README

Sabryr & frodstr
2020-05-04

This project is to create a wrapper for Pmetrics :
Original project: 
https://github.com/LAPKB/Pmetrics
http://www.lapk.org/pmetrics.php

##  For saga.sigma2.no using conda
login to saga.sigma2.no

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#rm -rf Pmetrics_test
git clone https://github.com/Sabryr/Pmetrics_test.git
cd Pmetrics_test

#Install Pmetrics R package from login node, this can not be done 
#on login node 
./pmetrics.sh install

#Edit job-pmetrics.slurm to point to data and set other run parameters
sbatch job-pmetrics.slurm 
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##  For saga.sigma2.no manual test

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#Install Pmetrics R package if not already done 
./pmetrics.sh install


conda deactivate &>/dev/null
conda deactivate &>/dev/null
module restore
module load Anaconda2/2019.03
source /cluster/software/Anaconda2/2019.03/etc/profile.d/conda.sh
conda activate /cluster/work/support/sabryr/conda/pmetrics/R-3.6.0
export LD_LIBRARY_PATH=/cluster/work/support/sabryr/conda/pmetrics/R-3.6.0/lib:/cluster/software/imkl/2018.1.163-iimpi-2018a/mkl/lib/intel64_lin:$LD_LIBRARY_PATH
export R_LIBS=/cluster/projects/nn9997k/sabryr/new_pmetrics/R
Run a test
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./pmetrics.sh 2 110 Examples/src/ex.csv Examples/src/model.txt
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How to clean build on SAGA
rm -rf R

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## For other systems
- Requirements
  - R 3.5.2
  - Fortran compiler
 
The script, pmetrics.sh	when loaunched for the first time will install 
all R librairies and a version of pmetrics.sh from 
https://github.com/Sabryr/Pmetrics branch debug

You can	edit this in the file:

pmetrics.rscript