From 1673ca04e902910c82575b62bdf99b2ecb3a4810 Mon Sep 17 00:00:00 2001 From: pvtroshin Date: Mon, 27 Jun 2011 13:29:22 +0000 Subject: [PATCH] remove settings as separate settings no longer required Add separate conf setting for engines and executables for dundee git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4334 e3abac25-378b-4346-85de-24260fe3988d --- dundee-conf/Engine.cluster.properties | 12 +++++ dundee-conf/Engine.local.properties | 7 +++ dundee-conf/Engine.local.sample.properties | 15 ------ dundee-conf/Executable.properties | 77 ++++++++++++++++++++++++---- dundee-conf/settings/ClustalLimits.xml | 18 ------- dundee-conf/settings/MafftLimits.xml | 43 ---------------- dundee-conf/settings/MuscleLimits.xml | 28 ---------- dundee-conf/settings/ProbconsLimits.xml | 13 ----- dundee-conf/settings/TcoffeeLimits.xml | 19 ------- 9 files changed, 87 insertions(+), 145 deletions(-) delete mode 100644 dundee-conf/Engine.local.sample.properties delete mode 100644 dundee-conf/settings/ClustalLimits.xml delete mode 100644 dundee-conf/settings/MafftLimits.xml delete mode 100644 dundee-conf/settings/MuscleLimits.xml delete mode 100644 dundee-conf/settings/ProbconsLimits.xml delete mode 100644 dundee-conf/settings/TcoffeeLimits.xml diff --git a/dundee-conf/Engine.cluster.properties b/dundee-conf/Engine.cluster.properties index 5264236..d75c228 100644 --- a/dundee-conf/Engine.cluster.properties +++ b/dundee-conf/Engine.cluster.properties @@ -7,5 +7,17 @@ engine.cluster.enable=true # Directory to use for temporary files storage # REQUIRED - cluster nodes must have access to this directory! # An absolute path is required + +# Please note that statistic web application will only be able to generate links +# to the job folders if this path is within JABA web application. +# JABAWS statistic application just assume that the last name in the path is the +# application folder in the root of JABAWS web application. cluster.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/jobsout + + +# Enable/disable cluster statistics collector +cluster.stat.collector.enable=true +# Maximum amount of time the job is considered running in hours +# Optional defaults to 7 days (168h) +cluster.stat.maxruntime=24 diff --git a/dundee-conf/Engine.local.properties b/dundee-conf/Engine.local.properties index a0c59d1..d9314c2 100644 --- a/dundee-conf/Engine.local.properties +++ b/dundee-conf/Engine.local.properties @@ -12,3 +12,10 @@ local.tmp.directory=/cluster/gjb_lab/fc/www-jws2/jaba/local_jobsout # OPTIONAL defaults to the number of cores for core number <=4 and # number of cores-1 for greater core numbers engine.local.thread.number=2 + +# Enable/disable cluster statistics collector +local.stat.collector.enable=true + +# Maximum amount of time the job is considered running in hours +# Optional defaults to 24 hours +local.stat.maxruntime=6 \ No newline at end of file diff --git a/dundee-conf/Engine.local.sample.properties b/dundee-conf/Engine.local.sample.properties deleted file mode 100644 index 1486480..0000000 --- a/dundee-conf/Engine.local.sample.properties +++ /dev/null @@ -1,15 +0,0 @@ -### Local Binaries root path ### -# enable or disable engine true | false -# OPTIONAL defaults to true -engine.local.enable=true - -# Directory to use for temporary files storage -# OPTIONAL defaults to java temporary directory -local.tmp.directory=D:\\workspace\\clusterengine\\testoutput - -# Number of threads for tasks execution (valid values between 1 and 2x cpu. -# Where x is a number of cores available in the system) -# OPTIONAL defaults to the number of cores for core number <=4 and -# number of cores -1 for greater core numbers -# TODO -engine.local.thread.number= diff --git a/dundee-conf/Executable.properties b/dundee-conf/Executable.properties index 3368475..caf7355 100644 --- a/dundee-conf/Executable.properties +++ b/dundee-conf/Executable.properties @@ -1,8 +1,8 @@ ### Clustal configuration ### -local.clustalw.bin.windows=binaries/clustalw2.exe +local.clustalw.bin.windows=binaries/windows/clustalw2.exe local.clustalw.bin=binaries/src/clustalw/src/clustalw2 -cluster.clustalw.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/clustalw/src/clustalw2 +cluster.clustalw.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalw/src/clustalw2 # Parameters names which come from RunnerConfig -> Parameters.xml file ultimately are all lowercased in comparison! # see engine.client.Util.getExecProperty() method for details # So they are case insensitive. @@ -13,11 +13,11 @@ clustalw.limits.file=conf/settings/ClustalLimits.xml clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M ### Muscle configuration ### -local.muscle.bin.windows=binaries/muscle.exe +local.muscle.bin.windows=binaries/windows/muscle.exe local.muscle.bin=binaries/src/muscle/muscle # Beware version of muscle on the cluster older and does not support some # of the newer version attributed thus, will not work with Muscle.java wrapper! -cluster.muscle.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/muscle/muscle +cluster.muscle.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/muscle/muscle #The environment variable MUSCLE_MXPATH can be used to specify a path where the matrices are stored # e.g. MUSCLE_MXPATH#binaries/matrices - but need to privide absolute path! muscle.-matrix.path=binaries/matrices @@ -28,21 +28,25 @@ muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M ### Mafft configuration ### #local.mafft.bin.windows= -local.mafft.bin=binaries/src/mafft/binaries/mafft -cluster.mafft.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/mafft/binaries/mafft -mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#/sw/bin/fasta34; +local.mafft.bin=binaries/src/mafft/scripts/mafft +cluster.mafft.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/mafft/scripts/mafft +# These paths will be converted to absolute if relative. +mafft.bin.env=MAFFT_BINARIES#binaries/src/mafft/binaries;FASTA_4_MAFFT#binaries/src/fasta34/fasta34; 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 + ### Tcoffee configuration ### local.tcoffee.bin=binaries/src/tcoffee/t_coffee_source/t_coffee -cluster.tcoffee.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/tcoffee/t_coffee_source/t_coffee +cluster.tcoffee.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/tcoffee/t_coffee_source/t_coffee #/sw/bin/t_coffee # Sub matrix support does not work #tcoffee.-matrix.path=binaries/matrices +# This variable is required by tcoffee +tcoffee.bin.env=HOME_4_TCOFFEE#jobsout; tcoffee.presets.file=conf/settings/TcoffeePresets.xml tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml tcoffee.limits.file=conf/settings/TcoffeeLimits.xml @@ -52,8 +56,63 @@ tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M - ### Probcons configuration ### #local.probcons.bin.windows= local.probcons.bin=binaries/src/probcons/probcons -cluster.probcons.bin=/homes/www-jws2/servers/tomcat-jaba/webapps/jabaws/binaries/src/probcons/probcons +cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/probcons #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 + +### Jronn configuration ### +local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe +local.jronn.bin=/sw/java/latest/bin/java +cluster.jronn.bin=/sw/java/latest/bin/java +jronn.jar.file=binaries/windows/jronn3.1.jar +# jronn.parameters.file=conf/settings/JronnParameters.xml +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 + + +### Disembl configuration Tisean - Disembl dependancy ### +#local.disembl.bin.windows= +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 + +### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### +#local.disembl.bin.windows= +local.globplot.bin=binaries/src/globplot/GlobPlot.py +cluster.globplot.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/globplot/GlobPlot.py +# Dundee only settings +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 + +### IUPred configuration ### +local.iupred.bin.windows=binaries/windows/iupred/iupred.exe +local.iupred.bin=binaries/src/iupred/iupred +# This must point to the directory where iupred binary is, with other files it depends on +#iupred.bin.env=IUPred_PATH#/homes/pvtroshin/workspace/jaba2/binaries/src/iupred +# This path will be converted to absolute if relative. +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 + +### AACon configuration ### +# This is just a path to the standard java executable +local.aacon.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe +local.aacon.bin=/sw/java/latest/bin/java +cluster.aacon.bin=/sw/java/latest/bin/java +# Path to the AACon library +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 diff --git a/dundee-conf/settings/ClustalLimits.xml b/dundee-conf/settings/ClustalLimits.xml deleted file mode 100644 index 28adf27..0000000 --- a/dundee-conf/settings/ClustalLimits.xml +++ /dev/null @@ -1,18 +0,0 @@ - - - compbio.runner.clustal.ClustalW - - Disable gap weighting (Speed-oriented) - 2000 - 1000 - - - 1000 - 1000 - - - # LocalEngineExecutionLimit # - 30 - 500 - - diff --git a/dundee-conf/settings/MafftLimits.xml b/dundee-conf/settings/MafftLimits.xml deleted file mode 100644 index 4cd787f..0000000 --- a/dundee-conf/settings/MafftLimits.xml +++ /dev/null @@ -1,43 +0,0 @@ - - - compbio.runner.mafft.Mafft - - 1000 - 1000 - - - L-INS-i (Accuracy-oriented) - 500 - 1000 - - - G-INS-i (Accuracy-oriented) - 500 - 1000 - - - E-INS-i (Accuracy-oriented) - 500 - 1000 - - - FFT-NS-i (Speed oriented) - 2000 - 1000 - - - FFT-NS-1 (Speed oriented) - 2000 - 1000 - - - NW-NS-PartTree-1 (Speed oriented) - 2000 - 1000 - - - # LocalEngineExecutionLimit # - 20 - 500 - - diff --git a/dundee-conf/settings/MuscleLimits.xml b/dundee-conf/settings/MuscleLimits.xml deleted file mode 100644 index 75d66d9..0000000 --- a/dundee-conf/settings/MuscleLimits.xml +++ /dev/null @@ -1,28 +0,0 @@ - - - compbio.runner.muscle.Muscle - - 1000 - 1000 - - - Protein alignment(Fastest speed) - 2000 - 1000 - - - Nucleotide alignment(Fastest speed) - 1000 - 3000 - - - Huge alignments (speed-oriented) - 2000 - 3000 - - - # LocalEngineExecutionLimit # - 20 - 500 - - diff --git a/dundee-conf/settings/ProbconsLimits.xml b/dundee-conf/settings/ProbconsLimits.xml deleted file mode 100644 index e530fb9..0000000 --- a/dundee-conf/settings/ProbconsLimits.xml +++ /dev/null @@ -1,13 +0,0 @@ - - - compbio.runner.probcons.Probcons - - 1000 - 1000 - - - # LocalEngineExecutionLimit # - 20 - 500 - - diff --git a/dundee-conf/settings/TcoffeeLimits.xml b/dundee-conf/settings/TcoffeeLimits.xml deleted file mode 100644 index 84b3f50..0000000 --- a/dundee-conf/settings/TcoffeeLimits.xml +++ /dev/null @@ -1,19 +0,0 @@ - - - compbio.runner.tcoffee.Tcoffee - - 1000 - 1000 - - - Quick align. Very fast approximate (Speed-oriented) - 1000 - 3000 - - - # LocalEngineExecutionLimit # - 15 - 400 - - - -- 1.7.10.2