Commit 3b9752b9 authored by Georges Kunstler's avatar Georges Kunstler
Browse files

changed location of bash files for run on cluster

parent 42999f9f
......@@ -22,3 +22,4 @@ docs/metadata/sites
GROWTH.MODEL.*
.Rapp.history
wc0.5/
Rscript_temp
### test jags
source('R/analysis/jags.run.R')
run.multiple.model.for.set.one.trait(model.files.jags.Tf.1, run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 200, warmup = 20, chains = 3,
init.TF = TRUE)
t1000 <- system.time(
res <- run.jags(model.files.jags.Tf.1, trait = 'Wood.density', type.filling = 'species',
init.TF = FALSE, cat.TF = FALSE, iter = 200,
warmup = 10, chains = 2,
thin = 1)
)
t1000.4 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.1,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 10000, warmup = 1000,
chains = 3, thin = 10,
init.TF = FALSE))
t1000.8 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.1,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 50000, warmup = 20,
chains = 3, thin = 50,
init.TF = FALSE))
## 50000 obs
run.multiple.model.for.set.one.trait(model.files.jags.Tf.1, run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 100000,
var.sample = 'ecocode.id',
iter = 200, warmup = 20, chains = 3,
init.TF = TRUE)
t10000 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.1,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 100000,
var.sample = 'ecocode.id',
iter = 200,
warmup = 10, chains = 2,
thin = 5,
init.TF = FALSE))
t10000.4 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.1,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 10000, warmup = 1000,
chains = 3, thin = 10,
init.TF = FALSE))
t10000.8 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.1,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 100000,
var.sample = 'ecocode.id',
iter = 50000, warmup = 20,
chains = 3, thin = 50,
init.TF = FALSE))
sample.vec <- c(5000, 10000, 50000)
t <- c(t1000['elapsed'], t1000.4['elapsed'], t1000.8['elapsed'])
t2 <- c(t10000['elapsed'], t10000.4['elapsed'], t10000.8['elapsed'])
pdf('time.jags.pdf')
plot(sample.vec, t, ylim = range(t, t2), type = 'b')
lines(sample.vec, t2, type = 'b', col = 'green')
dev.off()
###
run.multiple.model.for.set.one.trait(model.files.jags.Tf.2, run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 200, warmup = 20, chains = 3,
init.TF = TRUE)
t1000 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.2,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 5000,
warmup = 500, chains = 3,
thin = 5,
init.TF = FALSE))
t1000.4 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.2,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 10000, warmup = 1000,
chains = 3, thin = 10,
init.TF = FALSE))
t1000.8 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.2,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 50000, warmup = 20,
chains = 3, thin = 50,
init.TF = FALSE))
## 50000 obs
run.multiple.model.for.set.one.trait(model.files.jags.Tf.2, run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 100000,
var.sample = 'ecocode.id',
iter = 200, warmup = 20, chains = 3,
init.TF = TRUE)
t10000 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.2,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 100000,
var.sample = 'ecocode.id',
iter = 5000,
warmup = 500, chains = 3,
thin = 5,
init.TF = FALSE))
t10000.4 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.2,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 10000,
var.sample = 'ecocode.id',
iter = 10000, warmup = 1000,
chains = 3, thin = 10,
init.TF = FALSE))
t10000.8 <- system.time(
res <- run.multiple.model.for.set.one.trait(model.files.jags.Tf.2,
run.jags,
trait = 'Wood.density',
type.filling='species',
sample.size = 100000,
var.sample = 'ecocode.id',
iter = 50000, warmup = 20,
chains = 3, thin = 50,
init.TF = FALSE))
sample.vec <- c(5000, 10000, 50000)
t <- c(t1000['elapsed'], t1000.4['elapsed'], t1000.8['elapsed'])
t2 <- c(t10000['elapsed'], t10000.4['elapsed'], t10000.8['elapsed'])
pdf('time.jags.r.pdf')
plot(sample.vec, t, ylim = range(t, t2), type = 'b')
lines(sample.vec, t2, type = 'b', col = 'green')
dev.off()
###
......@@ -2,21 +2,21 @@
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > trait.workshop/gdata1$trait.sh
qsub trait.workshop/gdata1$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata1$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > Rscript_temp/gdata1$trait.sh
qsub Rscript_temp/gdata1$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata1$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > trait.workshop/gdata2$trait.sh
# qsub trait.workshop/gdata2$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata2$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
# qsub Rscript_temp/gdata2$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata2$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.log.rds');print('done')\"" > trait.workshop/gdata3$trait.sh
qsub trait.workshop/gdata3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata3$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata3$trait.sh
qsub Rscript_temp/gdata3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata3$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.log.rds');print('done')\"" > trait.workshop/gdata4$trait.sh
# qsub trait.workshop/gdata4$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata4$trait" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/gdata4$trait.sh
# qsub Rscript_temp/gdata4$trait.sh -l nodes=1:ppn=1,mem=8gb -N "gdata4$trait" -q opt32G -j oe
done
#!/bin/bash
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > trait.workshop/gdata1$trait.sh
bash trait.workshop/gdata1$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait);print('done')\"" > Rscript_temp/gdata1$trait.sh
bash Rscript_temp/gdata1$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > trait.workshop/gdata2$trait.sh
bash trait.workshop/gdata2$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE);print('done')\"" > Rscript_temp/gdata2$trait.sh
bash Rscript_temp/gdata2$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.csv');print('done')\"" > trait.workshop/gdata3$trait.sh
bash trait.workshop/gdata3$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, fname = 'data.all.csv');print('done')\"" > Rscript_temp/gdata3$trait.sh
bash Rscript_temp/gdata3$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.csv');print('done')\"" > trait.workshop/gdata4$trait.sh
bash trait.workshop/gdata4$trait.sh
echo "Rscript -e \"source('R/analysis/glmer.run.R'); load.and.save.data.for.glmer($trait, cat.TF=TRUE, fname = 'data.all.csv');print('done')\"" > Rscript_temp/gdata4$trait.sh
bash Rscript_temp/gdata4$trait.sh
done
......@@ -2,16 +2,16 @@
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
for trait in "'SLA'" "'Leaf.N'" "'Wood.density'" "'Max.height'" "'Seed.mass'"; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); load.and.save.data.for.lmer($trait);print('done')\"" > trait.workshop/data1$trait.sh
qsub trait.workshop/data1$trait.sh -l nodes=1:ppn=1,mem=8gb -N "data1$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); load.and.save.data.for.lmer($trait);print('done')\"" > Rscript_temp/data1$trait.sh
qsub Rscript_temp/data1$trait.sh -l nodes=1:ppn=1,mem=8gb -N "data1$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); load.and.save.data.for.lmer($trait, fname = 'data.all.log.rds');print('done')\"" > trait.workshop/data3$trait.sh
qsub trait.workshop/data3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "data3$trait" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); load.and.save.data.for.lmer($trait, fname = 'data.all.log.rds');print('done')\"" > Rscript_temp/data3$trait.sh
qsub Rscript_temp/data3$trait.sh -l nodes=1:ppn=1,mem=8gb -N "data3$trait" -q opt32G -j oe
done
......@@ -2,7 +2,7 @@
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
for trait in "SLA" "Leaf.N" "Wood.density" "Max.height" "Seed.mass"; do
......
#!/bin/bash
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
# test parameter
nbargs=$#
......@@ -19,23 +19,23 @@ samplesize=$1
for trait in "'SLA'" "'Wood.density'" "'Max.height'"; do
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(model.files.glmer.Tf.1, run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/glmerspecies1${trait}.sh
# qsub trait.workshop/glmerspecies1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall1${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(model.files.glmer.Tf.1, run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > Rscript_temp/glmerspecies1${trait}.sh
# qsub Rscript_temp/glmerspecies1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.2), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/glmerspecies2${trait}.sh
qsub trait.workshop/glmerspecies2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall2${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.2), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > Rscript_temp/glmerspecies2${trait}.sh
qsub Rscript_temp/glmerspecies2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall2${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.3), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > trait.workshop/glmerspecies3${trait}.sh
# qsub trait.workshop/glmerspecies3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall3${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.3), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id');print('done')\"" > Rscript_temp/glmerspecies3${trait}.sh
# qsub Rscript_temp/glmerspecies3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerall3${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(model.files.glmer.Tf.1, run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/glmerspeciesS1${trait}.sh
# qsub trait.workshop/glmerspeciesS1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS1${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(model.files.glmer.Tf.1, run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > Rscript_temp/glmerspeciesS1${trait}.sh
# qsub Rscript_temp/glmerspeciesS1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.2), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/glmerspeciesS2${trait}.sh
qsub trait.workshop/glmerspeciesS2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS2${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.2), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > Rscript_temp/glmerspeciesS2${trait}.sh
qsub Rscript_temp/glmerspeciesS2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS2${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.3), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > trait.workshop/glmerspeciesS3${trait}.sh
# qsub trait.workshop/glmerspeciesS3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS3${trait}" -q opt32G -j oe
# echo "/usr/local/R/R-3.0.1/bin/Rscript -e \"source('R/analysis/glmer.run.R');run.multiple.model.for.set.one.trait(c(model.files.glmer.Tf.3), run.glmer,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'species.id');print('done')\"" > Rscript_temp/glmerspeciesS3${trait}.sh
# qsub Rscript_temp/glmerspeciesS3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "glmerallS3${trait}" -q opt32G -j oe
......
......@@ -3,7 +3,7 @@
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
iter=50000
warmup=5000
......@@ -24,8 +24,8 @@ samplesize=$1
# "'Wood.density'" "'Max.height'" "'Seed.mass'" "'Leaf.N'"
for trait in "'SLA'" ; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(c(model.files.jags.Tf.0, model.files.jags.Tf.00), run.jags,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id',iter = $iter, warmup = $warmup, chains = 3, thin = $thin, init.TF = FALSE);print('done')\"" > trait.workshop/speciesjags${trait}.sh
qsub trait.workshop/speciesjags${trait}.sh -l nodes=1:ppn=1,mem=16gb -N "jags${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(c(model.files.jags.Tf.0, model.files.jags.Tf.00), run.jags,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id',iter = $iter, warmup = $warmup, chains = 3, thin = $thin, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesjags${trait}.sh
qsub Rscript_temp/speciesjags${trait}.sh -l nodes=1:ppn=1,mem=16gb -N "jags${trait}" -q opt32G -j oe
......
......@@ -3,7 +3,7 @@
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
iter=50000
warmup=5000
......@@ -24,8 +24,8 @@ samplesize=$1
#
for trait in "'SLA'" "'Wood.density'" "'Max.height'" "'Seed.mass'" "'Leaf.N'"; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(c(model.files.jags.Tf.1), run.jags,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id',iter = $iter, warmup = $warmup, chains = 3, thin = $thin, init.TF = TRUE);print('done')\"" > trait.workshop/speciesjags${trait}.sh
qsub trait.workshop/speciesjags${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "jags${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/jags.run.R'); run.multiple.model.for.set.one.trait(c(model.files.jags.Tf.1), run.jags,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode.id',iter = $iter, warmup = $warmup, chains = 3, thin = $thin, init.TF = TRUE);print('done')\"" > Rscript_temp/speciesjags${trait}.sh
qsub Rscript_temp/speciesjags${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "jags${trait}" -q opt32G -j oe
......
......@@ -3,7 +3,7 @@
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
# test parameter
......@@ -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
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 = $samplesize, var.sample = 'ecocode');print('done')\"" > Rscript_temp/species2${trait}.sh
qsub Rscript_temp/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
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,$trait,type.filling='species', sample.size = NA, var.sample = NA);print('done')\"" > Rscript_temp/species2T${trait}.sh
qsub Rscript_temp/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
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-3.1.1/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 = $samplesize, var.sample = 'sp.name');print('done')\"" > Rscript_temp/species2S${trait}.sh
qsub Rscript_temp/species2S${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "lmerall2S${trait}" -q opt32G -j oe
done
......@@ -3,7 +3,7 @@
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
iter=2000
warmup=1000
......@@ -23,14 +23,14 @@ samplesize=$1
# "'Wood.density'" "'Max.height'"
for trait in "'SLA'" ; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = FALSE);print('done')\"" > trait.workshop/speciesstanA1${trait}.sh
qsub trait.workshop/speciesstanA1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
qsub Rscript_temp/speciesstanA1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 2, init.TF = FALSE);print('done')\"" > trait.workshop/speciesstanA2${trait}.sh
qsub trait.workshop/speciesstanA2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA2${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 2, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA2${trait}.sh
qsub Rscript_temp/speciesstanA2${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA2${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 3, init.TF = FALSE);print('done')\"" > trait.workshop/speciesstanA3${trait}.sh
qsub trait.workshop/speciesstanA3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA3${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 3, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA3${trait}.sh
qsub Rscript_temp/speciesstanA3${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA3${trait}" -q opt32G -j oe
done
......@@ -3,7 +3,7 @@
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
iter=200
warmup=50
......@@ -23,8 +23,8 @@ samplesize=$1
# "'Wood.density'" "'Max.height'"
for trait in "'SLA'" ; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = TRUE);print('done')\"" > trait.workshop/speciesstanA1${trait}.sh
qsub trait.workshop/speciesstanA1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = TRUE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
qsub Rscript_temp/speciesstanA1${trait}.sh -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
......
......@@ -3,7 +3,7 @@
# read one variable
export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p trait.workshop
mkdir -p Rscript_temp
iter=100
warmup=20
......
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