fix bug in smoke_test and generate_bin_test script

smoke_test/generate_bin_test

@@ -14,14 +14,14 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi
 ' > $TESTCASE_DIR/bintest
 
 IFS_orig=$IFS

smoke_test/output_dir/anaconda/5.1.0-Python3.6-gcc5

+anaconda Command line client (version 1.6.9)

smoke_test/output_dir/gcc/4.9.3

+gcc (GCC) 4.9.3
+Copyright (C) 2015 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+

smoke_test/output_dir/gcc/5.4.0

+gcc (GCC) 5.4.0
+Copyright (C) 2015 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+

smoke_test/output_dir/gcc/8.1.0

+gcc (GCC) 8.1.0
+Copyright (C) 2018 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+

smoke_test/output_dir/java/1.8.0_77

+Unrecognized option: --version
+Error: Could not create the Java Virtual Machine.
+Error: A fatal exception has occurred. Program will exit.

smoke_test/output_dir/report.txt

+
+libjpeg-turbo 1.4.2 return non-zero exitcode 1 for testcase ./tests/libjpeg-turbo/bashcmd
+virtualgl 2.5.0 return non-zero exitcode 1 for testcase ./tests/virtualgl/bashcmd
+tigervnc 1.8.0 return non-zero exitcode 1 for testcase ./tests/tigervnc/bashcmd
+java 1.8.0_77 return non-zero exitcode 1 for testcase ./tests/java/bintest
+openblas 0.2.20 return non-zero exitcode 127 for testcase ./tests/openblas/bashcmd
+Summary
+Failed: 5
+Success 13
+No tests found: 0
+Failing because not enough tests succeeded

smoke_test/smoke_test

@@ -5,10 +5,10 @@ OUTPUT_DIR=${1:-output_dir}
 
 
 # select top 50 most used module by default
-NUM_MODULE=${2:-50}
+NUM_MODULE=${2:-10}
 
 declare -i TIMELIMIT
-BINTEST=false
+BINTEST=true
 TIMELIMIT=10
 TESTCASE_DIR='./tests'
 REPORT=$OUTPUT_DIR/'report.txt'
@@ -42,9 +42,8 @@ for i in $(head -n $NUM_MODULE $USAGE_REPORT); do
         echo "No testcase for $m found"  | tee -a $REPORT
 	num_notest+=1
     else
-        ALL_EXEC=$(ls -X $TESTCASE_DIR/$name)
-        for i in ${ALL_EXEC}; do
-            t_case=$TESTCASE_DIR/$name/$i 
+        ALL_EXEC=$(find $TESTCASE_DIR/$name -maxdepth 1 -executable -type f)
+        for t_case in ${ALL_EXEC}; do
             if [ $i ==  'bintest' ] && ! $BINTEST;then break;fi
             timeout $TIMELIMIT $t_case $ver &> $OUTPUT_DIR/$name/$ver 
             exitcode=$?

smoke_test/tests/anaconda/bintest

@@ -4,12 +4,12 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi
 

smoke_test/tests/atlas/bintest

@@ -4,12 +4,12 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi
 

smoke_test/tests/bedtools/bintest

@@ -4,12 +4,12 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi
 

smoke_test/tests/bintest

@@ -4,12 +4,12 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi
 

smoke_test/tests/bismark/bintest

@@ -4,12 +4,12 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi
 

smoke_test/tests/bowtie2/bintest

@@ -4,12 +4,12 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi
 

smoke_test/tests/cuda/bintest

@@ -4,12 +4,12 @@ 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 $(ls -X $bin); do
-        if [[ $i == $name ]]; then NAME_EXEC_EXIST=true;fi
+    for i in $(find $bin -maxdepth 1 -executable -type f ); do
+        if [[ $(basename $i) == $name ]]; then 
+            $i --version;
+            exit $?
+        fi
     done
 done
 
-if $NAME_EXEC_EXIST; then
-    $name --version
-fi