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Commit e18168a2 authored by Julien  GUGLIELMINI's avatar Julien GUGLIELMINI
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small fixes

parent 8e7e191f
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...@@ -12,6 +12,8 @@ readonly VERSION=0.5 ...@@ -12,6 +12,8 @@ readonly VERSION=0.5
bold=$(tput bold) bold=$(tput bold)
normal=$(tput sgr0) normal=$(tput sgr0)
ALL_ARGS=($@)
display_usage() { display_usage() {
echo "wGRR version ${VERSION}" echo "wGRR version ${VERSION}"
echo "${bold}USAGE:${normal} $ZSH_ARGZERO -f <fasta_file> [OPTIONS]" echo "${bold}USAGE:${normal} $ZSH_ARGZERO -f <fasta_file> [OPTIONS]"
...@@ -156,7 +158,7 @@ echo "[INFO] -- wGRR version ${VERSION}" ...@@ -156,7 +158,7 @@ echo "[INFO] -- wGRR version ${VERSION}"
if [[ $BATCHFLAG == 0 ]] ; then if [[ $BATCHFLAG == 0 ]] ; then
echo "[INFO] -- The command is:" echo "[INFO] -- The command is:"
echo "[INFO] -- ./wGRR "$@ echo "[INFO] -- ./wGRR ${ALL_ARGS}"
if [[ $THREADS -gt $(nproc) ]] ; then if [[ $THREADS -gt $(nproc) ]] ; then
echo "[ERROR] -- You required $THREADS threads but your machine has $(nproc) cores." echo "[ERROR] -- You required $THREADS threads but your machine has $(nproc) cores."
...@@ -301,6 +303,7 @@ else ...@@ -301,6 +303,7 @@ else
REQMEM="" REQMEM=""
echo "[INFO] -- Estimating required memory" echo "[INFO] -- Estimating required memory"
M1=$(awk -f wGRR.awk -v MINP=1 -v MAXP=10 -v OUT=$OUT -v MEM=1 $OUT.allpairs.txt $PRT $OUT.m8) M1=$(awk -f wGRR.awk -v MINP=1 -v MAXP=10 -v OUT=$OUT -v MEM=1 $OUT.allpairs.txt $PRT $OUT.m8)
echo $M1
REQMEM=$(bc -l <<< $(numfmt --from=iec $M1)*($ARRAYSIZE/10) | numfmt --to=iec | awk '{U=$0;gsub(/[^A-Za-z]/,"",U);V=$0;gsub(/[A-Za-z]+$/,"",V);split(V,a,".");n=split(a[1],b,"");c=b[1]+1;i=1;while(++i<=n){c=c"0"}print c""U}') REQMEM=$(bc -l <<< $(numfmt --from=iec $M1)*($ARRAYSIZE/10) | numfmt --to=iec | awk '{U=$0;gsub(/[^A-Za-z]/,"",U);V=$0;gsub(/[A-Za-z]+$/,"",V);split(V,a,".");n=split(a[1],b,"");c=b[1]+1;i=1;while(++i<=n){c=c"0"}print c""U}')
echo "[INFO] -- $REQMEM per job required" echo "[INFO] -- $REQMEM per job required"
duration=$SECONDS duration=$SECONDS
......
...@@ -296,6 +296,6 @@ END { ...@@ -296,6 +296,6 @@ END {
} }
} }
if(MEM){ if(MEM){
system("ps -www -o rss=,command= | grep wGRR.awk | grep "OUT" | sort -rn | awk '{print $1;exit}' | numfmt --to=iec" ) system("ps -wo rss,comm | grep wGRR.awk | grep "OUT" | sort -rn | awk '{print $1;exit}' | numfmt --from-unit=1024 --to=iec" )
} }
} }
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