Add simple functionality check of lmod modules
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check_lmod_modules.sh
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171
check_lmod_modules.sh
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#!/bin/bash -l
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#
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# Copyright (c) 2022 Christoph Niethammer <niethammer@hlrs.de>
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#
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# Script checking an lmod based module environment for problems during module loading/unloading
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#
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function print_usage() {
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echo "Script checking the module environment for problems during module loading/unloading"
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echo "usage: $0 [MODULE_PATTERN] [--exclude PATTERN]"
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}
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# Command line options:
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declare -a modulespecs # check only subset of modules
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declare -a exclude_pattern # exclude modules with given pattern, e.g. nightly builds
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while [[ $# -gt 0 ]]
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do
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key="$1"
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case $key in
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--exclude-pattern|--exclude)
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exclude_patterns+=($2)
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shift 2
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;;
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-h|--help)
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print_usage
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exit 0
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;;
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*)
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modulespecs+=($1)
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shift
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;;
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esac
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done
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# definitions for color output if outputting to tty
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if [ -t 1 ] ; then
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Color_Off='\e[0m' # Text Reset
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IGreen='\e[0;92m' # Intense Green
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IRed='\e[0;91m' # Intense Red
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IMagenta='\e[0;95m' # magenta
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fi
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# intermediate files, logfiles
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LOGDIR=${LOGDIR:=$PWD}
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tmpdir=/tmp/check_modules-$USER
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mkdir -p $tmpdir
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logfile="$LOGDIR/check_modules.log" # logfile with detailed information
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module_load_logfile="$tmpdir/.module_load.log" # output of 'module load commands
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module_rm_logfile="$tmpdir/.module_rm.log" # output of 'module rm' commands
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module_clean_env_file="$tmpdir/.module_clean_env" # original environment
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# safe the original environment
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set > $module_clean_env_file
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module save check_modules
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# list of all failed modules
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failed_modules=()
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echo "--------------------" | tee $logfile
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echo "Module environment check" | tee -a $logfile
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echo "--------------------" | tee -a $logfile
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echo "Date: $(date)" | tee -a $logfile
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echo "Host: $(/bin/hostname)" | tee -a $logfile
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echo "USER: $USER" | tee -a $logfile
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echo "Logfile: $logfile" | tee -a $logfile
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echo "--------------------" | tee -a $logfile
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echo Modulespecs: ${modulespecs[@]} | tee -a $logfile
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echo Exclude: ${exclude_patterns[@]} | tee -a $logfile
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echo "--------------------" | tee -a $logfile
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echo "Environment:" >> $logfile
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cat $module_clean_env_file >> $logfile
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echo "--------------------" >> $logfile
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for modulespec in ${modulespecs[@]}
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do
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for m_original in $(module -t spider $modulespec 2>&1); do
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match=0
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for exclude_pattern in ${exclude_patterns[@]}
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do
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if [[ "$m_original" =~ "$exclude_pattern" ]]; then
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echo -e "Skipping $m_original (matches $exclude_pattern) ... ${IMagenta} skipped${Color_Off}"
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match=1
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continue
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fi
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done
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if [ $match == 1 ]; then
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continue
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fi
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if [[ $m_original =~ ^[A-Za-z] ]]; then # skip any non module line in output
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m=$(echo $m_original | sed -e 's/(.*)//') # Remove aliases e.g. (default)
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echo "Checking $m_original ... "
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echo "Checking $m_original ... " >> $logfile
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readarray deps < <( module spider $m_original |& grep '^ ')
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for dep in "${deps[@]}" ; do
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dep=${dep//[$'\t\r\n']}
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echo -n "... with deps $dep ..."
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echo "... with deps $dep ..." >> $logfile
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module load $dep >>$logfile 2>&1
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cmd="module load $m"
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echo $cmd >> $logfile
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$cmd > $module_load_logfile 2>&1
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cat $module_load_logfile >> $logfile
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module li >>$logfile 2>&1
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# check if module was loaded and did not report errors during loading
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if module -t li 2>&1 | grep $m >/dev/null && ! grep ERROR $module_load_logfile >/dev/null ; then
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cmd="module rm $m"
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echo $cmd >> $logfile
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$cmd > $module_rm_logfile 2>&1
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cat $module_rm_logfile >> $logfile
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module li >>$logfile 2>&1
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# check if module was unloaded
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if module -t li 2>&1 | grep $m > /dev/null; then
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echo -e "${IRed}unloading failed${Color_Off}"
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echo "ERROR: unloading module '$m' failed" >> $logfile
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failed_modules=(${failed_modules[@]} "$m_original [$dep]")
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else
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echo -e "${IGreen}success${Color_Off}"
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echo "SUCCESS" >> $logfile
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fi
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else
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echo -e "${IRed}loading failed${Color_Off}"
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echo "ERROR: loading module '$m' failed" >> $logfile
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failed_modules=(${failed_modules[@]} "$m [$dep]")
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fi
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module unload $dep >>$logfile 2>&1
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# clean up module environment
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cmd="module purge"
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echo $cmd >> $logfile
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$cmd >>$logfile 2>&1
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module li >>$logfile 2>&1
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echo "Resetting environment ..." >>$logfile
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# Reset the complete environment manually to overcome problems with
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# inconsistent internal caches of the module command after module purge.
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#source $module_clean_env_file 2>/dev/null
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module restore check_modules 2>/dev/null
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# clean up intermediate files
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rm -f $module_load_logfile
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rm -f $module_rm_logfile
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echo >>$logfile 2>&1
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done
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fi
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done
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done
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# clean up file storing the initial environment
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rm -f $module_clean_env_file
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rm -rf $tmpdir
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echo "----------------------------------------"
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echo "Summary of failed modules (${#failed_modules[@]}):"
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echo "----------------------------------------"
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for m in ${failed_modules[@]}; do
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echo "$m"
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done
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echo "----------------------------------------"
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