As you can see, you have an embarrassment of riches in the replies. Some of them are purposefully terse and idiomatic because it's something of a sport here when a SoPW doesn't give code attempts. :P If you work with one of them and have follow-up questions, don't hesitate to ask, but post whatever code you tried to use.

You got an interesting but terminally slothful, half-right dose of self-congratulation regarding the use of a database. This is not necessary of course as several of the replies neatly addressed your actual question, and need, and are trivial to adapt to many other requirements if you can follow the code.

That said, some persons find SQL a more natural way of working with data so it is an interesting and potentially useful thing to do; there is no try®. Like so many things, it is semi-trivial in Perl if you know how. Building on previous answers, here's how–

#!/usr/bin/env perl
use strict;
use warnings;
use Text::CSV_XS "csv";
use DBI;

my $csv_file = shift || die "Give a CSV file with sample data\n";

my $dbh = DBI->connect("dbi:SQLite::memory:"); # DB is ":memory:"

$dbh->do(<<"");
    CREATE TABLE sampleData( sample, input, amount )

my $insert_h = $dbh->prepare(<<"");
    INSERT INTO sampleData VALUES( ?, ?, ? )

csv( in => "test.csv",
     on_in => sub {
         my @values = @{ $_[1] };
         $insert_h->execute(@values) if @values == 3;
     });

my $tallies = $dbh->selectall_arrayref(<<"");
    SELECT  sample
           ,input
           ,SUM(amount)
      FROM  sampleData
  GROUP BY  sample, input
  ORDER BY  sample, input

csv( in => $tallies,
     out => "outputfile.csv" );
[download]

You will need fairly recent versions of a couple of these for this to run, Text::CSV_XS, DBD::SQLite.

An excellent overview of DBI recipes: DBI recipes. And a footnote for working with the data outside of Perl–

$dbh->sqlite_backup_to_file("newDBname.sqlite");
# ^^^ To go from ":memory:" to a file. Then you also have access to
# the DB via the command line with the sqlite executable.
# moo@cow[2574]~>sqlite3 "newDBname.sqlite"
# sqlite> select * from sampleData;
# 3211111|100|3.2
# 3211112|101|3.2
# ...et cetera...
[download]

Update: s/CVS/CSV/g for @all_the_nodes;#!!!