:59:03] Writing local files
[09:59:04] Completed 73000 out of 100000 steps  (73)
[10:04:45] Writing local files
[10:04:45] Completed 74000 out of 100000 steps  (74)
[10:10:26] Writing local files
[10:10:26] Completed 75000 out of 100000 steps  (75)
[10:16:07] Writing local files
[10:16:07] Completed 76000 out of 100000 steps  (76)
[10:21:48] Writing local files
[10:21:48] Completed 77000 out of 100000 steps  (77)
[10:27:28] Writing local files
[10:27:28] Completed 78000 out of 100000 steps  (78)
[10:33:08] Writing local files
[10:33:08] Completed 79000 out of 100000 steps  (79)
[10:38:50] Writing local files
[10:38:50] Completed 80000 out of 100000 steps  (80)
[10:44:30] Writing local files
[10:44:30] Completed 81000 out of 100000 steps  (81)
[10:50:10] Writing local files
[10:50:10] Completed 82000 out of 100000 steps  (82)
[10:55:51] Writing local files
[10:55:51] Completed 83000 out of 100000 steps  (83)
[11:01:32] Writing local files
[11:01:33] Completed 84000 out of 100000 steps  (84)
[11:07:12] Writing local files
[11:07:13] Completed 85000 out of 100000 steps  (85)
[11:12:53] Writing local files
[11:12:53] Completed 86000 out of 100000 steps  (86)
[11:18:34] Writing local files
[11:18:34] Completed 87000 out of 100000 steps  (87)
[11:24:15] Writing local files
[11:24:15] Completed 88000 out of 100000 steps  (88)
[11:29:57] Writing local files
[11:29:57] Completed 89000 out of 100000 steps  (89)
[11:35:39] Writing local files
[11:35:39] Completed 90000 out of 100000 steps  (90)
[11:41:19] Writing local files
[11:41:20] Completed 91000 out of 100000 steps  (91)
[11:46:59] Writing local files
[11:46:59] Completed 92000 out of 100000 steps  (92)
[11:52:41] Writing local files
[11:52:41] Completed 93000 out of 100000 steps  (93)
[11:58:23] Writing local files
[11:58:23] Completed 94000 out of 100000 steps  (94)
[12:04:04] Writing local files
[12:04:04] Completed 95000 out of 100000 steps  (95)
[12:09:44] Writing local files
[12:09:44] Completed 96000 out of 100000 steps  (96)
[12:15:25] Writing local files
[12:15:25] Completed 97000 out of 100000 steps  (97)
[12:21:05] Writing local files
[12:21:05] Completed 98000 out of 100000 steps  (98)
[12:26:46] Writing local files
[12:26:46] Completed 99000 out of 100000 steps  (99)
[12:32:27] Writing local files
[12:32:27] Completed 100000 out of 100000 steps  (100)
[12:32:27] Writing final coordinates.
[12:32:28] Past main M.D. loop
[12:33:28] 
[12:33:28] Finished Work Unit:
[12:33:28] - Reading up to 715604 from "work/wudata_02.arc": Read 715604
[12:33:28] - Reading up to 26400 from "work/wudata_02.xtc": Read 26400
[12:33:28] goefile size: 0
[12:33:28] logfile size: 13867
[12:33:28] Leaving Run
[12:33:29] - Writing 960846 bytes of core data to disk...
[12:33:29]   ... Done.
[12:33:29] - Shutting down core
[12:33:29] 
[12:33:29] Folding@home Core Shutdown: FINISHED_UNIT
[12:33:33] CoreStatus = 64 (100)
[12:33:33] Sending work to server



Keep on Folding!!

 
Checked all the logs... SSE Boost OK

Guess they're just slow.
It's like watching a cake baking. You're never happy till it's done and you get to eat it.... though I don't really wanna eat any proteins.....
 
BakedON said:
Checked all the logs... SSE Boost OK

Guess they're just slow.
It's like watching a cake baking. You're never happy till it's done and you get to eat it.... though I don't really wanna eat any proteins.....
Click to expand...
in that case, may i suggest the ultra-pure-starvation diet, my good sir? ;)


 
BakedON said:
Yikes.... I have a handfull of 1.8Ghz machines that are just CHOKING on these little 84 pointers. :eek:
They're running like 12m/frame.... which ends up being like 20 hours I guess so I shouldn't complain too much. SOme of them seem to stall though and take a few extra hours at random. My 2.8Ghz P4 got one and kicked it out in under 8 hours so I guess I shouldn't be worried.... I guess that seems right.
Anyone else have problems with these little guys or am I asking too much from my 1.8's?
Click to expand...

P42.0A, 8 min/frame :)
 
Do your 1.8s have SSE2? Cause that's what speeds up these proteins.

Oldbenwa


Edit-

P4-2.53 - 6:31/frame.
P4-1.4 - 7:32/frame
 
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