nievergeltlab
7/25/2017 - 3:47 PM

Use all cores within a node via a loop E.g. Given N jobs, with K cores, run jobs 1-K, wait for all to finish, then run K+1 - N

Use all cores within a node via a loop

E.g. Given N jobs, with K cores, run jobs 1-K, wait for all to finish, then run K+1 - N

loop_cores.sh
content_copyfile_download
ncommands=22
nodesize=6
nodeuse=$(($nodesize ))
totjobs=$(( ($ncommands + $nodeuse - 1 ) / $nodeuse ))


 for i in $(seq 1 1 $totjobs)
 do
  jstart=$((($i-1)*$nodesize +1))
  jstop=$(($i*$nodesize))

  min=$([ $ncommands -le $jstop ] && echo "$ncommands" || echo "$jstop")
  jstop=$min
  for j in $(seq $jstart 1 $jstop)
  do
   fileline=$(cat $genotype_loc | awk -v lineno=$j 'NR==lineno {print}')
   chrom=$(echo $fileline | awk 'BEGIN {FS="_m"} {print $NF}')
   echo "Using $fileline to make PRS for chromosome $chrom"
   $plink2_loc --bfile $fileline --score $weights --q-score-file $threshold --q-score-range $range --out "$output_loc"/"$study"_"$sourcedat"_chr"$chrom"  &  
  done
  wait #wait for jobs to finish before starting next set
 
 done