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Commit a2bef31c authored by iker_martin's avatar iker_martin
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Major refactor in Checkrun.sh: Added description; Allows limit time for... 

Major refactor in Checkrun.sh: Added description; Allows limit time for launched jobs; Detected errors by the script are now saved at errores.txt so users can see them; Now calls auxiliary scripts for common steps; Other minor changes.
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Exec/CheckRun.sh
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#!/bin/bash
dir="/home/martini/malleability_benchmark/"
cores=20
partition="P1"
# Checks if all the runs in the current working directory performed under a
# Slurm manager have been performed correctly and if some runs can be corrected
# they are launched again
# Parameter 1 - Maximum index of the runs
# Parameter 2 - Amount of repetitions per index/run
# Parameter 3 - Total stages in all runs. #FIXME The amount of stages must be equal across all the runs, must be modified in the future.
# Parameter 4 - Total groups of processes in all runs #FIXME The amount of groups must be equal across all the runs, must be modified in the future.
# Parameter 5 - Maximum valid iteration time across all runs. If an iteration time
# Parameter 1 - Common name of the configuration files
# Parameter 2 - Maximum index of the runs
# Parameter 3 - Amount of repetitions per index/run
# Parameter 4 - Total stages in all runs. #FIXME The amount of stages must be equal across all the runs, must be modified in the future.
# Parameter 5 - Total groups of processes in all runs #FIXME The amount of groups must be equal across all the runs, must be modified in the future.
# Parameter 6 - Maximum valid iteration time across all runs. If an iteration time
# is higher, that particular repetition inside the run is cleaned and
# launched again.
# Parameter 7(Optional) - Maximum amount of time in seconds needed by a single execution. Default value is 0, which indicates infinite time.
# Must be a positive integer.
#====== Do not modify the following values =======
codeDir="Codes/"
execDir="Exec/"
ResultsDir="Results/"
cores=$(bash $dir$execDir/BashScripts/getCores.sh $partition)
maxIndex=$1
totalEjGrupo=$2 #Total de ejecuciones por grupo
total_stages=$3
total_groups=$4
maxTime=$5 #Maximo tiempo que se considera válido
if [ "$#" -lt "6" ]
then
echo "Not enough arguments"
echo "Usage -> bash CheckRun Common_Name maxIndex total_repetitions total_groups total_stages max_iteration_time [limit_time]"
exit -1
fi
common_name=$1
maxIndex=$2
totalEjGrupo=$3 #Total de ejecuciones por grupo
total_stages=$4
total_groups=$5
maxTime=$6 #Maximo tiempo que se considera válido
limit_time=$((0))
if [ $# -ge 7 ] #Max time per execution in seconds
then
limit_time=$(($7*$qty/60+1))
fi
exec_lines_basic=6
iter_lines_basic=3
exec_total_lines=$(($exec_lines_basic+$total_stages+$total_groups))
iter_total_lines=$(($iter_lines_basic+$total_stages*2+1))
exec_remove=$(($exec_lines_basic+$total_stages+$total_groups-1))
iter_remove=$(($iter_lines_basic+$total_stages-1))
iter_remove=$(($iter_lines_basic+$total_stages))
if [ "$#" -lt "5" ]
then
echo "Not enough arguments"
echo "Usage -> bash CheckRun maxIndes total_repetitions total_groups total_stages max_iteration_time"
exit -1
fi
#Check if there are fatal errors during executions
grep -i -e fatal -e error -e abort -e == slurm* > errores2.txt
......@@ -46,13 +58,14 @@ if [ "$qty" -gt "0" ]
then
echo "Found Fatal errors during execution. Aborting"
echo "Read file errors2 to see the errors and in which files"
echo "FAILURE"
exit -2
fi
#Check if the number of output files is correct.
#If the number is not correct is a fatal error and the user
# is informed in which runs the amount does not match, and
# then the scripts exit.
# then the scripts exits.
#The user must figure out what to do with those runs.
qtyG=$(ls R*_Global.out | wc -l)
qtyG=$(($qtyG * 2))
......@@ -75,21 +88,22 @@ else
echo "Files do not match at Run $i -- diff=$diff" >> errores2.txt
fi
done
echo "FAILURE"
exit -1
fi
rm errores2.txt
# Check if there is any negative execution time
# Only invalid IDs are stored
rm -f errores.txt
touch errores.txt
rm -f tmp.txt
touch tmp.txt
exec_ids=($(grep -n "T_total" R*_Global.out | grep - | cut -d '_' -f1 | cut -d 'R' -f2))
exec_line=($(grep -n "T_total" R*_Global.out | grep - | cut -d ':' -f2))
for ((i=${#exec_ids[@]}-1; i>=0; i--))
do
first_line=$((${exec_line[$i]}-$exec_remove))
last_line=$(($first_line+$exec_total_lines-1))
echo "${exec_ids[$i]}:$first_line:$last_line" >> errores.txt
echo "${exec_ids[$i]}:$first_line:$last_line" >> tmp.txt
done
# Check if there is any iter time higher than expected
......@@ -107,25 +121,29 @@ do
first_line=$(($first_line/$iter_total_lines))
first_line=$(($first_line*$exec_total_lines+1))
last_line=$(($first_line+$exec_total_lines-1))
echo "${iter_ids[$i]}:$first_line:$last_line" >> errores.txt
echo "${iter_ids[$i]}:$first_line:$last_line" >> tmp.txt
fi
done
#Clean data from collected erroneous executions
qty=$(wc -l errores.txt | cut -d ' ' -f1)
qty=$(wc -l tmp.txt | cut -d ' ' -f1)
if [ "$qty" -gt 0 ];
then
echo "Se han encontrado errores de ejecución leves. Volviendo a ejecutar"
echo "Found minor execution errors. Executing again. Review file errores.txt."
echo "CHECKRUN -- Found errors" >> errores.txt
while IFS="" read -r lineRun || [ -n "$lineRun" ]
do
#Obtain data of erroneous execution
run=$(echo $lineRun | cut -d ':' -f1)
echo "Run $run had an erroneous execution, cleaning bad data."
echo "Run$run----------------------------------------------" >> errores.txt
#1 - Delete erroneous lines in Global file
first_line=$(echo $lineRun | cut -d ':' -f2)
last_line=$(echo $lineRun | cut -d ':' -f3)
sed -n ''$first_line','$last_line'p' R${run}_Global.out >> errores.txt
sed -i ''$first_line','$last_line'd' R${run}_Global.out
#2 - Translate line numbers to Local files type
......@@ -135,10 +153,12 @@ then
#3 - Delete erroneous lines in Local files
for ((j=0; j<total_groups; j++));
do
sed -n ''$first_line','$last_line'p' R${run}_G${j}* >> errores.txt
sed -i ''$first_line','$last_line'd' R${run}_G${j}*
done
echo "--------------------------------------------------" >> errores.txt
done < errores.txt
done < tmp.txt
fi
#Check if all repetitions for each Run have been executed
......@@ -152,43 +172,24 @@ do
qtyEx=$(grep T_total R"$run"_Global.out | wc -l)
if [ "$qtyEx" -ne "$totalEjGrupo" ];
then
#1 - Obtain config file name and repetitions to perform
diff=$(($totalEjGrupo-$qtyEx))
qty_missing=$(($qty_missing+$diff))
config_file="config$run.ini"
config_file="$common_name$run.ini"
#1 - Obtain maximum number of processes for the run
max_numP=-1
for ((j=0; j<total_groups; j++));
do
resize_info=$(grep "\[resize$j\]" -n $config_file | cut -d ":" -f1)
first_line=$(echo $resize_info | cut -d " " -f1)
last_line=$(echo $resize_info | cut -d " " -f2)
range_lines=$(( last_line - first_line ))
numP=$(head -$last_line $config_file | tail -$range_lines | cut -d ';' -f1 | grep Procs | cut -d '=' -f2)
if [ "$numP" -gt "$max_numP" ];
then
max_numP=$numP
fi
done
#3 - Obtain needed nodes for the number of processes
node_qty=$(($max_numP / $cores))
if [ "$node_qty" -eq "0" ];
then
node_qty=1
fi
#2 - Obtain number of nodes needed
node_qty=$(bash $dir$execDir/BashScripts/getMaxNodesNeeded.sh $config_file $cores)
#3 - Launch execution
echo "Run$run lacks $diff repetitions"
use_extrae=0
sbatch -N $node_qty $dir$execDir./generalRun.sh $dir $config_file $use_extrae $run $diff
sbatch -p $partition -N $node_qty -t $limit_time $dir$execDir./generalRun.sh $dir $cores $config_file $use_extrae $run $diff
fi
else
echo "File R${run}_Global.out does not exist -- Could it be it must still be executed?"
fi
done
if [ "$qty_missing" -eq "0" ];
then
echo "SUCCESS"
......
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