Here you go:

#! perl -slw
use strict;
use List::Util qw[ sum ];
use Data::Dump qw[ pp ]; $Data::Dump::WIDTH = 1000;

my %chemsAndFlows;
while( <DATA> ) {
    my( $chem, $mach, $flow ) = split ' ';
    next if $flow == 0;
    push @{ $chemsAndFlows{ $chem } }, $flow;
}

@$_ = sort{ $a <=> $b } @$_ for values %chemsAndFlows; #pp \%chemsAndF
+lows;

## Greedy;
our $MACHMAX //= 11000;
my( $iMach, %machsAssigned ) = 0;
while( keys %chemsAndFlows ) {
    my( $machTotal, $mach ) = ( 0, sprintf "E%03d", ++$iMach);

    for my $chem ( keys %chemsAndFlows ) {
        for my $iFlow ( reverse 0 .. $#{ $chemsAndFlows{ $chem } } ) {
            my $flow = $chemsAndFlows{ $chem }[ $iFlow ];
            die "MACHMAX too small for $chem:$flow" unless $flow < $MA
+CHMAX;
            if( ( $machTotal + $flow ) <= $MACHMAX ) {
                $machTotal += $flow;
                push @{ $machsAssigned{ $mach }{ $chem } }, $flow;
                splice @{ $chemsAndFlows{ $chem } }, $iFlow, 1;
                delete $chemsAndFlows{ $chem } unless @{ $chemsAndFlow
+s{ $chem } };
            }
        }
    }
}
$_->{ ' total' } = sum( map @$_, values %$_ )for values %machsAssigned
+;
pp \%machsAssigned;

#1st column is unique chemical identifier 2nd column is unique machine
+ identifier 3rd column is processing seconds
__DATA__
[download]

Append your posted data at the end after the __DATA__ line.