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

diff --git a/dundee-conf/Executable.properties b/dundee-conf/Executable.properties
index caf7355..5d388db 100644 (file)
--- 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\r
 clustalw.parameters.file=conf/settings/ClustalParameters.xml\r
 clustalw.limits.file=conf/settings/ClustalLimits.xml\r
-clustalw.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+clustalw.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
+\r
+######                 CLUSTAL OMEGA CONFIGURATION                ######\r
+local.clustalo.bin.windows=binaries/windows/clustalo/clustalo.exe\r
+local.clustalo.bin=binaries/src/clustalo/src/clustalo\r
+cluster.clustalo.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/clustalo/src/clustalo\r
+## This parameters specifies the directory where the matrices files are stored   \r
+#clustalo.presets.file=conf/settings/ClustaloPresets.xml\r
+clustalo.parameters.file=conf/settings/ClustaloParameters.xml\r
+clustalo.limits.file=conf/settings/ClustaloLimits.xml\r
+## ClustalO can be executed on multiple CPUs if run on the cluster. \r
+## This parameter specifies the number of CPUs to use\r
+clustalo.cluster.cpunum=4\r
+## This reserves a slot with CPUNUM on the cluster for the task\r
+clustalo.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00  \r
+\r
 \r
 ### Muscle configuration ###\r
 local.muscle.bin.windows=binaries/windows/muscle.exe\r
@@ -24,7 +39,7 @@ muscle.-matrix.path=binaries/matrices
 muscle.presets.file=conf/settings/MusclePresets.xml\r
 muscle.parameters.file=conf/settings/MuscleParameters.xml\r
 muscle.limits.file=conf/settings/MuscleLimits.xml\r
-muscle.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+muscle.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 ### Mafft configuration ###\r
 #local.mafft.bin.windows=\r
@@ -36,7 +51,7 @@ mafft.--aamatrix.path=binaries/matrices
 mafft.presets.file=conf/settings/MafftPresets.xml\r
 mafft.parameters.file=conf/settings/MafftParameters.xml\r
 mafft.limits.file=conf/settings/MafftLimits.xml\r
-mafft.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+mafft.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 \r
 ### Tcoffee configuration ###\r
@@ -51,7 +66,7 @@ tcoffee.presets.file=conf/settings/TcoffeePresets.xml
 tcoffee.parameters.file=conf/settings/TcoffeeParameters.xml\r
 tcoffee.limits.file=conf/settings/TcoffeeLimits.xml\r
 tcoffee.cluster.cpunum=4\r
-tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00  \r
+tcoffee.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=1700M -l h_cpu=24:00:00  \r
 \r
 ### Probcons configuration ###\r
 #local.probcons.bin.windows=\r
@@ -60,7 +75,7 @@ cluster.probcons.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/probcons/prob
 #Probcons does not support matrix loading - unrecognised option reported! \r
 probcons.parameters.file=conf/settings/ProbconsParameters.xml\r
 probcons.limits.file=conf/settings/ProbconsLimits.xml\r
-probcons.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+probcons.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 ### Jronn configuration ### \r
 local.jronn.bin.windows=D:\\Java\\jdk1.6.0_24\\bin\\java.exe \r
@@ -71,7 +86,7 @@ jronn.jar.file=binaries/windows/jronn3.1.jar
 jronn.limits.file=conf/settings/JronnLimits.xml\r
 #TODO jronn.jvm.options=-Xms32M -Xmx512M\r
 jronn.cluster.cpunum=4\r
-jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l h_vmem=1700M -l ram=1700M -l h_cpu=24:00:00\r
+jronn.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=4000M -l h_cpu=24:00:00\r
 \r
 \r
 ### Disembl configuration Tisean - Disembl dependancy ### \r
@@ -80,7 +95,7 @@ local.disembl.bin=binaries/src/disembl/DisEMBL.py
 cluster.disembl.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/disembl/DisEMBL.py\r
 # disembl.parameters.file=conf/settings/DisemblParameters.xml\r
 disembl.limits.file=conf/settings/DisemblLimits.xml\r
-disembl.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+disembl.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 ### GlobPlot configuration Tisean - GlobPlot and Disembl dependancy ### \r
 #local.disembl.bin.windows= \r
@@ -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 \r
 # globplot.parameters.file=conf/settings/GlobPlotParameters.xml\r
 globplot.limits.file=conf/settings/GlobPlotLimits.xml\r
-globplot.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+globplot.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 ### IUPred configuration ### \r
 local.iupred.bin.windows=binaries/windows/iupred/iupred.exe \r
@@ -102,7 +117,7 @@ iupred.bin.env=IUPred_PATH#binaries/src/iupred
 cluster.iupred.bin=/homes/pvtroshin/workspace/jaba2/binaries/src/iupred/iupred\r
 iupred.parameters.file=conf/settings/IUPredParameters.xml\r
 iupred.limits.file=conf/settings/IUPredLimits.xml\r
-iupred.cluster.settings=-l h_cpu=24:00:00 -l h_vmem=6000M -l ram=6000M\r
+iupred.cluster.settings=-l h_cpu=24:00:00 -l ram=6000M\r
 \r
 ### AACon configuration ###\r
 # This is just a path to the standard java executable \r
@@ -114,5 +129,5 @@ aacon.jar.file=binaries/windows/aaconservation.jar
 aacon.parameters.file=conf/settings/AAConParameters.xml\r
 aacon.presets.file=conf/settings/AAConPresets.xml\r
 aacon.limits.file=conf/settings/AAConLimits.xml\r
-#TODO jronn.jvm.options=-Xms32M -Xmx512M\r
 aacon.cluster.cpunum=4\r
+aacon.cluster.settings=-q 64bit-pri.q -pe smp 4 -l ram=4000M -l h_cpu=24:00:00\r