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mwoodbri/covid-sim.pbs.sh Secret

Last active August 6, 2020 13:00
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covid-sim.pbs.sh
#!/bin/bash
#PBS -l walltime=03:00:00,select=1:ncpus=32:mem=62g
source ~/anaconda3/etc/profile.d/conda.sh
# conda create --yes --name covid-sim cmake python=3 r-sp
conda activate covid-sim
git clone --branch v0.14.0 --depth 1 https://github.com/mrc-ide/covid-sim.git
cd covid-sim/data
# https://github.com/mrc-ide/covid-sim/issues/378
export CXXFLAGS="-D__STDC_FORMAT_MACROS"
./run_sample.py United_Kingdom
Rscript ../Rscripts/PlotRuns.R
Rscript ../Rscripts/CompareRuns.R
rsync -a . $EPHEMERAL/${PBS_JOBNAME}.${PBS_JOBID%.pbs}/
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