Commit 42999f9f authored by Georges Kunstler's avatar Georges Kunstler
Browse files

clean to git on cluster

parent af84e86f
load.model <- function () {
list(name="lmer.LOGLIN.ER.AD.Tf.fixed.biomes.species",
var.BLUP = 'biomes.id',
lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+biomes.id+Tf+Tf:biomes.id+logD+sumBn+sumBn:biomes.id+sumTfBn+sumTfBn:biomes.id+sumTnBn+sumTnBn:biomes.id+sumTnTfBn.abs+sumTnTfBn.abs:biomes.id+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)))
lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+biomes.id+Tf+Tf:biomes.id+logD+sumBn+sumBn:biomes.id+sumTfBn+sumTfBn:biomes.id+sumTnBn+sumTnBn:biomes.id+sumTnTfBn.abs+sumTnTfBn.abs:biomes.id+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)"))
}
load.model <- function () {
list(name="lmer.LOGLIN.ER.AD.Tf.fixed.species",
var.BLUP = 'biomes.id',
lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+logD+sumBn+sumTfBn+sumTnBn+sumTnTfBn.abs+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)))
lmer.formula.tree.id=formula("logG~1+(1|set.id)+(1|species.id)+(1|plot.id)+Tf+logD+sumBn+sumTfBn+sumTnBn+sumTnTfBn.abs+(1|species.id) +(logD-1|species.id) +(sumBn-1|species.id)"))
}
#!/bin/sh
# Georges Kunstler
# 12/08/2013
# commande de soumission de jobs sur le cluster via qsub
# incremente par un numero d'ordre du fichier de donnees
# lancement ./jobJAGS.sh debut fin racineR subdir
# ou
# debut est l'indice du premier fichier à traiter
# fin est l'indice du dernier fichier à traiter
# racineR est le début du nom du fichier R
# subdir est la subdirectory ou run R
# les fichiers à traiter seront de la forme racine.Z.R
# ou Z est compris entre debut et fin
# test d'absence de parametre
nbargs=$#
echo "nombre d'arguments="$nbargs
if [ $nbargs -eq 0 ]
then
echo " il manque des parametres de lancement il en faut 4"
echo " usage :"
echo " ./jobJAGS.sh 1 5 racineR subdir"
exit 100
else
if [ $nbargs -lt 3 ]
then
echo " il faut 4 parametres indice de debut, indice de fin et la racine R"
echo " usage :"
echo " ./jobJAGS.sh 3 8 racineR subdir"
exit 100
fi
fi
# initialisation
# echo "lancer "$1" jobs"
JOB=R
REP=/data1/kunstler/workshop/
EXP=export
LD=LD_LIBRARY_PATH=/usr/lib64/R/library
NAME=Rcran
# boucle
min=$1
max=$2
for n in `seq $min $max`; do
# constitution du nom du fichier de donnees
DATA=$3$n.R
cd workshop
#ls
echo " $EXP $LD ; $JOB CMD BATCH $DATA"
echo " $EXP $LD ; $JOB CMD BATCH $DATA" |qsub -l nodes=1:ppn=1 -N "$NAME$n" -q opt32G -j oe
cd /data1/kunstler/
#echo " n vaut="$n
done
......@@ -22,13 +22,13 @@ samplesize=$1
#
for trait in "'SLA'" "'Wood.density'" "'Max.height'" "'Seed.mass'" "'Leaf.N'"; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1,model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode');print('done')\"" > trait.workshop/species2${trait}.sh
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode');print('done')\"" > trait.workshop/species2${trait}.sh
qsub trait.workshop/species2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1,model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = NA, var.sample = NA);print('done')\"" > trait.workshop/species2T${trait}.sh
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = NA, var.sample = NA);print('done')\"" > trait.workshop/species2T${trait}.sh
qsub trait.workshop/species2T${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2T${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'sp.name');print('done')\"" > trait.workshop/species2S${trait}.sh
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'sp.name');print('done')\"" > trait.workshop/species2S${trait}.sh
qsub trait.workshop/species2S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2S${trait}" -q opt32G -j oe
done
#!/bin/bash
# Georges Kunstler 14/05/2014
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
# "'Seed.mass'" "'Leaf.N'"
for trait in "'SLA'" "'Wood.density'" "'Max.height'"; do
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1,model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/species1${trait}.sh
# qsub trait.workshop/species1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall1${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.3,model.files.lmer.Tf.4), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/species2${trait}.sh
# qsub trait.workshop/species2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.5, run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/species3${trait}.sh
# qsub trait.workshop/species3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall3${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.1, model.files.lmer.Tf.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/species1S${trait}.sh
# qsub trait.workshop/species1S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall1S${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.3, model.files.lmer.Tf.4), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/species2S${trait}.sh
# qsub trait.workshop/species2S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2S${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.5, run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/speciesS3${trait}.sh
# qsub trait.workshop/speciesS3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerallS3${trait}" -q opt32G -j oe
# CAT model
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.CAT.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id', cat.TF = TRUE);print('done')\"" > trait.workshop/speciesCAT1${trait}.sh
qsub trait.workshop/speciesCAT1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerallCAT1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(c(model.files.lmer.Tf.CAT.2), run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id', cat.TF = TRUE);print('done')\"" > trait.workshop/speciesCATS1${trait}.sh
qsub trait.workshop/speciesCATS1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerallCATS1${trait}" -q opt32G -j oe
done
#!/bin/bash
# Georges Kunstler 14/05/2014
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
# test parameter
nbargs=$#
echo "number of arguments="$nbargs
if [ $nbargs -ne 1 ]
then
echo "need one and only one argument"
echo " usage :"
echo " ./launch_all_lmer.sh sample.size"
exit 100
fi
samplesize=$1
# "'Seed.mass'" "'Leaf.N'"
for trait in "'SLA'" "'Wood.density'" "'Max.height'"; do
for biome in "'Temperate rain forest'" "'Temperate grassland desert'" "'Tropical rain forest'" "'Tropical forest savanna'" "'Boreal forest'" "'Woodland shrubland'" "'Temperate forest'"; do
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.1, run.lmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id', select.biome = $biome);print('done')\"" > trait.workshop/species1${trait}_"${biome}".sh
qsub trait.workshop/species1${trait}_"${biome}".sh -l nodes=1:ppn=1,mem=8gb -N "lmerall1${trait}" -q opt32G -j oe
done
done
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