From 161310a131961fe7cd2fd04e1ccc4e2251c472c2 Mon Sep 17 00:00:00 2001
From: jgugliel <julien.guglielmini@pasteur.fr>
Date: Tue, 6 Jun 2023 14:04:27 +0200
Subject: [PATCH] Added more checks for the sbatch version (scratch folder
existence, number of threads for the main script)
---
wGRR | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/wGRR b/wGRR
index a719527..02c7a5d 100755
--- a/wGRR
+++ b/wGRR
@@ -7,7 +7,7 @@ trap 'rm -rf "$tmp"' EXIT
export LC_ALL=C
SECONDS=0
-readonly VERSION=1.4
+readonly VERSION=1.4.1
bold=$(tput bold)
green=$(tput setaf 2)
@@ -136,7 +136,7 @@ while getopts :fTsji:p:o:t:a:m:l:C:I: option ; do
case $option in
i) PRT="$OPTARG"; if [[ ! -s $PRT ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Fasta file '$PRT' not found or empty (option -i)." ; exit 1 ; fi ;;
p) MMPATH="$OPTARG" ;;
- o) OUT="$OPTARG"; if [[ -f "$OUT".wgrr.final.txt ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "File $OUT.wgrr.final.txt already exists. Change option -o or remove this file and relaunch." ; exit 1 ; fi ;;
+ o) OUT="$OPTARG"; if [[ -f "$OUT".wgrr.final.txt ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "File $OUT.wgrr.final.txt already exists. Change option -o or remove this file and relaunch." ; exit 1 ; elif [[ ${OUT} =~ / ]] ; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "You cannot use a path as a prefix with -o option. Please use a simple string instead." ; exit 1 ; fi ;;
t) THREADS="$OPTARG"; if [[ ! $THREADS =~ ^[0-9]+$ ]]; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Number of threads $THREADS must be an integer (option -t)." ; exit 1 ; fi ;;
a) ARRAYSIZE="$OPTARG"; if [[ ! $ARRAYSIZE =~ ^[0-9]+$ ]]; then if [[ $ARRAYSIZE != "AUTO" ]] ; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "Number of genomes comparisons $ARRAYSIZE must be an integer (option -a)." ; exit 1 ; fi ; fi ;;
l) IDLIST="$OPTARG"; if [[ ! -s ${IDLIST} ]] ; then printf "${bold}${red}%-17s -- %s\n${normal}" "[ERROR]" "File ${IDLIST} not found or empty (option -l)." ; exit 1 ; fi ;;
@@ -180,7 +180,10 @@ if [[ $? -eq 1 ]] ; then
tmp=$(mktemp -d tmp-XXXXXX)
else
if [[ `hostname` == "maestro-"* ]] ; then
- tmp=$(mktemp -p $MYSCRATCH -d tmp-XXXXXXXX)
+ if [[ ! -d ${APPASCRATCH}/${USER} ]] ; then
+ mkdir ${APPASCRATCH}/${USER}
+ fi
+ tmp=$(mktemp -p ${APPASCRATCH}/${USER} -d tmp-XXXXXXXX)
else
tmp=$(mktemp -d tmp-XXXXXXXX)
fi
@@ -198,7 +201,7 @@ fi
# Get system total memory if not in sbatch
TOTALMEM=0
-if [[ $BATCHFLAG==0 ]] ; then
+if [[ $BATCHFLAG == 0 ]] ; then
if [[ $SLURM_JOBID != "" ]] ; then
TOTALMEM=$(sacct -j $SLURM_JOBID -o ReqMem | awk 'NR==3{print $1;exit}' | numfmt --from=iec)
else
@@ -212,6 +215,9 @@ if [[ $BATCHFLAG==0 ]] ; then
fi
fi
fi
+elif [[ $(nproc) -gt 1 ]] ; then
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "You requested $(nproc) threads (sbatch -c $(nproc)) but wGRR main script will use only one in sbatch mode." | tee -a ${OUT}.wgrr.log
+ printf "${bold}${yellow}%-17s -- %s\n${normal}" "[WARNING]" "You should not use the -c option of sbatch when running wGRR this way." | tee -a ${OUT}.wgrr.log
fi
printf "%-17s -- %s\n" "["$(textifyDuration $SECONDS)"]" "wGRR version ${VERSION}" | tee -a ${OUT}.wgrr.log
--
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