<?php
set_time_limit(0);

require_once "blablabla/app/Mage.php";//my path here
umask(0);
Mage::app();


$sku="876297-6";  //some Sku
$_product = Mage::getModel('catalog/product')->loadByAttribute('sku',$sku);

$param = array(
101=>array(
'position'=>3
),
102=>array(
'position'=>5
)
);
$_product->setRelatedLinkData($param);
$_product->save();

echo "Great!!";

 ?>