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uplinger
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

Jm, can you post the stderr here? The percentage increases could have been because it was in a part of the application that could not allow for updates to fraction complete. Interesting that it was on the full percentages though.

As for length of the work units, these were test ones and BETA estimates are always way off even if I try :( This large set of work units had MANY types of workunits which does not help with sizing either.

Thanks,
-Uplinger
[Feb 26, 2014 5:15:34 PM]   Link   Report threatening or abusive post: please login first  Go to top 
JmBoullier
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

Jm, can you post the stderr here?

Here it is, with its associated Result Status line.

No problem with different WU durations, I was only mentioning them as mere facts in case it could help.
And every time I talk of estimated total durations I mean real-serious-human estimates, not the fancy-ridiculous-childish estimates computed by DrA's "smart" algorithm. laughing

BETA_ BETA_ 9999970_ 0476_ 1-- JmB-6600-Ub64 Pending Validation 26/02/14 05:56:00 26/02/14 10:24:53 1.76 / 1.78 27.4 / 0.0

Result Log

Result Name: BETA_ BETA_ 9999970_ 0476_ 1--
<core_client_version>7.2.7</core_client_version>
<![CDATA[
<stderr_txt>
{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{
A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A
}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}
... *** shortened to keep the post short enough *** ...
ExplicitStartingGeneSignatures = D E

//Starting Gene Signature
//Options are: explicitGeneSignatureSearch, explicitFrequencyRandomSearch,
// randomFixedLengthSearch, randomSearch, sequentialSearch,
StartingGeneSignatureAlgorithm = randomFixedLengthSearch

//For random and random fixed length, explicit frequency search and explicit frequency
//fixed search, define how many starting gene signatures to start with
SearchAlgorithmNumberToCreate = 1

//Only for sequential search, define the starting position
SearchAlgorithmSequentialStartPosition = 304

//Permutation Algorithm
//Permutations can have two sets of groups, in most cases only one is used.
//e.g. A user can define a group to permutate (group A) and another to
//pull from
RunPermutationAlgorithm = 1
PermutationGroups = F
PermutationGroupsForReplacement = F

//Options are:
// insertOneGeneFromGroup, insertOneGeneRandomly, insertEnumerateFromGroup, insertGreedyRandomly
// insertGreedyFromGroup, insertSimulatedAnnealingFromGroup, insertSimulatedAnnealingRandomly,
// deleteOneGeneFromGroup, deleteOneGeneRandomly, deleteEnumerateFromGroup, deleteGreedyRandomly,
// deleteGreedyFromGroup, deleteSimulatedAnnealingFromGroup, deleteSimulatedAnnealingRandomly,
// replaceFromGroupToGroup, replaceFromRandomlyToRandomly, replaceFromRandomlyToRandomlyGreedy,
// replaceFromRandomlyToRandomlySimulatedAnnealing, replaceFromRandomlyToGroup,
// replaceFromRandomlyToGroupGreedy, replaceFromRandomlyToGroupSimulatedAnnealing,
// replaceFromGroupToRandomly, runRandomGreedy, runRandomSimulatedAnnealing,
PermutationAlgorithm = replaceFromRandomlyToRandomlyGreedy

//Number of permutations to run PER starting gene signature
PermutationsNumIterations = 100

//Insert Delete Replace
OptimizationAlgorithmFrequency = 0 0 1

NReps = 10
// VMethod : string (CV) : validation method {LOO - leave-one-out validation, CV - cross-validation, OOB - "out of bag" validation, NFCV - N-fold CV}
//VMethod = LOO
//VMethod = CV
//VMethod = OOB
VMethod = NFCV
ModelType = SVM
SvmArgs = "-v 0 -c 0.1 -t 1 -d 4 -r 1 "
MinFitness = -1
RSeed = 5002
SvmLearnLimit = 250000


[08:00:29] Initializing
[08:00:32] Running
[08:00:32] EvaluateFitnessOfStartingGeneSignatures 1
INFO: WcgLearnLimit(250000) reached. 1.6010120170067239 0.0160643694816827
INFO: WcgLearnLimit(250000) reached. 1.5909506812240579 0.1324036373030140
[08:01:23]: Computing pass 0
INFO: WcgLearnLimit(250000) reached. 1.5079339110216097 0.0285698829095509
INFO: WcgLearnLimit(250000) reached. 1.1835485626907030 0.6990818839840358
INFO: WcgLearnLimit(250000) reached. 0.8788766349289290 0.1662673666291994
INFO: WcgLearnLimit(250000) reached. 1.4006863939043797 0.0877988938518683
INFO: WcgLearnLimit(250000) reached. 0.4338224176754011 0.0129167985287495
INFO: WcgLearnLimit(250000) reached. 0.6009846607630607 0.0057879033774952
INFO: WcgLearnLimit(250000) reached. 0.2737196207199304 0.0114022287671105
INFO: WcgLearnLimit(250000) reached. 1.0603640642002574 0.1034979197465873
INFO: WcgLearnLimit(250000) reached. 1.1720460343385639 0.0010550046654316
INFO: WcgLearnLimit(250000) reached. 1.3743308812772739 0.1167968593135811
INFO: WcgLearnLimit(250000) reached. 1.7652385435966309 0.0127503800875957
INFO: WcgLearnLimit(250000) reached. 0.9359360172466040 0.3751339717327937
INFO: WcgLearnLimit(250000) reached. 0.3036501448068520 0.0191665714664850
INFO: WcgLearnLimit(250000) reached. 1.0222109506030392 0.0010347525658290
INFO: WcgLearnLimit(250000) reached. 1.7414016861339405 0.0443018683508853
INFO: WcgLearnLimit(250000) reached. 0.8973642246473901 0.0173853053292987
INFO: WcgLearnLimit(250000) reached. 1.5364974785948107 0.0109519376383105
INFO: WcgLearnLimit(250000) reached. 0.5750262792498688 0.0351036035860943
INFO: WcgLearnLimit(250000) reached. 0.9373486767144641 0.0120101479024015
INFO: WcgLearnLimit(250000) reached. 0.9285691468685400 0.1785323672447703
INFO: WcgLearnLimit(250000) reached. 0.8684761145668745 0.0032792220790725
INFO: WcgLearnLimit(250000) reached. 1.0832972700536629 0.0446349917638145
INFO: WcgLearnLimit(250000) reached. 0.4655490454961182 0.2820631263075484
INFO: WcgLearnLimit(250000) reached. 0.8652376281752368 0.0027157327876921
INFO: WcgLearnLimit(250000) reached. 0.9315738020886783 0.1641739348415285
INFO: WcgLearnLimit(250000) reached. 0.8212574574081373 0.0553695525231888
INFO: WcgLearnLimit(250000) reached. 1.3728237018003711 0.0055804769763199
INFO: WcgLearnLimit(250000) reached. 1.1718425155213481 0.0624291799199455
INFO: WcgLearnLimit(250000) reached. 1.7197414149086399 0.0657542596636631
INFO: WcgLearnLimit(250000) reached. 0.2918640534680890 0.0315810903048259
INFO: WcgLearnLimit(250000) reached. 0.6203915338192019 0.0160002176053240
INFO: WcgLearnLimit(250000) reached. 0.5821023026037437 0.0687805378966004
INFO: WcgLearnLimit(250000) reached. 0.6509102162090130 0.1411484930795268
INFO: WcgLearnLimit(250000) reached. 1.6337488219592586 0.3804094193473020
... *** shortened to keep the post short enough *** ...
INFO: WcgLearnLimit(250000) reached. 0.8838747420472828 0.1387978458565158
INFO: WcgLearnLimit(250000) reached. 0.9258677862535478 0.0355698852881687
INFO: WcgLearnLimit(250000) reached. 1.5630310083088261 0.0023840340255106
INFO: WcgLearnLimit(250000) reached. 1.7064953066330020 0.0507768284696795
INFO: WcgLearnLimit(250000) reached. 1.2349308277935052 0.2525758724696061
INFO: WcgLearnLimit(250000) reached. 1.3916346945716214 0.0331879766317797
INFO: WcgLearnLimit(250000) reached. 0.4134370873505162 0.0157807744554930
INFO: WcgLearnLimit(250000) reached. 0.8396884894027608 0.0574902915832354
INFO: WcgLearnLimit(250000) reached. 0.9526968732461683 0.0643282959490534
INFO: WcgLearnLimit(250000) reached. 1.0081183659285671 0.0020207185020809
INFO: WcgLearnLimit(250000) reached. 1.5758918940045987 0.1997952868405264
[09:51:09] Exiting PermutateGeneSignature
[09:51:09] Writing final output
[09:51:09] Closing Output Stream
[09:51:09] Cleaning up
Result.out = 19961.000000
Run complete, CPU time: 6319.006078
09:51:09 (21039): called boinc_finish

</stderr_txt>
]]>
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pvh513
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

I received 72 beta WUs, of which 44 have been returned so far. All 44 are still in PV jail. Is validation on hold? I saw that for many WUs two results are in, but validation hasn't happened yet...
[Feb 26, 2014 5:54:59 PM]   Link   Report threatening or abusive post: please login first  Go to top 
LCB001
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

I seem to have a stuck WU here.

Beta_Beta_9999961_0096

CPU time at last checkpoint: 01:47:32
CPU time: 14:12:57
Elapsed time: 14:13:21

stderr;

Commandline = projects/www.worldcommunitygrid.org/wcgrid_beta17_7.29_windows_x86_64 -SettingsFile BETA_9999961_0096.txt -DatabaseFile dataset-GDS2771-v1.txt
Settings File
//Master Settings Template

//Project Details
DateOfDesign = 08052013
Designer = Mike
WorkOrderID = 1426

//Work Unit Parameters
DatasetID = GDS2771-v1
NumberOfGenesInStartingSignature = 15
NumberOfGenesInSignatureMin = 12
NumberOfGenesInSignatureMax = 18

//Frequency/Group Vector for Genes
//UseFrequencyVector = 0
GroupVectorValues = {A}{A}{A}{A D}{A}{A}{A F}{A}{A}{A}{A}{A}{A}{A}{A}{A E}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}

Shortened out to make it easier

{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}{A}
ExplicitStartingGeneSignatures = D E

//Starting Gene Signature
//Options are: explicitGeneSignatureSearch, explicitFrequencyRandomSearch,
// randomFixedLengthSearch, randomSearch, sequentialSearch,
StartingGeneSignatureAlgorithm = explicitGeneSignatureSearch

//For random and random fixed length, explicit frequency search and explicit frequency
//fixed search, define how many starting gene signatures to start with
SearchAlgorithmNumberToCreate = 304

//Only for sequential search, define the starting position
SearchAlgorithmSequentialStartPosition = 304

//Permutation Algorithm
//Permutations can have two sets of groups, in most cases only one is used.
//e.g. A user can define a group to permutate (group A) and another to
//pull from
RunPermutationAlgorithm = 1
PermutationGroups = F
PermutationGroupsForReplacement = F

//Options are:
// insertOneGeneFromGroup, insertOneGeneRandomly, insertEnumerateFromGroup, insertGreedyRandomly
// insertGreedyFromGroup, insertSimulatedAnnealingFromGroup, insertSimulatedAnnealingRandomly,
// deleteOneGeneFromGroup, deleteOneGeneRandomly, deleteEnumerateFromGroup, deleteGreedyRandomly,
// deleteGreedyFromGroup, deleteSimulatedAnnealingFromGroup, deleteSimulatedAnnealingRandomly,
// replaceFromGroupToGroup, replaceFromRandomlyToRandomly, replaceFromRandomlyToRandomlyGreedy,
// replaceFromRandomlyToRandomlySimulatedAnnealing, replaceFromRandomlyToGroup,
// replaceFromRandomlyToGroupGreedy, replaceFromRandomlyToGroupSimulatedAnnealing,
// replaceFromGroupToRandomly, runRandomGreedy, runRandomSimulatedAnnealing,
PermutationAlgorithm = replaceFromRandomlyToRandomlySimulatedAnnealing

//Number of permutations to run PER starting gene signature
PermutationsNumIterations = 304

//Insert Delete Replace
OptimizationAlgorithmFrequency = 0 0 1

NReps = 10
// VMethod : string (CV) : validation method {LOO - leave-one-out validation, CV - cross-validation, OOB - "out of bag" validation, NFCV - N-fold CV}
VMethod = LOO
//VMethod = CV
//VMethod = OOB
//VMethod = NFCV
ModelType = SVM
SvmArgs = "-v 0 -c 0.1 -t 2 -g 0.1 "
MinFitness = -1
RSeed = 4000
SvmLearnLimit = 750000


[22:18:30] Initializing
[22:18:36] Running
[22:18:36] EvaluateFitnessOfStartingGeneSignatures 2
[22:18:45]: Computing pass 0
[22:46:03]: Computing pass 1


It seems to be stuck at pass 1.
The WU is still running if you need more...
----------------------------------------

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JmBoullier
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

LCB001,
What you show looks like what I have reported just before yours.
Are you also seeing round percentages, obviously increasing more slowly?
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LCB001
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

LCB001,
What you show looks like what I have reported just before yours.
Are you also seeing round percentages, obviously increasing more slowly?

Oops, knew I forgot to mention something.

Percentage done is Not incrementing on this one, seems stuck at 88.486% at least for the last couple of hours since I started keeping an eye on it.

If you need anything else just holler...
----------------------------------------

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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

For result name
BETA_ BETA_ 9999965_ 0897_ 0--
I unchecked "leave applications in memory while suspended." and closed the BOINC manager.

When I restarted my Window 7 machine's BOINC manager I waited an hour & exited a second time. Both times the application jumped to 0.500 but then recovered - just like most people are reportiong I thought of this as rugged testing but then I started worrying that perhaps my result would actually confuse the tech and waste his or her time - so I am posting my actions just in case.
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ccandido
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

WU BETA_ BETA_ 9999960_ 0738_ 0--
did not return to normal from the 0.5% progress thing
and did not make any checkpoint
----------------------------------------


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ccandido
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

I received 72 beta WUs, of which 44 have been returned so far. All 44 are still in PV jail. Is validation on hold? I saw that for many WUs two results are in, but validation hasn't happened yet...



Yes, if you read previous messages from uplinger you will see that validation is on hold. You'll have to wait a bit more, as I think it will start to validate today
----------------------------------------


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branjo
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Re: Mapping Cancer Markers Beta Test - Version 7.29 [ Issues Thread ]

No problem so far, shrubbing on Win7 64-bit i7-3770 7.2.39 and Mac OS X 10.9.2 i5-2500S 7.0.65 chicken

Re "0,5% case" after rebooting: it stucks on it regardless on checkpoint for majority of WU's. Even when I rebooted with tasks without checkpoints, they started at 0,5% thinking

Tasks on Mac OS X went to normal percentage muuuuuuch sooner than those on Windoze nerd

Cheers and good luck peace
----------------------------------------

Crunching@Home since January 13 2000. Shrubbing@Home since January 5 2006

----------------------------------------
[Edit 1 times, last edit by branjo at Feb 26, 2014 10:16:04 PM]
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