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  Thread: Linux for the Leishmaniasis (DSFL) project?

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Ingleside
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Re: Linux for the Leishmaniasis (DSFL) project?
Hello ZoSo,
Are your Intel CPUs using hyperthreading?

He did state it's a Q6600, meaning an older quad-core that doesn't have hyperthreading.

This will present the appearance of terrible inefficiency, but in reality the CPU will produce about 15% more per unit time than it would without hyperthreading. Since this is done by using 2 threads per unit time, the reported efficiency will be 115% / 2 or 57% efficiency per task if both tasks are treated equally. If one task is favored, then the other task will look even worse.

confused

Hmm, are you telling me Linux works differently in this regard than windows does? Atleast under windows, all tasks is at 99% efficiency running on a HT-computer, as long as doesn't use computer for other things than crunching that is.
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"I make so many mistakes. But then just think of all the mistakes I don't make, although I might."
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[Edit 1 times, last edit by Ingleside at Sep 10, 2011 3:41:42 PM]
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Former Member
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Re: Linux for the Leishmaniasis (DSFL) project?
Since badges are based on CPU time, the fact that windows may run the same work unit a little longer is a plus, in my opinion.

My main concern is why some work units run with terrible efficiency. e.g.

http://my.core.com/~zoso/WCG/DSFL_poorEfficiency.png **

C2Q6660 is an Intel Q6600 running fedora 32-bit with the fedora-issued BOINC 6.10.45; I have 2 other machines with that same version of fedora and BOINC, but with AMD processors, that I've never seen get 'stuck' with such poor efficiency (~12%) work units.

** Click on link to see 'big' screenshot.

ZoSo, no problem with DSFL on Ubuntu Nasty 11.04 with 6.12.33 client here, about 75 completed, 100% result, and getting about 99.2-99.6% efficiency per BT. It looks like it's not efficiency, it's having the appearance that your science apps are not getting the time [hung in a loop I doubt as that would still show CPU use]. If you open up system monitor there are 2 apps, the control [wcg_dsfl_6.19_i686-pc-linux-gnu] that maybe take 1 minute over the whole job and the worker app [wcg_dsfl_vina_6.19_i686-pc-linux-gnu] which is the one that would use all the spare cycles. Maybe, as with FAAH, the security software is interfering. Ran a ClamAV scan whilst BOINC was running, and it had no problem, but have no Firewall (sits in the router).

edit: On closer look at the target 8 results, the Elapsed time of 6-9 hours is kind of normal for this target. Is it the CEP lost CPU time syndrome reborn? Presume these tasks validate, then look in the Result Status page and click on such a result WU name to see the quorum and the CPU time the wingman took.

--//--
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[Edit 1 times, last edit by Former Member at Sep 10, 2011 4:08:16 PM]
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KWSN - A Shrubbery
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Re: Linux for the Leishmaniasis (DSFL) project?
edit: On closer look at the target 8 results, the Elapsed time of 6-9 hours is kind of normal for this target. Is it the CEP lost CPU time syndrome reborn? Presume these tasks validate, then look in the Result Status page and click on such a result WU name to see the quorum and the CPU time the wingman took.

--//--

That was what I noticed as well. Under 1 hour completion on a target 8 would be exceptional speed. Even my fastest system takes about 5-7 hours on those.
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Distributed computing volunteer since September 27, 2000
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Former Member
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Re: Linux for the Leishmaniasis (DSFL) project?
ZoSo, further to me previous post also click on the status link of such a short running DSFL task to get the result log. Please post a copy so we can read the actual [your] walltimes and the times each job takes in CPU seconds.

--//--
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Former Member
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Re: Linux for the Leishmaniasis (DSFL) project?
ZoSo, further to me previous post also click on the status link of such a short running DSFL task to get the result log. Please post a copy so we can read the actual [your] walltimes and the times each job takes in CPU seconds.

--//--







Result Log  

Result Name: DSFL_ 00000008_ 0000040_ 0150_ 0-- 
 
<core_client_version>6.10.45</core_client_version>
<![CDATA[
<stderr_txt>
INFO: No state to restore. Start from the beginning.
[08:50:31] Number of tasks = 68
[08:50:31] Starting job 0,CPU time is 0.000000.
[08:50:31] ZINC19788368.pdbqt size = 29 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[08:58:56] Finished Job #0 cpu time used 66.195936
[08:58:56] Starting job 1,CPU time is 66.195936.
[08:58:56] ZINC19788368.pdbqt size = 29 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[09:07:21] Finished Job #1 cpu time used 65.330068
[09:07:21] Starting job 2,CPU time is 131.526004.
[09:07:21] ZINC19788368.pdbqt size = 29 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[09:15:48] Finished Job #2 cpu time used 66.276924
[09:15:48] Starting job 3,CPU time is 197.802928.
[09:15:48] ZINC19788368.pdbqt size = 29 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[09:24:09] Finished Job #3 cpu time used 66.122947
[09:24:09] Starting job 4,CPU time is 263.925875.
[09:24:09] ZINC19788410.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[09:29:49] Finished Job #4 cpu time used 65.447050
[09:29:49] Starting job 5,CPU time is 329.372925.
[09:29:49] ZINC19788410.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[09:35:29] Finished Job #5 cpu time used 65.507041
[09:35:29] Starting job 6,CPU time is 394.879966.
[09:35:29] ZINC19788410.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[09:41:10] Finished Job #6 cpu time used 65.811995
[09:41:10] Starting job 7,CPU time is 460.691961.
[09:41:10] ZINC19788410.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[09:46:54] Finished Job #7 cpu time used 65.899981
[09:46:54] Starting job 8,CPU time is 526.591942.
[09:46:54] ZINC19788419.pdbqt size = 35 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[10:04:37] Finished Job #8 cpu time used 66.112949
[10:04:37] Starting job 9,CPU time is 592.704891.
[10:04:37] ZINC19788419.pdbqt size = 35 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[10:22:25] Finished Job #9 cpu time used 65.872985
[10:22:25] Starting job 10,CPU time is 658.577876.
[10:22:25] ZINC19788419.pdbqt size = 35 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[10:40:07] Finished Job #10 cpu time used 65.416055
[10:40:07] Starting job 11,CPU time is 723.993931.
[10:40:07] ZINC19788419.pdbqt size = 35 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[10:57:39] Finished Job #11 cpu time used 65.936976
[10:57:39] Starting job 12,CPU time is 789.930907.
[10:57:40] ZINC19788461.pdbqt size = 25 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[11:04:52] Finished Job #12 cpu time used 65.741005
[11:04:52] Starting job 13,CPU time is 855.671912.
[11:04:52] ZINC19788461.pdbqt size = 25 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[11:12:06] Finished Job #13 cpu time used 65.959972
[11:12:06] Starting job 14,CPU time is 921.631884.
[11:12:06] ZINC19788461.pdbqt size = 25 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[11:19:15] Finished Job #14 cpu time used 66.054958
[11:19:15] Starting job 15,CPU time is 987.686842.
[11:19:15] ZINC19788461.pdbqt size = 25 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[11:26:25] Finished Job #15 cpu time used 66.025962
[11:26:25] Starting job 16,CPU time is 1053.712804.
[11:26:25] ZINC19788465.pdbqt size = 28 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[11:35:54] Finished Job #16 cpu time used 65.734006
[11:35:54] Starting job 17,CPU time is 1119.446810.
[11:35:54] ZINC19788465.pdbqt size = 28 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[11:45:19] Finished Job #17 cpu time used 65.868986
[11:45:19] Starting job 18,CPU time is 1185.315796.
[11:45:19] ZINC19788465.pdbqt size = 28 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[11:54:49] Finished Job #18 cpu time used 66.138945
[11:54:49] Starting job 19,CPU time is 1251.454741.
[11:54:49] ZINC19788465.pdbqt size = 28 7 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[12:04:14] Finished Job #19 cpu time used 65.940975
[12:04:14] Starting job 20,CPU time is 1317.395716.
[12:04:14] ZINC19788532.pdbqt size = 31 8 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[12:14:00] Finished Job #20 cpu time used 65.925977
[12:14:00] Starting job 21,CPU time is 1383.321693.
[12:14:00] ZINC19788532.pdbqt size = 31 8 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[12:23:47] Finished Job #21 cpu time used 66.039960
[12:23:47] Starting job 22,CPU time is 1449.361653.
[12:23:48] ZINC19788532.pdbqt size = 31 8 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[12:33:29] Finished Job #22 cpu time used 66.355912
[12:33:29] Starting job 23,CPU time is 1515.717565.
[12:33:29] ZINC19788532.pdbqt size = 31 8 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[12:43:25] Finished Job #23 cpu time used 66.148943
[12:43:25] Starting job 24,CPU time is 1581.866508.
[12:43:25] ZINC19788574.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[12:50:32] Finished Job #24 cpu time used 65.769001
[12:50:32] Starting job 25,CPU time is 1647.635509.
[12:50:32] ZINC19788574.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[12:57:42] Finished Job #25 cpu time used 66.251928
[12:57:42] Starting job 26,CPU time is 1713.887437.
[12:57:42] ZINC19788574.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[13:04:46] Finished Job #26 cpu time used 66.076954
[13:04:46] Starting job 27,CPU time is 1779.964391.
[13:04:46] ZINC19788574.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[13:11:50] Finished Job #27 cpu time used 66.023962
[13:11:50] Starting job 28,CPU time is 1845.988353.
[13:11:50] ZINC19788576.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[13:18:50] Finished Job #28 cpu time used 65.771001
[13:18:50] Starting job 29,CPU time is 1911.759354.
[13:18:50] ZINC19788576.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[13:25:49] Finished Job #29 cpu time used 66.149943
[13:25:49] Starting job 30,CPU time is 1977.909297.
[13:25:49] ZINC19788576.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[13:32:45] Finished Job #30 cpu time used 65.773000
[13:32:45] Starting job 31,CPU time is 2043.682297.
[13:32:45] ZINC19788576.pdbqt size = 26 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[13:39:45] Finished Job #31 cpu time used 65.489044
[13:39:45] Starting job 32,CPU time is 2109.171341.
[13:39:45] ZINC19788580.pdbqt size = 29 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[13:51:32] Finished Job #32 cpu time used 65.495043
[13:51:32] Starting job 33,CPU time is 2174.666384.
[13:51:32] ZINC19788580.pdbqt size = 29 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:03:14] Finished Job #33 cpu time used 66.291922
[14:03:14] Starting job 34,CPU time is 2240.958306.
[14:03:14] ZINC19788580.pdbqt size = 29 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:15:00] Finished Job #34 cpu time used 65.894982
[14:15:00] Starting job 35,CPU time is 2306.853288.
[14:15:00] ZINC19788580.pdbqt size = 29 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:26:42] Finished Job #35 cpu time used 65.821993
[14:26:42] Starting job 36,CPU time is 2372.675281.
[14:26:42] ZINC19788609.pdbqt size = 22 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:31:12] Finished Job #36 cpu time used 65.713010
[14:31:12] Starting job 37,CPU time is 2438.388291.
[14:31:12] ZINC19788609.pdbqt size = 22 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:35:49] Finished Job #37 cpu time used 66.141944
[14:35:49] Starting job 38,CPU time is 2504.530235.
[14:35:49] ZINC19788609.pdbqt size = 22 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:40:21] Finished Job #38 cpu time used 65.699012
[14:40:21] Starting job 39,CPU time is 2570.229247.
[14:40:21] ZINC19788609.pdbqt size = 22 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:44:49] Finished Job #39 cpu time used 66.254927
[14:44:49] Starting job 40,CPU time is 2636.484174.
[14:44:49] ZINC19788635.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:51:03] Finished Job #40 cpu time used 65.849989
[14:51:03] Starting job 41,CPU time is 2702.334163.
[14:51:03] ZINC19788635.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[14:57:16] Finished Job #41 cpu time used 66.072955
[14:57:16] Starting job 42,CPU time is 2768.407118.
[14:57:16] ZINC19788635.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[15:03:31] Finished Job #42 cpu time used 66.196936
[15:03:31] Starting job 43,CPU time is 2834.604054.
[15:03:31] ZINC19788635.pdbqt size = 20 1 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[15:09:50] Finished Job #43 cpu time used 66.222932
[15:09:50] Starting job 44,CPU time is 2900.826986.
[15:09:50] ZINC19788638.pdbqt size = 25 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[15:19:34] Finished Job #44 cpu time used 66.189937
[15:19:34] Starting job 45,CPU time is 2967.016923.
[15:19:34] ZINC19788638.pdbqt size = 25 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[15:29:10] Finished Job #45 cpu time used 65.902981
[15:29:10] Starting job 46,CPU time is 3032.919904.
[15:29:10] ZINC19788638.pdbqt size = 25 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[15:38:46] Finished Job #46 cpu time used 65.473046
[15:38:46] Starting job 47,CPU time is 3098.392950.
[15:38:46] ZINC19788638.pdbqt size = 25 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[15:48:27] Finished Job #47 cpu time used 65.687014
[15:48:27] Starting job 48,CPU time is 3164.079964.
[15:48:27] ZINC19788659.pdbqt size = 31 4 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[15:59:00] Finished Job #48 cpu time used 65.378061
[15:59:00] Starting job 49,CPU time is 3229.458025.
[15:59:00] ZINC19788659.pdbqt size = 31 4 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:09:45] Finished Job #49 cpu time used 66.314918
[16:09:45] Starting job 50,CPU time is 3295.772943.
[16:09:45] ZINC19788659.pdbqt size = 31 4 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:20:23] Finished Job #50 cpu time used 66.057957
[16:20:23] Starting job 51,CPU time is 3361.830900.
[16:20:23] ZINC19788659.pdbqt size = 31 4 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:31:03] Finished Job #51 cpu time used 66.244929
[16:31:03] Starting job 52,CPU time is 3428.075829.
[16:31:03] ZINC19788664.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:35:40] Finished Job #52 cpu time used 65.616024
[16:35:40] Starting job 53,CPU time is 3493.691853.
[16:35:40] ZINC19788664.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:40:14] Finished Job #53 cpu time used 66.101950
[16:40:14] Starting job 54,CPU time is 3559.793803.
[16:40:14] ZINC19788664.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:44:46] Finished Job #54 cpu time used 65.596027
[16:44:46] Starting job 55,CPU time is 3625.389830.
[16:44:46] ZINC19788664.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:49:18] Finished Job #55 cpu time used 66.018963
[16:49:18] Starting job 56,CPU time is 3691.408793.
[16:49:18] ZINC19788666.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:53:54] Finished Job #56 cpu time used 66.221932
[16:53:54] Starting job 57,CPU time is 3757.630725.
[16:53:54] ZINC19788666.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[16:58:28] Finished Job #57 cpu time used 65.582030
[16:58:28] Starting job 58,CPU time is 3823.212755.
[16:58:28] ZINC19788666.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[17:03:01] Finished Job #58 cpu time used 66.294921
[17:03:01] Starting job 59,CPU time is 3889.507676.
[17:03:01] ZINC19788666.pdbqt size = 21 6 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[17:07:36] Finished Job #59 cpu time used 65.725008
[17:07:36] Starting job 60,CPU time is 3955.232684.
[17:07:36] ZINC19788674.pdbqt size = 28 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[17:16:11] Finished Job #60 cpu time used 65.971970
[17:16:11] Starting job 61,CPU time is 4021.204654.
[17:16:11] ZINC19788674.pdbqt size = 28 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[17:24:43] Finished Job #61 cpu time used 65.749004
[17:24:43] Starting job 62,CPU time is 4086.953658.
[17:24:43] ZINC19788674.pdbqt size = 28 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[17:33:15] Finished Job #62 cpu time used 66.069955
[17:33:15] Starting job 63,CPU time is 4153.023613.
[17:33:15] ZINC19788674.pdbqt size = 28 5 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[17:41:47] Finished Job #63 cpu time used 66.264926
[17:41:47] Starting job 64,CPU time is 4219.288539.
[17:41:47] ZINC19788677.pdbqt size = 34 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[17:53:37] Finished Job #64 cpu time used 65.750004
[17:53:37] Starting job 65,CPU time is 4285.038543.
[17:53:37] ZINC19788677.pdbqt size = 34 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[18:05:28] Finished Job #65 cpu time used 65.340066
[18:05:28] Starting job 66,CPU time is 4350.378609.
[18:05:28] ZINC19788677.pdbqt size = 34 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[18:17:16] Finished Job #66 cpu time used 65.700012
[18:17:16] Starting job 67,CPU time is 4416.078621.
[18:17:16] ZINC19788677.pdbqt size = 34 3 ../../projects/www.worldcommunitygrid.org/dsfl.target_00000008.pdbqt size = 13522 0
[18:29:01] Finished Job #67 cpu time used 65.936976
18:29:01 (1448): called boinc_finish

</stderr_txt>
]]>



Is that what you had in mind?

Thanks.

edit1:
The firewall settings on that machine are exactly the same as the other 2 machines running that version of fedora and BOINC.
There is no AV running on that machine (ClamAV is running on 1 of the others).
The last AVC Denial from SELinux on it was 51 days ago.
----------------------------------------
[Edit 1 times, last edit by Former Member at Sep 11, 2011 12:42:54 AM]
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