#!/bin/bash
#PBS -A GEO106
#PBS -N Decomp
#PBS -j oe
#PBS -l walltime=02:30:00,nodes=9
##PBS -l walltime=01:00:00,nodes=18
##PBS -l gres=widow2%widow3
##PBS -q killable
##PBS -q debug

#cd /tmp/work/$USER
date

cd $PBS_O_WORKDIR

#LBPM_WIA_INSTALL_DIR=/lustre/atlas/proj-shared/geo106/build-eos-LBPM-WIA

LBPM_WIA_INSTALL_DIR=$PROJWORK/geo106/Eos-LBPM-WIA

#echo "PBS_O_WORKDIR: `echo $PBS_O_WORKDIR`"
source $MODULESHOME/init/bash
module swap PrgEnv-intel PrgEnv-gnu


export LD_LIBRARY_PATH=${CRAY_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH}

  # directory structure should be set up 
  #   directories must include PATTERN within the name (change as needed)
  #   each directory must contain
  #      - Domain.in -- file that specifies parallel domain
  #      - Segmented.in -- file that specifies input file
  #      - 8-bit binary file with the digital geometry
  LIST=$(ls | grep PATTERN)

  # integer labels for the solid phase and the non-wetting phase
  SOLID=0
  NWP=1

  # loop over directories and generate input files for parallel simulation
  # performs domain decomposition based on Domain.in
  # number of processors must match simulation
  NUMPROCS=144
  for i in $LIST; do
     echo $i
     cd $i
     aprun -n $NUMPROCS $LBPM_WIA_INSTALL_DIR/bin/lbpm_segmented_decomp $SOLID $NWP

     mkdir -p MEDIA
     cp ID* MEDIA
     cd ..
  done


exit;