I assume you are refering to the ship that Phillip and his mother leave on, the S. S. Hato. We can find the answer to your question in Chapter Two of this excellent novel. In this chapter, we are told that Phillip and his mother are leaving their father behind because of the way that war seems ever more likely. Therefore, they are going to leave on this ship, which is describe in the following paragraph:
Early Friday morning, we boarded the S. S. Hato in St Anna Channel. She was a small Dutch freighter with a high bow and stern, and a bridge house in the middle between two well decks... She had a long stack and always puffed thick, black smoke.
This is of course the ship that will be torpedoed by the Germans at the beginning of Chapter Three, resulting in Phillip finding himself stranded on the sea with nobody else except for Timothy. Thus their relationship begins, and Phillip is forced to confront his own prejudices and to get along with Timothy and work together for their mutual survival.