Commit a1ea35f2 authored by kunstler's avatar kunstler
Browse files

launch stan

parent 8c493678
......@@ -22,26 +22,35 @@ samplesize=$1
# "'Seed.mass'" "'Leaf.N'"
for trait in "'SLA'" "'Wood.density'" "'Max.height'" ; do
# ALL data
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allf${trait}.sh
# biomes data
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$trait, sample.size = $samplesize, var.sample = 'biomes');print('done')\"" > Rscript_temp/allf${trait}.sh
qsub Rscript_temp/allf${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f${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(model.files.lmer.Tf.3[2], run.lmer,$trait);print('done')\"" > Rscript_temp/allf2${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(model.files.lmer.Tf.3[2], run.lmer,$trait, sample.size = $samplesize, var.sample = 'biomes');print('done')\"" > Rscript_temp/allf2${trait}.sh
qsub Rscript_temp/allf2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.fb${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(model.files.lmer.Tf.3[3], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allf3${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(model.files.lmer.Tf.3[3], merge.biomes.TF = TRUE, run.lmer,$trait, sample.size = $samplesize, var.sample = 'biomes');print('done')\"" > Rscript_temp/allf3${trait}.sh
qsub Rscript_temp/allf3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.fb2${trait}" -q opt32G -j oe
# ALL data All census
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.4[1], run.lmer,$trait, select.one.census = FALSE);print('done')\"" > Rscript_temp/allcensus${trait}.sh
qsub Rscript_temp/allcensus${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.census${trait}" -q opt32G -j oe
# # ALL data
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.3[1], run.lmer,$trait);print('done')\"" > Rscript_temp/allf${trait}.sh
# qsub Rscript_temp/allf${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.f${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(model.files.lmer.Tf.3[2], run.lmer,$trait);print('done')\"" > Rscript_temp/allf2${trait}.sh
# qsub Rscript_temp/allf2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.fb${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(model.files.lmer.Tf.3[3], merge.biomes.TF = TRUE, run.lmer,$trait);print('done')\"" > Rscript_temp/allf3${trait}.sh
# qsub Rscript_temp/allf3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.fb2${trait}" -q opt32G -j oe
# # ALL data All census
# echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/lmer.run.R'); run.multiple.model.for.set.one.trait(model.files.lmer.Tf.4[1], run.lmer,$trait, select.one.census = FALSE);print('done')\"" > Rscript_temp/allcensus${trait}.sh
# qsub Rscript_temp/allcensus${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.census${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(model.files.lmer.Tf.4[2], run.lmer,$trait, select.one.census = FALSE);print('done')\"" > Rscript_temp/allcensus2${trait}.sh
qsub Rscript_temp/allcensus2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.censusb${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(model.files.lmer.Tf.4[2], run.lmer,$trait, select.one.census = FALSE);print('done')\"" > Rscript_temp/allcensus2${trait}.sh
# qsub Rscript_temp/allcensus2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.censusb${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(model.files.lmer.Tf.4[3], merge.biomes.TF = TRUE, run.lmer,$trait,select.one.census = FALSE);print('done')\"" > Rscript_temp/allcensus3${trait}.sh
qsub Rscript_temp/allcensus3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.censusb2${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(model.files.lmer.Tf.4[3], merge.biomes.TF = TRUE, run.lmer,$trait,select.one.census = FALSE);print('done')\"" > Rscript_temp/allcensus3${trait}.sh
# qsub Rscript_temp/allcensus3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "lmerall2all.censusb2${trait}" -q opt32G -j oe
......
......@@ -23,14 +23,15 @@ 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 = $warmup, chains = 1, chain_id = 1, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
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.2[3], run.stan,$trait,type.filling='species', sample.size = NA,iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = FALSE, merge.biomes.TF = TRUE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
qsub Rscript_temp/speciesstanA1${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA1${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 = $warmup, chains = 1, chain_id = 2, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA2${trait}.sh
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.2[3], run.stan,$trait,type.filling='species', sample.size = NA,iter = $iter, warmup = $warmup, chains = 1, chain_id = 2, init.TF = FALSE, merge.biomes.TF = TRUE);print('done')\"" > Rscript_temp/speciesstanA2${trait}.sh
qsub Rscript_temp/speciesstanA2${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA2${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 = $warmup, chains = 1, chain_id = 3, init.TF = FALSE);print('done')\"" > Rscript_temp/speciesstanA3${trait}.sh
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.2[3], run.stan,$trait,type.filling='species', sample.size = NA,iter = $iter, warmup = $warmup, chains = 1, chain_id = 3, init.TF = FALSE, merge.biomes.TF = TRUE);print('done')\"" > Rscript_temp/speciesstanA3${trait}.sh
qsub Rscript_temp/speciesstanA3${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA3${trait}" -q opt32G -j oe
done
......@@ -5,8 +5,8 @@ export LD_LIBRARY_PATH=/usr/lib64/R/library
mkdir -p Rscript_temp
iter=200
warmup=50
iter=2000
warmup=500
# test parameter
nbargs=$#
echo "number of arguments="$nbargs
......@@ -20,10 +20,10 @@ fi
samplesize=$1
# "'Wood.density'" "'Max.height'"
for trait in "'SLA'" ; do
#
for trait in "'SLA'" "'Wood.density'" "'Max.height'"; do
echo "/usr/local/R/R-3.1.1/bin/Rscript -e \"source('R/analysis/stan.run.R'); run.multiple.model.for.set.one.trait(model.files.stan.Tf.1, run.stan,$trait,type.filling='species', sample.size = $samplesize, var.sample = 'ecocode',iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = TRUE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
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.2[3], run.stan,$trait,type.filling='species', sample.size = NA, iter = $iter, warmup = $warmup, chains = 1, chain_id = 1, init.TF = TRUE, merge.biomes.TF = TRUE);print('done')\"" > Rscript_temp/speciesstanA1${trait}.sh
qsub Rscript_temp/speciesstanA1${trait}.sh -d ~/trait.competition.workshop -l nodes=1:ppn=1,mem=8gb -N "stanallA1${trait}" -q opt32G -j oe
......
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