From eed2331a64a7c043792e667e6d7205bcfe88fb89 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Thu, 4 Aug 2011 14:38:34 +0000 Subject: [PATCH] Get rid of v_hmem settings git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4475 e3abac25-378b-4346-85de-24260fe3988d --- dundee-conf/Executable.properties | 35 +++++++++++++++++++++++++---------- 1 file changed, 25 insertions(+), 10 deletions(-) diff --git a/dundee-conf/Executable.properties b/dundee-conf/Executable.properties index caf7355..5d388db 100644 --- a/dundee-conf/Executable.properties +++ b/dundee-conf/Executable.properties @@ -10,7 +10,22 @@ clustalw.-matrix.path=binaries/matrices clustalw.presets.file=conf/settings/ClustalPresets.xml clustalw.parameters.file=conf/settings/ClustalParameters.xml clustalw.limits.file=conf/settings/ClustalLimits.xml -clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +clustalw.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M + +###### CLUSTAL OMEGA CONFIGURATION ###### +local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe +local.clustalo.bin=binaries/src/clustalo/src/clustalo +cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo +## This parameters specifies the directory where the matrices files are stored +#clustalo.presets.file=conf/settings/ClustaloPresets.xml +clustalo.parameters.file=conf/settings/ClustaloParameters.xml +clustalo.limits.file=conf/settings/ClustaloLimits.xml +## ClustalO can be executed on multiple CPUs if run on the cluster. +## This parameter specifies the number of CPUs to use +clustalo.cluster.cpunum=4 +## This reserves a slot with CPUNUM on the cluster for the task +clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 + ### Muscle configuration ### local.muscle.bin.windows=binaries/windows/muscle.exe @@ -24,7 +39,7 @@ muscle.-matrix.path=binaries/matrices muscle.presets.file=conf/settings/MusclePresets.xml muscle.parameters.file=conf/settings/MuscleParameters.xml muscle.limits.file=conf/settings/MuscleLimits.xml -muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +muscle.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M ### Mafft configuration ### #local.mafft.bin.windows= @@ -36,7 +51,7 @@ mafft.--aamatrix.path=binaries/matrices mafft.presets.file=conf/settings/MafftPresets.xml mafft.parameters.file=conf/settings/MafftParameters.xml mafft.limits.file=conf/settings/MafftLimits.xml -mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M ### Tcoffee configuration ### @@ -51,7 +66,7 @@ tcoffee.presets.file=conf/settings/TcoffeePresets.xml tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml tcoffee.limits.file=conf/settings/TcoffeeLimits.xml tcoffee.cluster.cpunum=4 -tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 +tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00 ### Probcons configuration ### #local.probcons.bin.windows= @@ -60,7 +75,7 @@ cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/prob #Probcons does not support matrix loading - unrecognised option reported! probcons.parameters.file=conf/settings/ProbconsParameters.xml probcons.limits.file=conf/settings/ProbconsLimits.xml -probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M ### Jronn configuration ### local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe @@ -71,7 +86,7 @@ jronn.jar.file=binaries/windows/jronn3.1.jar jronn.limits.file=conf/settings/JronnLimits.xml #TODO jronn.jvm.options=-Xms32M -Xmx512M jronn.cluster.cpunum=4 -jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00 +jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=4000M -l h_cpu=24:00:00 ### Disembl configuration Tisean - Disembl dependancy ### @@ -80,7 +95,7 @@ local.disembl.bin=binaries/src/disembl/DisEMBL.py cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py # disembl.parameters.file=conf/settings/DisemblParameters.xml disembl.limits.file=conf/settings/DisemblLimits.xml -disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M ### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### #local.disembl.bin.windows= @@ -90,7 +105,7 @@ cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/Glob globplot.bin.env=PYTHONPATH#/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/biopython-1.50 # globplot.parameters.file=conf/settings/GlobPlotParameters.xml globplot.limits.file=conf/settings/GlobPlotLimits.xml -globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M ### IUPred configuration ### local.iupred.bin.windows=binaries/windows/iupred/iupred.exe @@ -102,7 +117,7 @@ iupred.bin.env=IUPred_PATH#binaries/src/iupred cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred iupred.parameters.file=conf/settings/IUPredParameters.xml iupred.limits.file=conf/settings/IUPredLimits.xml -iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M +iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M ### AACon configuration ### # This is just a path to the standard java executable @@ -114,5 +129,5 @@ aacon.jar.file=binaries/windows/aaconservation.jar aacon.parameters.file=conf/settings/AAConParameters.xml aacon.presets.file=conf/settings/AAConPresets.xml aacon.limits.file=conf/settings/AAConLimits.xml -#TODO jronn.jvm.options=-Xms32M -Xmx512M aacon.cluster.cpunum=4 +aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=4000M -l h_cpu=24:00:00 -- 1.7.10.2