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Commit bbfc064f authored by Andreas Hamacher's avatar Andreas Hamacher
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Added listdeps, which output a list softwares that depend on the any given... 

Added listdeps, which output a list softwares that depend on the any given module. Added software_usage, which count the number of occurence for each modules in module logging and sort them in desceding order. Added smoke_test, which is the driver for running test cases under smoke_test/tests folder
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xnat-utils/0.2.1
xnat-utils/0.2.5
xnat-utils/0.2.6
xnat-utils/0.4.5
xnat-utils/0.4.6
xnat-utils/0.4.9
xnat-utils/0.5.3
xnat-utils/0.5.5
xvfb/1.19.3
yade/1.20.0-cpu
yade/1.20.0-gpu
yade/2019-06-20
yade/2019-06-20-cpu
yade/yade-daily-may-2019
yasm/1.2.0-4
yasm/1.3.0
zetastitcher/0.3.3
zlib/1.2.11
zoem/11-166
zoltan/3.83
zopfli/1.0.3
zstd/1.4.0
smoke_test/batch_app_report 0 → 100755
+ 6
− 0
View file @ bbfc064f
#!/bin/bash
inputfile=$1
for app in $(cat $inputfile); do
version=$(ls /usr/local/Modules/modulefiles/$app)
mtime=360 ./application_report $app $version
done
smoke_test/generate_bin_test
+ 25
− 11
View file @ bbfc064f
#!/bin/bash #!/bin/bash
NUM_MODULE=${2:-100} # NUM_MODULE does not necessarily corresponds to the output of `ls -l $TESTCASE_DIR | wc -l` because
# 1. one folder is created for each software but NUM_MODULE pick combinations of from software/version
# 2. if a software does not modify PATH variable then there is no bintest generated for them, the number of those softwares are printed at the end
NUM_MODULE=${1:-100}
TESTCASE_DIR='./tests' TESTCASE_DIR='./tests'
APPLICATION_LIST='./application_list.txt'
USAGE_REPORT=software_usage.txt # USAGE_REPORT=software_usage.txt
if [ ! -f $USAGE_REPORT ]; then # if [ ! -f $USAGE_REPORT ]; then
software_usage $USAGE_REPORT # software_usage $USAGE_REPORT
fi # fi
echo '#!/bin/bash echo '#!/bin/bash
name=$( realpath $0 | xargs dirname | xargs basename ) name=$( realpath $0 | xargs dirname | xargs basename )
ver=${1:-"default"} ver=${1:-"default"}
...@@ -15,7 +18,7 @@ bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p") ...@@ -15,7 +18,7 @@ bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
NAME_EXEC_EXIST=false NAME_EXEC_EXIST=false
for bin in $bin_dirs; do for bin in $bin_dirs; do
for i in $(find $bin -maxdepth 1 -executable -type f ); do for i in $(find $bin -maxdepth 1 -executable -type f ); do
if [[ $(basename $i) == $name ]]; then if [[ $(basename $i) == $name ]]; then
$i --version; $i --version;
exit $? exit $?
fi fi
...@@ -24,17 +27,28 @@ done ...@@ -24,17 +27,28 @@ done
' > $TESTCASE_DIR/bintest ' > $TESTCASE_DIR/bintest
echo "Starting generate bintest for $NUM_MODULE softwares"
declare -i NUM_LIB=0
declare -i GENERATED_NUM=0
IFS_orig=$IFS IFS_orig=$IFS
IFS=$'\n' IFS=$'\n'
for i in $(head -n $NUM_MODULE $USAGE_REPORT); do for i in $(head -n $NUM_MODULE $APPLICATION_LIST); do
m=$(sed -n 's/\(.*\)\/\(.*\) - \(.*\)/\1 \2/p' <<< $i) m=$(sed -n 's/\(.*\)\/\(.*\)/\1 \2/p' <<< $i)
name=$(cut -f1 -d' ' <<< $m) name=$(cut -f1 -d' ' <<< $m)
ver=$(cut -f2 -d' ' <<< $m) ver=$(cut -f2 -d' ' <<< $m)
MODIFED_PATH=$(module show $name/$ver 2>&1 | sed -n 's/.* PATH \(.*\)/\1/p') MODIFIED_PATH=$(module show $name/$ver 2>&1 | sed -n 's/.* PATH \(.*\)/\1/p')
if [ -z ${MODIFIED_PATH+_} ]; then if ! [ -z "${MODIFIED_PATH}" ]; then
mkdir -p $TESTCASE_DIR/$name mkdir -p $TESTCASE_DIR/$name
cp $TESTCASE_DIR/bintest $TESTCASE_DIR/$name/bintest cp $TESTCASE_DIR/bintest $TESTCASE_DIR/$name/bintest
chmod u+x $TESTCASE_DIR/$name/bintest chmod u+x $TESTCASE_DIR/$name/bintest
GENERATED_NUM+=1
else
NUM_LIB+=1
fi fi
done done
IFS=$IFS_orig IFS=$IFS_orig
echo "Successfully generated bintests for $GENERATED_NUM applications"
echo "There are $NUM_LIB libraries (does not modify PATH), no testcases generated for them"
smoke_test/generate_modules_list 0 → 100755
+ 14
− 0
View file @ bbfc064f
#!/bin/bash
TARGET_MODULEPATH="/usr/local/Modules/modulefiles"
OUTPUT_PATH="application_list.txt"
echo "" > $OUTPUT_PATH
MODULEPATH=$TARGET_MODULEPATH module avail -t 2>&1 | python -c "
import sys
with open('$OUTPUT_PATH', 'w') as fout:
for line in sys.stdin:
linelist = line.split('/')
if len(linelist) != 2:
continue
linelist[-1] = linelist[-1].replace('(default)','')
fout.write('/'.join(linelist))
"
\ No newline at end of file
smoke_test/python/avg_install.py 0 → 100755
+ 32
− 0
View file @ bbfc064f
#!/usr/bin/env python3
# run module load python/3.8.5-gcc8-static first
from pathlib import Path
import os
import pandas as pd
import time
import datetime
import collections
import numpy as np
nweek = 12
modulepath = Path('/usr/local/Modules/modulefiles')
softwares = list(modulepath.glob('*/'))
modulefiles = [list(i.glob('**/[!.]*')) for i in softwares if i.is_dir() and os.access(i, os.R_OK)]
lastm = {datetime.datetime.fromtimestamp(j.stat().st_mtime): j for i in modulefiles for j in i}
today = datetime.date.today()
week = datetime.timedelta(weeks=1)
interval = np.array([today - week*i for i in range(nweek+1)][::-1])
def quantize_week(date):
week = interval[:-1][(interval[:-1] <= date) & (date < interval[1:])]
return week.item()
byweek = collections.defaultdict(list)
for k, v in lastm.items():
mod_day = datetime.date(*k.timetuple()[:3])
if mod_day >= interval[0]:
byweek[quantize_week(mod_day)].append(v)
avg_install = np.mean([len(i) for i in byweek.values()])
print(avg_install)
smoke_test/smoke_test
+ 109
− 25
View file @ bbfc064f
#!/bin/bash #!/bin/bash
# each application will create a folder under OUTPUT_DIR # each application will create a folder under OUTPUT_DIR
OUTPUT_DIR=${1:-output_dir} declare -i NUM_MODULE
declare -i DEFAULT_NUM_MODULE
declare -i TIMEOUT
declare -i DEFAULT_TIMEOUT
DEFAULT_OUTPUT_DIR='./output_dir'
DEFAULT_NUM_MODULE=100
DEFAULT_TESTCASE_DIR='./tests'
DEFAULT_TIMEOUT=10
DEFAULT_APPLICATION_LIST='./application_list.txt'
function usage {
echo "Run smoke test"
echo "Usage: $0"
echo " -a <list of applications to test>. This should point to a file with lines of '<name>/<version>', it can be generated using either generate_modules_list or software_usage.default: $DEFAULT_APPLICATION_LIST"
echo " -n <number of modules to test>. Specify a large number to test all softwares, default: $DEFAULT_NUM_MODULE"
echo " -o <output directory>, Output file will be generated at OUTPUT_DIR/report.txt, default: $DEFAULT_OUTPUT_DIR"
echo " -t <testcases directories>.Testcases will be loaded from this directory. default: $DEFAULT_TESTCASE_DIR"
echo " -T <timout period in seconds>, default: $DEFAULT_TIMEOUT"
exit 1
}
while getopts ":n:a:o:t:T:" opt; do
case "$opt" in
a)
APPLICATION_LIST=$OPTARG
;;
o)
OUTPUT_DIR="$OPTARG"
;;
n)
NUM_MODULE=$OPTARG
;;
t)
TESTCASE_DIR=$OPTARG
;;
T)
TIMEOUT=$OPTARG
;;
*)
usage
;;
esac
done
if [ -z $APPLICATION_LIST ]; then
APPLICATION_LIST=$(realpath $DEFAULT_APPLICATION_LIST)
fi
# select top 50 most used module by default if [ -z $OUTPUT_DIR ]; then
NUM_MODULE=${2:-30} OUTPUT_DIR=$(realpath $DEFAULT_OUTPUT_DIR)
fi
if [ -z $NUM_MODULE ]; then
NUM_MODULE=$DEFAULT_NUM_MODULE
fi
if [ -z $TESTCASE_DIR ]; then
TESTCASE_DIR=$(realpath $DEFAULT_TESTCASE_DIR)
fi
if [ -z $TIMEOUT]; then
TIMEOUT=$DEFAULT_TIMEOUT
fi
declare -i TIMELIMIT
BINTEST=true BINTEST=true
TIMELIMIT=10
TESTCASE_DIR=$(realpath './tests')
OUTPUT_DIR=$(realpath $OUTPUT_DIR) REPORT="$OUTPUT_DIR/report.txt"
REPORT=$OUTPUT_DIR/'report.txt' FAILED_MODULE_LOGS="$OUTPUT_DIR/failed_modules.txt"
echo '' > $FAILED_MODULE_LOGS
echo '' > $REPORT
declare -i num_success=0 declare -i num_success=0
declare -i num_failed=0 declare -i num_failed=0
declare -i num_notest=0 declare -i num_notest=0
declare -i minor_error=0 declare -i minor_error=0
function generate_output_directory {
mkdir -p $OUTPUT_DIR
touch $REPORT
echo '' > $REPORT
echo "Test report created at $REPORT"
}
# function generate_software_usage {
# SOFTWARE_USAGE_PATH=software_usage.txt
# if [ ! -f $SOFTWARE_USAGE_PATH ]; then
# ./software_usage $SOFTWARE_USAGE_PATH
# fi
# }
mkdir -p $OUTPUT_DIR
touch $REPORT
echo $REPORT
echo '' > $REPORT
USAGE_REPORT=software_usage.txt
if [ ! -f $USAGE_REPORT ]; then
./software_usage $USAGE_REPORT
fi
declare -a modules
generate_output_directory
IFS_orig=$IFS IFS_orig=$IFS
IFS=$'\n' IFS=$'\n'
for i in $(head -n $NUM_MODULE $USAGE_REPORT); do
m=$(sed -n 's/\(.*\)\/\(.*\) - \(.*\)/\1 \2/p' <<< $i)
for i in $(head -n $NUM_MODULE $APPLICATION_LIST); do
# m=$(sed -n 's/\(.*\)\/\(.*\) - \(.*\)/\1 \2/p' <<< $i)
m=$(sed -n 's/\(.*\)\/\(.*\)/\1 \2/p' <<< $i)
name=$(cut -f1 -d' ' <<< $m) name=$(cut -f1 -d' ' <<< $m)
ver=$(cut -f2 -d' ' <<< $m) ver=$(cut -f2 -d' ' <<< $m)
printf "\n\n=========================\n"
if [ -z $name ]; then
continue
fi
echo "Testing $name/$ver ... "
module purge
module load $name/$ver module load $name/$ver
mkdir -p $OUTPUT_DIR/$name mkdir -p $OUTPUT_DIR/$name
echo '' > $OUTPUT_DIR/$name/$ver echo '' > $OUTPUT_DIR/$name/$ver
if [ ! -d $TESTCASE_DIR/$name ]; then if [ ! -d $TESTCASE_DIR/$name ]; then
echo "No testcase for $m found" | tee -a $REPORT echo "No testcase for $m found" | tee -a $REPORT
num_notest+=1 num_notest+=1
else else
ALL_EXEC=$(find $TESTCASE_DIR/$name -maxdepth 1 -executable -type f) ALL_EXEC=$(find $TESTCASE_DIR/$name -maxdepth 1 -executable -type f)
module_failed=false
for t_case in ${ALL_EXEC}; do for t_case in ${ALL_EXEC}; do
if [ $i == 'bintest' ] && ! $BINTEST;then break;fi if [ $i == 'bintest' ] && ! $BINTEST;then break;fi
orig_dir=$PWD orig_dir=$PWD
cd $(dirname $t_case) # in case the testcase need to compile some source from the directory cd $(dirname $t_case) # in case the testcase need to compile some source from the directory
timeout $TIMELIMIT $t_case $ver &> $OUTPUT_DIR/$name/$ver timeout $TIMEOUT $t_case $ver &> $OUTPUT_DIR/$name/$ver
exitcode=$? exitcode=$?
cd $orig_dir cd $orig_dir
if [ $exitcode -eq 0 ]; then if [ $exitcode -eq 0 ]; then
num_success+=1 num_success+=1
else else
if [ $exitcode -eq 1 ]; then if [ $exitcode -eq 1 ]; then
minor_error+=1 minor_error+=1
else else
num_failed+=1 num_failed+=1
module_failed=true
fi fi
echo "$m return non-zero exitcode $exitcode for testcase $t_case" 2>&1 | tee -a $REPORT echo "$m return non-zero exitcode $exitcode for testcase $t_case" 2>&1 | tee -a $REPORT
fi fi
done done
if $module_failed ; then
echo "$name/$ver failed"
echo "$name/$ver" >> $FAILED_MODULE_LOGS
fi
fi fi
module purge module unload $name/$ver
printf "Done"
done done
IFS=$IFS_orig IFS=$IFS_orig
echo "Summary" 2>&1 | tee -a $REPORT echo "Testcase summary" 2>&1 | tee -a $REPORT
echo "Failed: $num_failed" 2>&1 | tee -a $REPORT echo "Failed: $num_failed" 2>&1 | tee -a $REPORT
echo "Success: $num_success" 2>&1 | tee -a $REPORT echo "Success: $num_success" 2>&1 | tee -a $REPORT
echo "minor error: $minor_error, this is often due to executable not having --version option" 2>&1 | tee -a $REPORT echo "minor error: $minor_error, this is often due to executable not having --version option" 2>&1 | tee -a $REPORT
...@@ -78,5 +163,4 @@ if [ "$num_success" -lt $(( $NUM_MODULE / 2 )) ]; then ...@@ -78,5 +163,4 @@ if [ "$num_success" -lt $(( $NUM_MODULE / 2 )) ]; then
echo "Failing because not enough tests succeeded" 2>&1 | tee -a $REPORT echo "Failing because not enough tests succeeded" 2>&1 | tee -a $REPORT
exit 2 exit 2
fi fi
[ -f TAIR10_chr1.fas ] && rm TAIR10_chr1.fas
[ "$num_failed" -eq "0" ] [ "$num_failed" -eq "0" ]
smoke_test/software_usage.txt 0 → 100644
+ 1201
− 0
View file @ bbfc064f
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