Physical hardship is a military term used to define situations that may not in themselves be imminently dangerous, or hazardous, but that may cause "extreme physical discomfort or distress" that cannot be mitigated by protective or defensive equipment or machinery.
Duty involving a physical hardship is duty that may not in itself be hazardous, but causes extreme physical discomfort or distress and is not adequately alleviated by protective or mechanical devices. (U.S. Office of Personnel Management)
While there is no direct mention of "physical hardship" in O’Flaherty story, "The Sniper," it is a military term and as such has a bearing on understanding this military story. There are a number of instances of physical hardship that the Republican sniper experiences. The first is hunger: "He was eating a sandwich hungrily. He had eaten nothing since morning." Another is heat and discomfort as he was all day on a long summer day on the rooftop behind the parapet of a tall building: "the long summer day of fasting and watching on the roof."
More severe physical hardships--duty in which "protective or mechanical devices" cannot alleviate the discomfort or distress of the duty--occur after he is shot (for foolishly giving in to lighting a match and holding it to a cigarette). His wound from the rifle shot of the opposite sniper is not fatal but clearly causes significant physical hardship. Along with the searing pain comes the physical hardship and difficulty of performing his assigned duty with a numbed and broken forearm. The physical hardship is increased when he has to be his own doctor and tend to his painful wound himself.
A paroxysm of pain swept through him. He placed the cotton wadding over the wound and wrapped the dressing over it. He tied the ends with his teeth.
Further physical hardship comes when he fires at the enemy sniper on the opposite rooftop; when his "teeth chattered" and he "gibbered"; and when he cursed the war, himself and everybody: "cursing the war, cursing himself, cursing everybody." As he runs across the street during his escape--detouring to see the face of the sniper whose life he took--he faces the physical hardship of being pelted by machine gun fire.