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kelley |
1.1 |
#/bin/bash
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# ------------------------------------------------------------------------------- #
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# resubmitConfig.sh -- creates a config file to resubmit jobs that failed #
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# #
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# description: This script will search the output dir for the given condor script #
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# and determine which files do not exist. It uses this list of #
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# missing files to create a new sumission script. This script #
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# is the same name as the original script except with an _resubmit #
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# appended to the name #
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# #
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# usage: ./resubmitConfig.sh <condor_script_file> #
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# #
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# <condor_script_file> is the originially submitted condor script #
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# #
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# #
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# ------------------------------------------------------------------------------- #
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# input
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# ------------------------------------------------------------------------------- #
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condor_script_filename=$1
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if [ ! -f "$condor_script_filename" ]; then
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echo "File $condor_script_filename not found. Exiting"
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exit 1
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fi
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# get the arguments lines from the original submission
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# ------------------------------------------------------------------------------- #
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# get the list of args into an array
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index=0
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while read line ; do
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fgolf |
1.2 |
if [ -n "$(echo $line | grep argument)" ]; then
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#arg_list[$index]=$(echo $line | sed s/\"\"/\\\\\"\\\\\"/g) # don't need this anymore?
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arg_list[$index]=$(echo $line)
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index=$(($index+1))
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fi
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done < "${condor_script_filename}"
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kelley |
1.1 |
num_args=${#arg_list[@]}
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# get output path
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fgolf |
1.2 |
output_path=$(echo ${arg_list[0]} | awk '{print $7}' | sed s/\"//g)
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kelley |
1.1 |
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# output files to find -- if found, the index is stored
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for (( i=0; i < $num_args; i++ ));
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do
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fgolf |
1.2 |
input_file=$(echo ${arg_list[$i]} | awk '{print $2}')
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kelley |
1.1 |
file=$(basename ${input_file})
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fgolf |
1.2 |
#echo find $output_path -type f -name $file
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kelley |
1.1 |
if [ ! $(find $output_path -type f -name $file) ]; then
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index_of_missing_files=(${index_of_missing_files[@]} $i)
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fi
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done
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# form the resubmissing script
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# ------------------------------------------------------------------------------- #
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# if there are missing files, create the resubmit script
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num_missing_files=${#index_of_missing_files[@]}
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if [ ${num_missing_files} -gt 0 ]; then
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# same name as originial condor script with _resubmit appended
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condor_resubmit_script_filename=${condor_script_filename%.*}_resubmit.cmd
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echo Missing ${num_missing_files} / ${num_args} files
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echo creating resumit list: $condor_resubmit_script_filename
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# do the same header as original file
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head -n 15 $condor_script_filename > $condor_resubmit_script_filename
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for (( i=0; i < ${num_missing_files}; i++ ));
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do
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cat >> $condor_resubmit_script_filename << EOF
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executable=wrapper.sh
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transfer_executable=True
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${arg_list[${index_of_missing_files[$i]}]}
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queue
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EOF
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done
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else
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echo "No missing files"
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fgolf |
1.2 |
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# create a blank resubmit script
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condor_resubmit_script_filename=${condor_script_filename%.*}_resubmit.cmd
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head -n 15 $condor_script_filename > $condor_resubmit_script_filename
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kelley |
1.1 |
fi
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