Trains were running with delays as the Thursday night rush hour ended after being marred by cancellations due to a signal problem in or near the tunnels out of Penn Station, the Long Island Rail Road said.

A wire problem caused the signal system to break down about 5 p.m., leading to more than 15 train cancellations and the temporary suspension of westbound service between Jamaica and Penn stations, said LIRR spokesman Salvatore Arena.

Westbound service was back up at 7:10 p.m., he said.

Eastbound service was operating close to schedule by 8:15 p.m., he said.

It was the second time this week riders crammed into Penn Station for long waits and crowded rides home due to LIRR problems. On Tuesday, a disabled train at Penn Station marred the rush hour with cancellations and delays that lasted until after the official rush hour ended.

Thursday’s bout of cancellations set off a familiar soundtrack of complaints — bad communications, crowded cars and bad service.

“LIRR is the worst monopoly in NYC,” tweeted BlueCollarBlueShirts, also known as Sean McCaffrey, 33, a construction worker from Lynbrook.

On the train platform could be seen 10 police officers — a rare sight, said the rider, theorizing they were waiting for “rough riders” among the “miserable” crush of people bumping into each other with the slightest movement.

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“I’m so numb to this. I’m used to it,” said McCaffrey, who’s been commuting more than 15 years.

The LIRR had temporarily suspended westbound service to free up tracks to take eastbound commuters home, an effort to avoid a buildup of passengers waiting at Penn Station, Arena said.

The seriousness and nature of the wire problem was not immediately clear, Arena said.

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The MTA had cross-honored fares on subways for westbound riders, authorities said.