smoke_test/generate_bin_test

+#!/bin/bash
+# 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'
+
+APPLICATION_LIST='./application_list.txt'
+# USAGE_REPORT=software_usage.txt
+# if [ ! -f $USAGE_REPORT ]; then
+#     software_usage $USAGE_REPORT
+# fi
+echo '#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+' > $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=$'\n'
+for i in $(head -n $NUM_MODULE $APPLICATION_LIST); do
+    m=$(sed -n 's/\(.*\)\/\(.*\)/\1 \2/p' <<< $i)
+    name=$(cut -f1 -d' ' <<< $m)
+    ver=$(cut -f2 -d' ' <<< $m)
+    MODIFIED_PATH=$(module show $name/$ver 2>&1 | sed -n 's/.* PATH \(.*\)/\1/p')
+    if ! [ -z "${MODIFIED_PATH}" ]; then
+        mkdir -p $TESTCASE_DIR/$name
+        cp $TESTCASE_DIR/bintest $TESTCASE_DIR/$name/bintest
+        chmod u+x $TESTCASE_DIR/$name/bintest
+        GENERATED_NUM+=1
+    else
+        NUM_LIB+=1
+    fi
+
+done
+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

+#!/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/listdeps

+#!/bin/bash
+
+# This script does not detect implicit dependency 
+# For example, if A -> B -> openmpi/1.10.7-mlx, only module B will be detected  
+set -e
+software=$1
+if [ -z $1 ]; then 
+    echo 'please specify target software'
+    echo 'input can be either '
+    echo 'listdeps <name>'
+    echo 'OR'
+    echo 'listdeps <name> <version>'
+    exit 1
+fi
+version=$2
+if [ ! -z ${version} ]; then
+    version=( $version )
+else 
+    version=( $(ls /usr/local/Modules/modulefiles/$software) )
+fi 
+
+mkdir -p $software
+for ver in ${version[@]}; do touch $software/$ver;done
+
+for i in $(ls -d /usr/local/*/); do
+    name=$(basename $i)
+    if [[ -r "/usr/local/Modules/modulefiles/$name" ]]; then
+        vers=$(ls /usr/local/Modules/modulefiles/$name)
+    fi 
+    for ver in ${vers[@]}; do
+        load_ver=$(module show $name/$ver 2>&1 | sed -n "s/module.*load\ ${software}\/\(.*\)/\1/p")
+        if [ ! -z $load_ver ] && [ -f $software/$load_ver ]; then 
+            echo $name/$ver >> $software/$load_ver
+        fi
+    done
+done
+set +e

smoke_test/python/avg_install.py

+#!/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

+#!/bin/bash
+# each application will create a folder under 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
+
+if [ -z $OUTPUT_DIR ]; then
+    OUTPUT_DIR=$(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
+
+BINTEST=true
+
+
+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_failed=0
+declare -i num_notest=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 $SOFTWARE_USAGE_PATH
+#     fi
+# }
+
+
+
+
+generate_output_directory
+
+
+IFS_orig=$IFS
+IFS=$'\n'
+
+
+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' ' <<< $m)
+    ver=$(cut -f2 -d' ' <<< $m)
+    printf "\n\n=========================\n"
+    if [ -z $name ]; then
+        continue
+    fi
+
+    echo "Testing $name/$ver ... "
+
+
+    module purge
+    module load $name/$ver
+    mkdir -p $OUTPUT_DIR/$name
+    echo '' > $OUTPUT_DIR/$name/$ver
+    if [ ! -d $TESTCASE_DIR/$name ]; then
+        echo "No testcase for $m found"  | tee -a $REPORT
+        num_notest+=1
+    else
+        ALL_EXEC=$(find $TESTCASE_DIR/$name -maxdepth 1 -executable -type f)
+        module_failed=false
+        for t_case in ${ALL_EXEC}; do
+            if [ $i ==  'bintest' ] && ! $BINTEST;then break;fi
+            orig_dir=$PWD
+            cd $(dirname $t_case) # in case the testcase need to compile some source from the directory
+            timeout $TIMEOUT $t_case $ver &> $OUTPUT_DIR/$name/$ver
+            exitcode=$?
+            cd $orig_dir
+            if [ $exitcode -eq 0 ]; then
+                num_success+=1
+            else
+                if [ $exitcode -eq 1 ]; then
+                    minor_error+=1
+                else
+                    num_failed+=1
+                    module_failed=true
+                fi
+                echo "$m return non-zero exitcode $exitcode for testcase $t_case" 2>&1 | tee -a $REPORT
+            fi
+        done
+        if $module_failed ; then
+            echo "$name/$ver failed"
+            echo "$name/$ver" >> $FAILED_MODULE_LOGS
+        fi
+    fi
+    module unload $name/$ver
+
+    printf "Done"
+
+done
+IFS=$IFS_orig
+
+echo "Testcase summary" 2>&1 | tee -a $REPORT
+echo "Failed: $num_failed" 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 "Num applications that has no test case: $num_notest" 2>&1 | tee -a $REPORT
+if [ "$num_success" -lt $(( $NUM_MODULE / 2 )) ]; then
+    echo "Failing because not enough tests succeeded" 2>&1 | tee -a $REPORT
+    exit 2
+fi
+[ "$num_failed" -eq "0" ]

smoke_test/software_usage

+#!/bin/bash
+
+# This script will count the number of occurence for all modules in logging and sort the them in desceding order
+timestamp=$(date | sed 's/ /_/g' | sed 's/\:/\_/g' )
+output=${1:-${timestamp}.txt}
+MODULE_LOGGING_PATH=/projects/pMOSP/module_logging
+#MODULE_LOGGING_PATH=/home/luhanc/module_logging
+
+userlist=$(ls -d $MODULE_LOGGING_PATH/*/)
+declare -A modules
+modules=()
+for userpath in $userlist
+do 
+    if [[ -r $userpath ]]
+    then 
+        logfiles=$(ls $userpath/module_log_*)
+        for logfile in $logfiles
+        do 
+            for i in $(cat $logfile | tr ':' '\n')
+            do 
+                (( modules["$i"] ++ ))
+            done
+        done
+    fi
+done
+
+for k in "${!modules[@]}"
+do
+    echo $k ' - ' ${modules["$k"]}
+done |
+sort -rn -k3 > $output

smoke_test/software_usage.txt

+libjpeg-turbo/1.4.2  -  5855
+gcc/5.4.0  -  5723
+virtualgl/2.5.0  -  5586
+tigervnc/1.8.0  -  5061
+openmpi/1.10.7-mlx  -  2368
+gcc/8.1.0  -  2162
+gcc/4.9.3  -  2063
+anaconda/5.1.0-Python3.6-gcc5  -  1635
+openblas/0.2.20  -  1510
+fftw/3.3.5-gcc5  -  1419
+hdf5/1.10.0-patch1  -  1301
+atlas/3.10.2-gcc5  -  1299
+singularity/3.2.1  -  1198
+gcc/6.1.0  -  1181
+fftw/3.3.4-gcc  -  1155
+fftw/3.3.5-gcc  -  1072
+fsl/6.0.3  -  1025
+lapack/3.6.1-gcc5  -  1023
+cuda/7.5  -  1018
+atlas/3.10.2-gcc4  -  936
+geos/3.6  -  912
+python/3.7.3-system  -  889
+lapack/3.6.1-gcc4  -  841
+htslib/1.9-gcc5  -  836
+samtools/1.9-gcc5  -  820
+mpfr/3.1.5  -  785
+gmp/6.1.2  -  780
+picard/2.9.2  -  779
+libtiff/3.9.7  -  774
+fsl/5.0.11  -  771
+gsl/2.2-system  -  740
+deeptools/3.1.2  -  731
+bowtie2/2.2.9  -  710
+gsl/2.2-gcc4  -  709
+python/3.6.6-gcc5  -  705
+cuda/10.1  -  700
+cutadapt/0.16  -  699
+bismark/v0.19.1  -  663
+openmpi/1.10.3-gcc4-mlx-verbs  -  657
+fastqc/0.11.7  -  620
+bedtools/2.26.0  -  608
+htseq/0.10.0  -  601
+htslib/1.9  -  561
+cuda/8.0.61  -  557
+samtools/1.9  -  551
+cuda/9.1  -  540
+anaconda/2019.03-Python3.7-gcc5  -  533
+samtools/1.7  -  516
+wxwidgets/3.0.3  -  507
+python/2.7.12-gcc4  -  502
+matlab/r2018a  -  490
+ctffind/4.1.8  -  471
+cuda/10.0  -  464
+openmpi/1.10.3-gcc5-mlx  -  461
+matlab/r2019b  -  459
+perl/5.28.0  -  456
+cmake/3.5.2-gcc5  -  456
+anaconda/5.0.1-Python2.7-gcc5  -  451
+merantk/1.2.1  -  440
+gsl/2.2-gcc5  -  438
+python/3.6.2  -  433
+libmaus/0.0.196  -  433
+biobambam/0.0.191  -  432
+cmake/3.5.2  -  418
+singularity/3.5.2  -  412
+bcftools/1.8  -  392
+ucsc-genome-tools/201806  -  391
+qt/5.7.1-gcc5  -  386
+python/2.7.15-gcc5  -  383
+R/3.6.0-mkl  -  382
+singularity/3.1.0  -  369
+ants/20190910  -  369
+python/3.7.2-gcc6  -  354
+bwa/0.7.17-gcc5  -  354
+mrtrix/3.0_rc3_latest  -  348
+mesa/default  -  343
+blast/2.7.1  -  338
+boost/1.67.0-gcc5  -  330
+freesurfer/6.0  -  327
+fsl/6.0.1  -  320
+python/3.5.2-gcc4  -  316
+matlab/r2015b  -  315
+gctf/1.06_cuda8  -  300
+mrtrix/3.0_rc3  -  279
+cuda/9.0  -  278
+trim_galore/0.4.5  -  275
+matlab/r2019a  -  275
+freesurfer/devel-20190128  -  269
+spm12/matlab2018a.r7487  -  267
+squashfs-tools/4.3-0.21  -  263
+cufflinks/2.2.1  -  259
+macs2/2.1.1.20160309  -  257
+eigen/3.3.7  -  257
+molden/5.7  -  251
+bwa/0.7.12  -  240
+virtualgl/2.5.2  -  229
+trim_galore/0.5.0  -  227
+spm12/matlab2015b.r6685  -  227
+tiff/4.0.8  -  222
+mrtrix3tissue/5.2.8  -  221
+ants/2.2.0  -  221
+mricron/30apr2016  -  218
+eigen/3.3.0  -  218
+vmd/1.9.4  -  211
+mrtrix3tissue/5.2.8-ubuntu  -  208
+motioncor2/2.1.10-cuda8  -  208
+squashfuse/0.1.103  -  205
+fsl/5.0.9  -  204
+cuda/8.0  -  202
+miniconda3/4.1.11-python3.5  -  199
+bedtools/2.27.1-gcc5  -  199
+singularity/3.5.3  -  198
+python/3.6.2-static  -  198
+cudnn/7.3.0-cuda9  -  196
+motioncor2/2.1.3.0-cuda101  -  189
+zlib/1.2.11  -  182
+bowtie2/2.3.5  -  179
+singularity/2.5.2  -  177
+spades/3.12.0  -  176
+fasttree/2.1.10  -  174
+pigz/2.3.4  -  172
+seqtk/1.3  -  170
+emboss/6.6.0  -  169
+python/3.5.2-gcc5  -  160
+pycharm/2018.3.3  -  160
+pilon/1.22  -  160
+lmdb/latest  -  158
+xnat-utils/0.5.5  -  157
+mafft/7.310  -  157
+cudnn/7.6.5-cuda10.1  -  157
+protobuf/master  -  154
+cmake/3.10.2-gcc5  -  154
+picard/2.19.0  -  151
+matlab/r2017a  -  150
+afni/17.0.11  -  149
+singularity/3.4.0  -  148
+python/2.7.12-gcc5  -  146
+fsleyes/0.32.0  -  146
+trimmomatic/0.38  -  142
+mc/4.8.21  -  140
+gnuplot/5.2.1  -  140
+cblas/20032302-gcc5  -  139
+cudnn/7.6.5.32-cuda10  -  137
+anaconda/2018.12-Python3.7-gcc6  -  135
+mricrogl/1.0.20170207  -  134
+prokka/1.13.3  -  133
+intel/2018u3  -  133
+relion/3.1_beta-latest  -  130
+R/3.5.1  -  130
+mash/2.1.1  -  128
+chrome/default  -  128
+gaussian/g16a03  -  126
+freesurfer/5.3  -  126
+mricrogl/20180623  -  124
+vt/0.57  -  123
+matlab/r2016a  -  122
+skesa/2.3  -  120
+gnuparallel/20190122  -  116
+fiji/current  -  115
+mkl/2018u3  -  111
+cmake/3.15.1-gcc5  -  111
+chimera/1.11  -  111
+gflags/master  -  110
+glog/master  -  109
+singularity/3.2.0  -  108
+cmake/3.10.2-gcc4  -  108
+cdhit/4.8.1  -  108
+velvet/1.2.10  -  107
+anaconda/5.0.1-Python3.6-gcc5  -  107
+snippy/4.3.8  -  104
+mlst/2.15  -  104
+flash/1.2.11-gcc5  -  103
+shovill/1.0.4  -  102
+freebayes/0.9.9  -  102
+python/2.7.11-gcc  -  101
+lighter/1.1.2  -  100
+gpucomputingsdk/4.0.17  -  100
+cryosparc/v2  -  100
+blas/3.8.0-gcc5  -  100
+kraken2/2.0.7-beta  -  99
+boost/1.72.0-gcc8  -  99
+rstudio/1.1.463-r3.6.0-mkl  -  98
+boost/1.62.0-gcc4  -  96
+avizo/9.5.0  -  96
+ants/2.3.1  -  96
+abricate/0.8.13  -  96
+itk/4.10.0-gcc4  -  95
+avizo/9.7  -  95
+tensorflow/2.0.0-gpu  -  94
+muscle/3.8.31  -  94
+megahit/1.1.3  -  93
+R/3.5.2-openblas  -  92
+samclip/0.2  -  91
+cutadapt/2.7  -  90
+libcublas/10.2.1.243-cuda10  -  89
+atom/1.39.1  -  89
+lapack/3.8.0-gcc5  -  88
+git/2.8.1  -  88
+singularity/3.0  -  85
+kraken/1.1.1  -  85
+freesurfer/6.0-patch  -  85
+pytorch/1.3-cuda10  -  84
+matlab/r2017b  -  84
+fsleyes/0.24.3  -  84
+snappy/master  -  83
+singularity/2.4.5  -  83
+perl/5.24.0  -  83
+vtk/7.0.0  -  82
+deeptools/3.1.3  -  82
+nullarbor/2.0.20181010  -  81
+fiji/20160808  -  81
+chimera/1.13  -  81
+relion/3.0-stable  -  80
+imod/4.9.9  -  80
+openmpi/3.1.4-mlx  -  79
+rdkit/2019.03.3.0  -  78
+matlab/r2019b-container  -  78
+fsl/6.0.0  -  77
+blast+/2.9.0  -  77
+snp-dists/0.6.3  -  76
+newick-utils/1.6  -  76
+dcm2niix/latest  -  76
+dsistudio/latest  -  74
+connectome/1.2.3  -  74
+centrifuge/1.0.4-beta  -  73
+jellyfish/1.1.12  -  72
+avizo/9.0.1  -  72
+anaconda/5.0.1-Python3.5-gcc5  -  72
+relion/3.1_beta  -  71
+chimera/1.14  -  71
+vcftools/0.1.15  -  70
+R/3.5.3-mkl  -  70
+convert3d/1.0.0  -  70
+3dslicer/4.10.2  -  70
+maven/3.3.9  -  69
+itk/ansto  -  69
+apex/latest  -  69
+R/3.4.3  -  68
+hdf5/1.10.5  -  68
+gatk/4.1.2.0  -  68
+mrtrix/0.3.15-gcc4  -  67
+minimap2/2.17-r954-dirty  -  67
+prank/170427  -  66
+itksnap/3.3.x  -  66
+relion/2.1  -  65
+quicktree/2.5  -  65
+mrtrix/3.0.0  -  65
+R/3.5.0  -  64
+opencv/3.4.1  -  63
+leveldb/master  -  63
+cmake/3.10.2-gcc4-system  -  63
+spm12/matlab2018a.r6685  -  62
+pytorch/1.1-cuda10  -  61
+mcl/11-294  -  61
+cmake/3.15.4-gcc8  -  61
+sra-tools/2.9.6  -  60
+rstudio/1.1.463  -  60
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smoke_test/tests/R/bashcmd

+#!/bin/bash
+R --version

smoke_test/tests/R/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/anaconda/bashcmd

+#!/bin/bash
+conda list 
+python -c 'import os;import sys;'
+

smoke_test/tests/anaconda/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/ants/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/atlas/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/bcftools/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/bedtools/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/biobambam/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/bismark/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+

smoke_test/tests/blast/bintest

+#!/bin/bash
+name=$( realpath $0 | xargs dirname | xargs basename )
+ver=${1:-"default"}
+bin_dirs=$(module show $name/$ver 2>&1 | sed -n "s/.* PATH \(.*\)/\1/p")
+NAME_EXEC_EXIST=false
+for bin in $bin_dirs; do
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
+    done
+done
+
+