the life with playstation [email protected] project concludes

Sunday, November 4th, 2012, was the last morning when [email protected] on Life With Playstation received my Playstation 3’s last completed work unit. One of the selling points for my reason of getting a PS3 was the capability of donating more CPU power to the distributed computing project.

I took these last screenshots to preserve the memory of the application on my Playstation. I continue to contribute to the project on a regular basis by donating the CPU power of Diode, my trusty file server that has been folding proteins since I built it back in 2007, and occasionally from c0rey foldman, my desktop computer with a Phenom quad-core processor.

I have built and used many desktop computers that have contributed to Stanford University’s [email protected] project. I started donating around 2001-2002 with an Athlon Thunderbird 1.4  processor that I still have stored away somewhere but has been retired for years. I have used a couple Athlon XP’s and a few Athlon 64 X2’s (including the one in Diode that still folds on), and an Phenom X4 that I burn up maybe a couple months a year these days when the temperature drops considerably.

I was excited to gain a Playstation 3 back in 2008, because that fulfilled my dream of having the machine that folded using the Cell, the multi-core processor used in the PS3. I managed to donate 1533+ work units over the years with my Playstation. The images provided here are a little deceiving. I had a system crash that required me to reinstall Life With Playstation and lose the completed count from the first round. I can only recall that I was in the triple digits before that unfortunate incident.

When I fired on the Playstation today, I wanted to see if any changes were made to Life With Playstation since I last checked on Sunday. I read the news around the end of October that the program was ending, so I was not surprised. I was waiting for the actual end date which had to have occurred some time this week if not today. I started the LWP application, and it required an immediate update. After the 11MB file downloaded and installed, running the program again displayed this message:

Folding proteins on my Cell microprocessor has finally ended. Technology is always evolving, and this milestone marks the end of a five-year relationship that I was proud to participate in.

^_^

On a numerological note: 1533 is the same sequence of numbers in 1.533GHz, the stable overclocked speed of the first processor I used for [email protected], my Athlon Thunderbird.

the 4 million points earned

I just checked my [email protected] stats, and I just reached 4 million points today. w00t! I’ve been folding since 2001, and points did not accumulate very quickly until multi-core processors surfaced. Typical work units will earn around 150-250 points each, but the ones I usually fold now will earn almost 2000 points each. Those numbers should give you an idea what it takes to get to 4 million points.

My donator rank based on Stanford’s [email protected] site is 1916 of 1374571, so that puts me in the top 0.001% of the project. I’ve been donating computing power to for 8+ years now and have invested in building computers especially for the cause. I deserve some bragging rights, right? =D Peace out.

the texas snow

Only in Texas will the weather be a comfortable ~70°F during the day, large gusts of wind come through in the late afternoon, and snow falls from the sky a half hour ’til midnight.

Mare took a picture of her Vespa as the snow started falling.

The bandwidth in the apartment is currently being eaten up with a 50MB upload to Stanford of a completed [email protected] work unit by c0rey and another one completed by Diode. The PS3 should be completing another one around 1:30AM.

To post this without having to put up with the lag from the large data transfers going on right now, I am mooching off a neighbor who is unaware of the importance of securing a wireless network.

To successfully rip The Dark Knight on DVD, make sure you’re using DVDFab Platinum 5.1.2.2. They thought they could stop us.

the foldman finishes his first fold

c0reyfoldman (machine ID 5) for sigmarevenge (Team 32):
May 24, 2008 9am – 1,760 points

[08:12:45]
[08:12:45] + Processing work unit
[08:12:45] Core required: FahCore_a1.exe
[08:12:45] Core found.
[08:12:45] Working on Unit 01 [May 22 08:12:45]
[08:12:45] + Working …
[08:12:45]
[08:12:45] *——————————*
[08:12:45] [email protected] Gromacs SMP Core
[08:12:45] Version 1.74 (November 27, 2006)
[08:12:45]
[08:12:45] Preparing to commence simulation
[08:12:45] – Ensuring status. Please wait.
[08:12:46] – Starting from initial work packet
[08:12:46]
[08:12:46] Project: 2605 (Run 9, Clone 179, Gen 54)
[08:12:46]
[08:12:46] Assembly optimizations on if available.
[08:12:46] Entering M.D.
[08:13:03] al work pa- Starting from initial work packet
[08:13:03]
[08:13:03] Project: 2605 (Run 9, Clone 179, Gen 54)
[08:13:03]
[08:13:04] Entering M.D.
NNODES=4, MYRANK=0, HOSTNAME=c0reyfoldman
NNODES=4, MYRANK=1, HOSTNAME=c0reyfoldman
NNODES=4, MYRANK=2, HOSTNAME=c0reyfoldman
NNODES=4, MYRANK=3, HOSTNAME=c0reyfoldman
NODEID=3 argc=15
NODEID=0 argc=15
NODEID=1 argc=15
NODEID=2 argc=15
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.

This inclusion of Gromacs code in the [email protected] Core is under
a special license (see http://folding.stanford.edu/gromacs.html)
specially granted to Stanford by the copyright holders. If you
are interested in using Gromacs, visit www.gromacs.org where
you can download a free version of Gromacs under
the terms of the GNU General Public License (GPL) as published
by the Free Software Foundation; either version 2 of the License,
or (at your option) any later version.

[08:13:10] Protein: Protein in POPC
[08:13:10] Writing local files
starting mdrun ‘Protein in POPC’
500000 steps, 1000.0 ps.

[08:13:11] Extra SSE boost OK.
[08:42:18] es
[08:42:19] Completed 5000 out of 500000 steps (1 percent)
[09:11:20] Writing local files
[09:11:21] Completed 10000 out of 500000 steps (2 percent)
[09:40:23] Writing local files
[09:40:24] Completed 15000 out of 500000 steps (3 percent)
[10:09:22] Writing local files
[10:09:23] Completed 20000 out of 500000 steps (4 percent)
[10:38:23] Writing local files
[10:38:23] Completed 25000 out of 500000 steps (5 percent)
[11:07:22] Writing local files
[11:07:22] Completed 30000 out of 500000 steps (6 percent)
[11:36:19] Writing local files
[11:36:19] Completed 35000 out of 500000 steps (7 percent)
[12:05:20] Writing local files
[12:05:20] Completed 40000 out of 500000 steps (8 percent)
[12:34:19] Writing local files
[12:34:19] Completed 45000 out of 500000 steps (9 percent)
[13:03:18] Writing local files
[13:03:18] Completed 50000 out of 500000 steps (10 percent)
[13:32:17] Writing local files
[13:32:17] Completed 55000 out of 500000 steps (11 percent)
[14:01:17] Writing local files
[14:01:17] Completed 60000 out of 500000 steps (12 percent)
[14:30:14] Writing local files
[14:30:14] Completed 65000 out of 500000 steps (13 percent)
[14:59:11] Writing local files
[14:59:11] Completed 70000 out of 500000 steps (14 percent)
[15:28:10] Writing local files
[15:28:10] Completed 75000 out of 500000 steps (15 percent)
[15:57:09] Writing local files
[15:57:09] Completed 80000 out of 500000 steps (16 percent)
[16:26:07] Writing local files
[16:26:07] Completed 85000 out of 500000 steps (17 percent)
[16:55:07] Writing local files
[16:55:07] Completed 90000 out of 500000 steps (18 percent)
[17:24:05] Writing local files
[17:24:05] Completed 95000 out of 500000 steps (19 percent)
[17:53:02] Writing local files
[17:53:02] Completed 100000 out of 500000 steps (20 percent)
[18:21:59] Writing local files
[18:22:00] Completed 105000 out of 500000 steps (21 percent)
[18:50:58] Writing local files
[18:50:58] Completed 110000 out of 500000 steps (22 percent)
[19:19:56] Writing local files
[19:19:56] Completed 115000 out of 500000 steps (23 percent)
[19:48:53] Writing local files
[19:48:53] Completed 120000 out of 500000 steps (24 percent)
[20:17:50] Writing local files
[20:17:50] Completed 125000 out of 500000 steps (25 percent)
[20:46:48] Writing local files
[20:46:48] Completed 130000 out of 500000 steps (26 percent)
[21:15:45] Writing local files
[21:15:45] Completed 135000 out of 500000 steps (27 percent)
[21:44:43] Writing local files
[21:44:43] Completed 140000 out of 500000 steps (28 percent)
[22:13:44] Writing local files
[22:13:44] Completed 145000 out of 500000 steps (29 percent)
[22:43:14] Writing local files
[22:43:14] Completed 150000 out of 500000 steps (30 percent)
[23:12:16] Writing local files
[23:12:16] Completed 155000 out of 500000 steps (31 percent)
[23:41:19] Writing local files
[23:41:19] Completed 160000 out of 500000 steps (32 percent)
[00:10:19] Writing local files
[00:10:19] Completed 165000 out of 500000 steps (33 percent)
[00:39:23] Writing local files
[00:39:23] Completed 170000 out of 500000 steps (34 percent)
[01:08:23] Writing local files
[01:08:23] Completed 175000 out of 500000 steps (35 percent)
[01:37:24] Writing local files
[01:37:24] Completed 180000 out of 500000 steps (36 percent)
[02:06:27] Writing local files
[02:06:27] Completed 185000 out of 500000 steps (37 percent)
[02:35:29] Writing local files
[02:35:29] Completed 190000 out of 500000 steps (38 percent)
[03:04:30] Writing local files
[03:04:30] Completed 195000 out of 500000 steps (39 percent)
[03:33:32] Writing local files
[03:33:32] Completed 200000 out of 500000 steps (40 percent)
[04:02:35] Writing local files
[04:02:35] Completed 205000 out of 500000 steps (41 percent)
[04:31:36] Writing local files
[04:31:36] Completed 210000 out of 500000 steps (42 percent)
[05:00:38] Writing local files
[05:00:38] Completed 215000 out of 500000 steps (43 percent)
[05:29:40] Writing local files
[05:29:40] Completed 220000 out of 500000 steps (44 percent)
[05:58:43] Writing local files
[05:58:43] Completed 225000 out of 500000 steps (45 percent)
[06:27:47] Writing local files
[06:27:47] Completed 230000 out of 500000 steps (46 percent)
[06:56:48] Writing local files
[06:56:48] Completed 235000 out of 500000 steps (47 percent)
[07:25:50] Writing local files
[07:25:50] Completed 240000 out of 500000 steps (48 percent)
[07:54:54] Writing local files
[07:54:54] Completed 245000 out of 500000 steps (49 percent)
[08:23:57] Writing local files
[08:23:57] Completed 250000 out of 500000 steps (50 percent)
[08:52:58] Writing local files
[08:52:59] Completed 255000 out of 500000 steps (51 percent)
[09:21:59] Writing local files
[09:21:59] Completed 260000 out of 500000 steps (52 percent)
[09:51:02] Writing local files
[09:51:02] Completed 265000 out of 500000 steps (53 percent)
[10:20:04] Writing local files
[10:20:04] Completed 270000 out of 500000 steps (54 percent)
[10:49:05] Writing local files
[10:49:06] Completed 275000 out of 500000 steps (55 percent)
[11:18:08] Writing local files
[11:18:08] Completed 280000 out of 500000 steps (56 percent)
[11:47:12] Writing local files
[11:47:12] Completed 285000 out of 500000 steps (57 percent)
[12:16:14] Writing local files
[12:16:14] Completed 290000 out of 500000 steps (58 percent)
[12:45:18] Writing local files
[12:45:18] Completed 295000 out of 500000 steps (59 percent)
[13:14:24] Writing local files
[13:14:24] Completed 300000 out of 500000 steps (60 percent)
[13:43:26] Writing local files
[13:43:26] Completed 305000 out of 500000 steps (61 percent)
[14:12:29] Writing local files
[14:12:29] Completed 310000 out of 500000 steps (62 percent)
[14:41:29] Writing local files
[14:41:29] Completed 315000 out of 500000 steps (63 percent)
[15:10:30] Writing local files
[15:10:30] Completed 320000 out of 500000 steps (64 percent)
[15:39:33] Writing local files
[15:39:33] Completed 325000 out of 500000 steps (65 percent)
[16:08:36] Writing local files
[16:08:36] Completed 330000 out of 500000 steps (66 percent)
[16:37:36] Writing local files
[16:37:36] Completed 335000 out of 500000 steps (67 percent)
[17:06:39] Writing local files
[17:06:39] Completed 340000 out of 500000 steps (68 percent)
[17:35:44] Writing local files
[17:35:44] Completed 345000 out of 500000 steps (69 percent)
[18:04:46] Writing local files
[18:04:46] Completed 350000 out of 500000 steps (70 percent)
[18:33:47] Writing local files
[18:33:47] Completed 355000 out of 500000 steps (71 percent)
[19:02:48] Writing local files
[19:02:48] Completed 360000 out of 500000 steps (72 percent)
[19:31:49] Writing local files
[19:31:49] Completed 365000 out of 500000 steps (73 percent)
[20:00:53] Writing local files
[20:00:53] Completed 370000 out of 500000 steps (74 percent)
[20:29:57] Writing local files
[20:29:57] Completed 375000 out of 500000 steps (75 percent)
[20:59:00] Writing local files
[20:59:00] Completed 380000 out of 500000 steps (76 percent)
[21:28:03] Writing local files
[21:28:04] Completed 385000 out of 500000 steps (77 percent)
[21:57:10] Writing local files
[21:57:10] Completed 390000 out of 500000 steps (78 percent)
[22:26:16] Writing local files
[22:26:16] Completed 395000 out of 500000 steps (79 percent)
[22:55:21] Writing local files
[22:55:21] Completed 400000 out of 500000 steps (80 percent)
[23:24:25] Writing local files
[23:24:25] Completed 405000 out of 500000 steps (81 percent)
[23:53:28] Writing local files
[23:53:28] Completed 410000 out of 500000 steps (82 percent)
[00:22:33] Writing local files
[00:22:33] Completed 415000 out of 500000 steps (83 percent)
[00:51:40] Writing local files
[00:51:40] Completed 420000 out of 500000 steps (84 percent)
[01:20:42] Writing local files
[01:20:42] Completed 425000 out of 500000 steps (85 percent)
[01:49:47] Writing local files
[01:49:47] Completed 430000 out of 500000 steps (86 percent)
[02:18:50] Writing local files
[02:18:50] Completed 435000 out of 500000 steps (87 percent)
[02:48:05] Writing local files
[02:48:05] Completed 440000 out of 500000 steps (88 percent)
[03:17:06] Writing local files
[03:17:06] Completed 445000 out of 500000 steps (89 percent)
[03:46:08] Writing local files
[03:46:08] Completed 450000 out of 500000 steps (90 percent)
[04:15:11] Writing local files
[04:15:12] Completed 455000 out of 500000 steps (91 percent)
[04:44:13] Writing local files
[04:44:13] Completed 460000 out of 500000 steps (92 percent)
[05:13:16] Writing local files
[05:13:16] Completed 465000 out of 500000 steps (93 percent)
[05:42:18] Writing local files
[05:42:18] Completed 470000 out of 500000 steps (94 percent)
[06:11:20] Writing local files
[06:11:20] Completed 475000 out of 500000 steps (95 percent)
[06:40:24] Writing local files
[06:40:24] Completed 480000 out of 500000 steps (96 percent)
[07:09:24] Writing local files
[07:09:25] Completed 485000 out of 500000 steps (97 percent)
[07:45:25] Writing local files
[07:45:25] Completed 490000 out of 500000 steps (98 percent)
[08:14:25] Writing local files
[08:14:25] Completed 495000 out of 500000 steps (99 percent)
[08:43:24] Writing local files
[08:43:24] Completed 500000 out of 500000 steps (100 percent)
[08:43:24] Writing final coordinates.

[08:43:25] Past main M.D. loop

M E G A – F L O P S A C C O U N T I N G

Parallel run – timing based on wallclock.
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces

Computing: M-Number M-Flops % of Flops
———————————————————————–
VdW(T) 1365206.268165 73721138.480910 16.7
RF Coul 548660.228024 18105787.524792 4.1
RF Coul [W3] 2041.717397 200088.304906 0.0
RF Coul + VdW(T) 608759.577645 39569372.546925 8.9
RF Coul + VdW(T) [W3] 286048.380738 37186289.495940 8.4
RF Coul + VdW(T) [W3-W3] 764537.359365 244651954.996800 55.3
Outer nonbonded loop 240018.112809 2400181.128090 0.5
1,4 nonbonded interactions 1059.002118 95310.190620 0.0
NS-Pairs 507354.520058 10654444.921218 2.4
Reset In Box 3876.077520 34884.697680 0.0
Shift-X 77423.154846 464538.929076 0.1
CG-CoM 1765.285305 51193.273845 0.0
Sum Forces 116280.232560 116280.232560 0.0
Bonds 13248.026496 569665.139328 0.1
Angles 15591.531183 2541419.582829 0.6
Propers 5376.010752 1231106.462208 0.3
Impropers 1006.002012 209248.418496 0.0
RB-Dihedrals 14114.028228 3486164.972316 0.8
Virial 38814.077628 698653.397304 0.2
Update 38760.077520 1201562.403120 0.3
Stop-CM 38760.000000 387600.000000 0.1
P-Coupling 38760.077520 232560.465120 0.1
Calc-Ekin 38760.155040 1046524.186080 0.2
Constraint-V 38760.077520 232560.465120 0.1
Constraint-Vir 25213.550427 605125.210248 0.1
Settle 8404.516809 2714658.929307 0.6
———————————————————————–
Total 442408314.354838 100.0
———————————————————————–

NODE (s) Real (s) (%)
Time: 174614.000 174614.000 100.0
2d00h30:14
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 20.475 2.534 0.495 48.504
[08:43:25] Will end MPI now
[08:44:25]
[08:44:25] Finished Work Unit:
[08:44:25] – Reading up to 3721200 from “work/wudata_01.arc”: Read 3721200
[08:44:25] – Reading up to 1775276 from “work/wudata_01.xtc”: Read 1775276
[08:44:25] goefile size: 0
[08:44:25] logfile size: 24717
[08:44:25] Leaving Run
[08:44:30] – Writing 5525593 bytes of core data to disk…
[08:44:30] … Done.
[08:44:55] – Shutting down core
[08:44:55]
[08:44:55] [email protected] Core Shutdown: FINISHED_UNIT
[0]0:Return code = 100
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Quit
[08:45:36] CoreStatus = 64 (100)
[08:45:36] Sending work to server

[08:45:36] + Attempting to send results
[08:57:45] + Results successfully sent
[08:57:45] Thank you for your contribution to [email protected]
[08:57:45] + Starting local stats count at 1

the brother to the rescue

My Debian machine completed a [email protected] work unit but wasn’t able to send it nor could it obtain a new work unit. I figured that Stanford’s [email protected] servers might be offline. When I checked, they were fully functional.

I figured that something was up with Diode, my Debian machine, when it couldn’t connect to the internet. This explained why it wasn’t able to send the work unit or receive a new one.

I did my search engine/forum hunt for a solution and tried the many command line solutions that the GNU/Linux wizards provided to no avail. It was time to bust out the big guns: call up my bro.

I really didn’t want to bug him so late at nite, but he helps me figure these kind of issues out and I was already not thinking straight since I had been tinkering without progress for a while by this time. I was able to access all of computers on the internal network, but Diode couldn’t communicate with the outside which was very odd.

My bro just told me to restart the router, and it solved everything. After digging myself into a really deep technical hole, the last thing on my mind was to reboot the router.

So I’m writing this on my Debian machine successfully connected to the internet as a way of saying thanks. All he really had to do was talk it through with me, and everything was fixed.

In other news, today was my mother’s birthday. Happy Birthday, Mom!