my $SMPP_count = int ((split (/\s+/,`cut -d "|" -f 1,10,13 SMSCDR*$
+date$hour$minute*.log |grep "Submit|GSM" |grep "$hour:$min:$sec" |sor
+t |uniq -c`)) [1]) + int ((split (/\s+/,`cut -d "|" -f 1,10,13 SMSCDR
+*$date$hour$minute*.log |grep "Submit|SMPP" |grep "$hour:$min:$sec" |
+sort |uniq -c`)) [1]);
[download]

Short answer: since you are using uniq -c as the last filter in you pipelines, you are interested in the first field. This field has leading whitespace. From the documentation of split:

As another special case, "split" emulates the default behavior of the command line tool awk when the PATTERN is either omitted or a literal string composed of a single space character (such as ' ' or "\x20", but not e.g. "/ /"). In this case, any leading whitespace in EXPR is removed before splitting occurs, and the PATTERN is instead treated as if it were "/\s+/"; in particular, this means that any contiguous whitespace (not just a single space character) is used as a separator.

Long answer: you are running

• 1 x perl
• 2 x /bin/sh (at each qx() or backtick ``)
• 4 x grep
• 2 x sort
• 2 x uniq

which makes for 11 processes in total, and you are reading each file that matches SMSCDR*$date$hour$minute*.log twice - to get a sum which perl happily would give you in a less convoluted way in just 1 process.

• cut -d "|" -f 1,10,13 would be (split '|', $_)[0,9,12]
• grep and sort are perl builtins
• use a hash (see perldata) and use its keys for uniqueness
• you can use the bultin glob to expand SMSCDR*$date$hour$minute*.log into a list of filenames

From your code I am guessing that your log files contain a timestamp in the first field, Submit occurs in the 10^th field, and you want lines which contain GSMor SMPP in the 13^th field.
Putting it all together, omitting uneccesary steps and not writing perl as if it were shell:

@ARGV = glob "SMSCDR*$date$hour$minute*.log";
my $SMPP_count;
my $stamp = "$hour:$min:$sec";
while(<>){
    chomp;
    my @ary = (split '|')[0,9,12];
    $SMPP_count++ 
        if  $ary[0] eq $stamp
        and $ary[1] eq "Submit"
        and $ary[2] =~ /(GSM|SMPP)/;
};
print $SMPP_count;
[download]

update: corrected code

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