Re: [Treebase-devel] Server sluggishness

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That seems reasonable to me.

On Fri, Jun 18, 2010 at 4:49 PM, Jon Auman <jon...@du...> wrote:
> I've noticed a lot of hung queries on the production treebase server over
> the last couple of weeks. The hung queries consume all available memory and
> CPU cycles. I propose that I put timeout limit on queries, so that postgres
> will automatically kill them if they go on to long. I propose 10 minutes.
> Does that seem reasonable?
> FYI. the stuck query is always as follows:
> select matrixcolu0_.MATRIXCOLUMN_ID as MATRIXCO1_26_10_,
> matrixcolu0_.VERSION as
> VERSION26_10_, matrixcolu0_.PHYLOCHAR_ID as PHYLOCHAR3_26_10_,
> matrixcolu0_.MATRIX_ID as MATRIX4_26_10_, matrixcolu0_.STATEFORMAT_ID as
> STATEFOR5_26_10_, phylochar1_.PHYLOCHAR_ID as PHYLOCHAR2_15_0_,
> phylochar1_.VERSION as VERSION15_0_, phylochar1_.Description as
> Descript4_15_0_,
> phylochar1_.LowerLimit as LowerLimit15_0_, phylochar1_.UpperLimit as
> UpperLimit15_0_, phylochar1_.TYPE as TYPE15_0_, characterm2_.MATRIX_ID as
> MATRIX2_6_1_, characterm2_.VERSION as VERSION6_1_, characterm2_.TB_MatrixID
> as
> TB4_6_1_, characterm2_.MATRIXDATATYPE_ID as MATRIXD18_6_1_,
> characterm2_.Description as Descript5_6_1_, characterm2_.GapSymbol as
> GapSymbol6_1_, characterm2_.MATRIXKIND_ID as MATRIXKIND19_6_1_,
> characterm2_.MissingSymbol as MissingS7_6_1_, characterm2_.NexusFileName as
> NexusFil8_6_1_, characterm2_.Published as Published6_1_,
> characterm2_.STUDY_ID
> as STUDY20_6_1_, characterm2_.Symbols as Symbols6_1_,
> characterm2_.TAXONLABELSET_ID as TAXONLA21_6_1_, characterm2_.Title as
> Title6_1_, characterm2_.ANCSTATESET_ID as ANCSTAT22_6_1_,
> characterm2_.CODONPOSITIONSET_ID as CODONPO23_6_1_, characterm2_.CHARSET_ID
> as
> CHARSET24_6_1_, characterm2_.TYPESET_ID as TYPESET25_6_1_,
> characterm2_.CHARWEIGHTSET_ID as CHARWEI26_6_1_, characterm2_.nChar as
> nChar6_1_, characterm2_.nTax as nTax6_1_, characterm2_.Aligned as
> Aligned6_1_,
> characterm2_.CaseSensitive as CaseSen17_6_1_, characterm2_.MATRIXTYPE as
> MATRIXTYPE6_1_, matrixdata3_.MATRIXDATATYPE_ID as MATRIXDA1_27_2_,
> matrixdata3_.VERSION as VERSION27_2_, matrixdata3_.PHYLOCHAR_ID as
> PHYLOCHAR4_27_2_, matrixdata3_.Description as Descript3_27_2_,
> phylochar4_.PHYLOCHAR_ID as PHYLOCHAR2_15_3_, phylochar4_.VERSION as
> VERSION15_3_, phylochar4_.Description as Descript4_15_3_,
> phylochar4_.LowerLimit
> as LowerLimit15_3_, phylochar4_.UpperLimit as UpperLimit15_3_,
> phylochar4_.TYPE
> as TYPE15_3_, ancstatese5_.ANCSTATESET_ID as ANCSTATE1_5_4_,
> ancstatese5_.VERSION as VERSION5_4_, ancstatese5_.Title as Title5_4_,
> codonposit6_.CodonPositionSet_ID as CodonPos1_14_5_, codonposit6_.VERSION as
> VERSION14_5_, codonposit6_.Title as Title14_5_, excludedch7_.CHARSET_ID as
> CHARSET2_9_6_, excludedch7_.VERSION as VERSION9_6_, excludedch7_.MATRIX_ID
> as
> MATRIX5_9_6_, excludedch7_.Title as Title9_6_, characterm8_.MATRIX_ID as
> MATRIX2_6_7_, characterm8_.VERSION as VERSION6_7_, characterm8_.TB_MatrixID
> as
> TB4_6_7_, characterm8_.MATRIXDATATYPE_ID as MATRIXD18_6_7_,
> characterm8_.Description as Descript5_6_7_, characterm8_.GapSymbol as
> GapSymbol6_7_, characterm8_.MATRIXKIND_ID as MATRIXKIND19_6_7_,
> characterm8_.MissingSymbol as MissingS7_6_7_, characterm8_.NexusFileName as
> NexusFil8_6_7_, characterm8_.Published as Published6_7_,
> characterm8_.STUDY_ID
> as STUDY20_6_7_, characterm8_.Symbols as Symbols6_7_,
> characterm8_.TAXONLABELSET_ID as TAXONLA21_6_7_, characterm8_.Title as
> Title6_7_, characterm8_.ANCSTATESET_ID as ANCSTAT22_6_7_,
> characterm8_.CODONPOSITIONSET_ID as CODONPO23_6_7_, characterm8_.CHARSET_ID
> as
> CHARSET24_6_7_, characterm8_.TYPESET_ID as TYPESET25_6_7_,
> characterm8_.CHARWEIGHTSET_ID as CHARWEI26_6_7_, characterm8_.nChar as
> nChar6_7_, characterm8_.nTax as nTax6_7_, characterm8_.Aligned as
> Aligned6_7_,
> characterm8_.CaseSensitive as CaseSen17_6_7_, characterm8_.MATRIXTYPE as
> MATRIXTYPE6_7_, typeset9_.TYPESET_ID as TYPESET1_37_8_, typeset9_.VERSION as
> VERSION37_8_, typeset9_.Title as Title37_8_, charweight10_.CHARWEIGHTSET_ID
> as
> CHARWEIG1_11_9_, charweight10_.VERSION as VERSION11_9_, charweight10_.Title
> as
> Title11_9_ from MATRIXCOLUMN matrixcolu0_ left outer join PHYLOCHAR
> phylochar1_
> on matrixcolu0_.PHYLOCHAR_ID=phylochar1_.PHYLOCHAR_ID left outer join MATRIX
> characterm2_ on matrixcolu0_.MATRIX_ID=characterm2_.MATRIX_ID left outer
> join
> MATRIXDATATYPE matrixdata3_ on
> characterm2_.MATRIXDATATYPE_ID=matrixdata3_.MATRIXDATATYPE_ID left outer
> join
> PHYLOCHAR phylochar4_ on matrixdata3_.PHYLOCHAR_ID=phylochar4_.PHYLOCHAR_ID
> left
> outer join ANCSTATESET ancstatese5_ on
> characterm2_.ANCSTATESET_ID=ancstatese5_.ANCSTATESET_ID left outer join
> CodonPositionSet codonposit6_ on
> characterm2_.CODONPOSITIONSET_ID=codonposit6_.CodonPositionSet_ID left outer
> join CHARSET excludedch7_ on characterm2_.CHARSET_ID=excludedch7_.CHARSET_ID
> left outer join MATRIX characterm8_ on
> excludedch7_.MATRIX_ID=characterm8_.MATRIX_ID left outer join TYPESET
> typeset9_
> on characterm2_.TYPESET_ID=typeset9_.TYPESET_ID left outer join
> CHARWEIGHTSET
> charweight10_ on
> characterm2_.CHARWEIGHTSET_ID=charweight10_.CHARWEIGHTSET_ID
> where matrixcolu0_.MATRIX_ID=$1 and matrixcolu0_.COLUMN_ORDER=$2
> -Jon
>
> -------------------------------------------------------
> Jon Auman
> Systems Administrator
> National Evolutionary Synthesis Center
> Duke University
> http:www.nescent.org
> jon...@ne...
> ------------------------------------------------------
>
>
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-- 
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