for (my $element = 0; $element<$total_element; $element++)
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Don't. Use the following instead:

for my $command (@run) {
...
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This is much saner, as you don't need to know about $total_element and cannot make errors by using $element in a wrong way.

Also, please check the return value from system instead of only querying $?. Use the following:

if (system( $run_cmd ) != 0) {
    print "Running command '$run_cmd' failed: $!/$?\n";
    $err = 1;
};
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