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  Thread: New Beta Starting 2011/07/22

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Crystal Pellet
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Re: New Beta Starting 2011/07/22
Hi Jean,

Because of the problems with the Linux version I specially observed the behaviour on my Linux dual core laptop.
I could do this often, because I received initially 4 tasks and my laptop seems to be reliable.
After the first 4, I got 11 resends (1 because of an abort).
The other 10 tasks were because of 2 wingmen, both inconclusive.
All my 15 returned tasks were valid.
The high number of 20 inconclusives to check (whereof 10 turned into invalid) is in line what other beta-testers noticed.

The CPU behaviour I noticed:
The first 20 seconds of every of the 8 jobs within a task, the CPU in BOINC is increased. Thereafter the cpu time isn't increased, only the elapsed time.
At a checkpoint the whole used cpu-time is reported to BOINC.
It looks like the 6.12 Linux version does not communicate most of the time with BOINC at all until a checkpoint. That also explains why it is not reacting on the BOINC SUSPEND command.

Some efficiency figures from mentioned 15 Linux tasks:
                  Task	        Elapsed	CPU-time  Returned	%
BETA_BETA_ace80_0000000_2159_1	2:08:20	1:50:32	07/29-23:22	83.90
BETA_BETA_ace80_0000000_0416_1	2:43:49	2:14:18	07/30-00:07	78.02
BETA_BETA_ace80_0000000_3641_1	2:43:47	2:11:42	07/30-02:08	75.64
BETA_BETA_ace80_0000000_4086_1	1:41:00	1:25:00	07/30-04:27	81.18
BETA_BETA_ace80_0000000_3837_2	2:33:23	2:16:02	07/30-06:22	87.25
BETA_BETA_ace80_0000000_1590_2	2:24:28	1:56:21	07/30-07:19	75.83
BETA_BETA_ace80_0000000_0998_2	0:53:44	0:44:41	07/30-08:24	79.75
BETA_BETA_ace80_0000000_4641_2	2:28:23	2:20:52	07/30-13:43	94.66
BETA_BETA_ace80_0000000_1210_2	2:53:14	2:37:19	07/30-14:50	89.88
BETA_BETA_ace80_0000000_1776_2	2:36:01	1:58:20	07/30-20:06	68.15
BETA_BETA_ace80_0000000_2191_2	2:09:03	1:48:03	07/30-20:29	80.56
BETA_BETA_ace80_0000000_1931_2	2:38:58	2:14:18	07/30-23:35	81.63
BETA_BETA_ace80_0000000_2951_2	3:37:51	2:53:45	07/31-00:29	74.62
BETA_BETA_ace80_0000000_3448_2	3:37:51	2:52:32	07/31-04:18	73.73
BETA_BETA_ace80_0000000_3177_2	2:24:39	1:57:36	07/31-04:40	77.00

Edit: 1 or 2 of the low efficiencies (probably task 1590 and/or 998) are caused by battling for cpu-time by 3 BOINC-processes on a dual core, whilst the BETA crunched on after the suspend command.
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[Edit 2 times, last edit by Crystal Pellet at Jul 31, 2011 9:53:44 AM]
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Crystal Pellet
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Re: New Beta Starting 2011/07/22
Jean, you are right about not counting 1 job to the total CPU-runtime. The final job (8) is not added up.
I got a BETA-resend on my Linux box again biggrin , and was able to follow what is happening.
During job 8 the shown CPU-time is not incrementing as mentioned before, but unlike at the checkpoints the CPU-time is not totalled up when job 8 and thus the whole task finishes.

BETA_ BETA_ ace80_ 0000000_ 2590_ 2-- 999763 Valid 31/07/11 11:05:50 31/07/11 14:18:44 2.44 41.5 / 46.1

Last task:
Elapsed time 11538 seconds
Recorded CPU-time 8767 seconds - efficiency 76%
CPU including job 8 10700 seconds - efficiency 93%


Result Log

Result Name: BETA_ BETA_ ace80_ 0000000_ 2590_ 2--

<core_client_version>6.10.17</core_client_version>
<![CDATA[
<stderr_txt>
INFO: No state to restore. Start from the beginning.
[13:06:21] Number of tasks = 8
[13:06:21] Starting job 0,CPU time is 0.000000.
[13:06:21] ZINC04857456.pdbqt size = 21 4 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[13:19:30] Finished Job #0 cpu time used 739.140000
[13:19:30] Starting job 1,CPU time is 739.140000.
[13:19:30] ZINC04857456.pdbqt size = 21 4 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[13:32:46] Finished Job #1 cpu time used 741.020000
[13:32:46] Starting job 2,CPU time is 1480.160000.
[13:32:47] ZINC04857456.pdbqt size = 21 4 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[13:45:52] Finished Job #2 cpu time used 738.850000
[13:45:52] Starting job 3,CPU time is 2219.010000.
[13:45:52] ZINC04857456.pdbqt size = 21 4 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[14:00:16] Finished Job #3 cpu time used 745.510000
[14:00:16] Starting job 4,CPU time is 2964.520000.
[14:00:16] ZINC04757091.pdbqt size = 34 5 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[14:34:15] Finished Job #4 cpu time used 1923.400000
[14:34:15] Starting job 5,CPU time is 4887.920000.
[14:34:15] ZINC04757091.pdbqt size = 34 5 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[15:08:26] Finished Job #5 cpu time used 1926.150000
[15:08:26] Starting job 6,CPU time is 6814.070000.
[15:08:26] ZINC04757091.pdbqt size = 34 5 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[15:44:21] Finished Job #6 cpu time used 1952.440000
[15:44:21] Starting job 7,CPU time is 8766.510000.
[15:44:21] ZINC04757091.pdbqt size = 34 5 ../../projects/www.worldcommunitygrid.org/beta13.target_ace.pdbqt size = 4660 0
[16:18:48] Finished Job #7 cpu time used 1932.600000
16:18:48 (29216): called boinc_finish

</stderr_txt>
]]>
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[Edit 1 times, last edit by Crystal Pellet at Jul 31, 2011 2:45:05 PM]
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BSD
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Re: New Beta Starting 2011/07/22
Are we done? Haven't seen any new betas in 2 hours. sad

I must of picked up the slack, that's when I got my two. biggrin

Both completed and validated, processing time appear to be correct. Each WU processed on a separate Linux x64 device, one with AMD x4 core and the other Intel x2 core CPU. Set CPU speed to 50% in manager preferences due to high heat and humidity in my local community area weather.
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[Edit 1 times, last edit by BSD at Jul 31, 2011 3:20:05 PM]
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nanoprobe
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Re: New Beta Starting 2011/07/22
Seeing a few resends. Any new full batches in the works?
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kateiacy
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Re: New Beta Starting 2011/07/22
These betas must be for the schistosomiasis project, since it involves docking.

http://www-03.ibm.com/press/us/en/pressrelease/32422.wss
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Bearcat
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Re: New Beta Starting 2011/07/22
Thanks for the link Kate. Interesting read.
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Crystal Pellet
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Re: New Beta Starting 2011/07/22
These betas must be for the schistosomiasis project, since it involves docking.

http://www-03.ibm.com/press/us/en/pressrelease/32422.wss

Good finding Kate!

Very likely, because they are using compounds from the ZINC database and in our slots we find 2 ZINC-targets.
One target for the 1st 4 jobs in a task and one target for the 2nd 4 jobs resulting in 8 Beta13.target_ace_ZINC********_*********_out.pdbqt files.

Schistosomiasis also known as bilharzia or snail fever.
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ski1939
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Re: New Beta Starting 2011/07/22
You are probably right since its an IBM press release.

I was thinking it might be for studying "AmpC beta-lactamases"

http://www.ncbi.nlm.nih.gov/pubmed/19136439

AmpC beta-lactamases are clinically important cephalosporinases encoded on the chromosomes of many of the Enterobacteriaceae and a few other organisms, where they mediate resistance to cephalothin, cefazolin, cefoxitin, most penicillins, and beta-lactamase inhibitor-beta-lactam
combinations.
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kateiacy
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Re: New Beta Starting 2011/07/22
I vaguely recalled this press release from just before C4CW started, so it wasn't hard to hunt it up. I'm just surprised that Falconet didn't beat me to it! biggrin
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Re: New Beta Starting 2011/07/22
The suspense, Oooh the suspense... is it this research project or is it something else. Can't tell, can't tell :O)

(meantime topping the C4CW target up with 3-4 days a day... must have sapphire, must have sapphire, oh precious ;P)

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