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(The following article by Mac Daniel was posted on the Boston Globe website on May 26.)

BOSTON — Massachusetts commuter-rail riders have been packed in like sardines amid sometimes stifling heat in recent weeks, as the Massachusetts Bay Transportation Authority struggles to correct a shortage of rail cars and broken air-conditioning systems.

The reason for the overcrowding, which riders said goes far beyond the usual crush at rush hour, is a shortage of trains as cars are outfitted with new wheels and rebuilt air-conditioning systems, said the MBTA’s general manager, Michael H. Mulhern.

The T has fined the contractor that operates commuter rail for the agency, the Massachusetts Bay Commuter Railroad Co., a total of $250,000 since January, for shortcomings in service. About 75 percent of the fines were for late trains and a lack of cars on popular lines at peak times, T officials said.

“It was so packed that people were screaming to people in the middle of the train to move in,” said Tara Gibbs of Grafton, a passenger on the 4:58 train to Worcester out of South Station, which normally has five double-decker cars but Monday night had only three, a loss of about 245 seats. “It’s unbelievable.”

Fixing the overcrowding problem has taken on new urgency for the region’s aging commuter rail fleet, because thousands of new riders are expected to try riding the rails the last week of July, when the Democratic National Convention triggers massive roadway closures. But Mulhern insisted the shortfall in cars and the mechanical problems would be fully addressed before July.

“There won’t be any fumbles,” Mulhern said.

Mulhern blamed the shortfall on late delivery of new wheel sets for some cars as well as the need to pull rail cars from service to repair faulty air conditioning systems. While the wheel replacement project was recently completed, T spokesman Joe Pesaturo said, the air-conditioning repairs continue to take cars off the tracks.

The Massachusetts Bay Commuter Railroad Co., which took over operations for commuter rail from Amtrak in July, operated 321 rail cars systemwide yesterday, 14 cars short of the T’s minimum operating requirements, according to Pesaturo. The system was five cars short on the north side (trains bound for North Station) and nine short on the south side (trains going to South Station). The T requires a minimum of 122 rail cars on northside lines and 213 on the south, for a total of 335.

On average, T officials said, single-level commuter rail cars have seating for 125, while double-decker cars have seating for 185. At its worst, the rail provider had 25 cars out of service in April, a minimum loss of 3,125 seats.

The consortium will challenge the penalties levied by the T, said spokeswoman Tara Frier She said the wheel repairs remain “99 percent resolved” while the air-conditioning repairs continue.

“I would love to say to you that all of our air conditioning is in 100 percent great shape, but the true test of any air-conditioning system is after we’ve had a heat wave for several days,” Frier said. “I don’t want to guarantee that we’re not going to have any air conditioning problems. . . . I can’t predict the future.”

The consortium, she added, has an on-time record of between 96 and 97 percent and has logged 1,000 more miles between breakdowns than Amtrak. Service will be first-rate for year-round passengers and for the heightened expectations for commuter rail during convention week, she said. North Station will be closed, forcing some 24,000 passengers to transfer to buses and the subway just north of the city, but all other lines should be operating normally.

Passengers interviewed this week, however, were dubious. To make matters worse, fares for commuter rail were recently boosted 25 percent, amid promises of better service. “A crowded train at rush hour is one thing. This situation is a serious problem,” says commuter Todd Glickman of Burlington, who normally takes the Lowell line to North Station, but during the convention week plans to drive to the Route 128 station in Dedham and catch a northbound train to South Station. That way he can avoid being transferred to a bus.

On the Lowell Line’s No. 308 train arriving at 7:44 a.m. yesterday at the Anderson Regional Transportation Center in Woburn, the six-car train offered enough room for everyone to get a seat. At West Medford, however — the inbound train’s last stop before North Station — boarding passengers were forced to stand, an act that had become the norm, according to passengers, even with six cars.

“It’s guaranteed that I stand up,” said Heidi Davis of West Medford as she rode into North Station for her job at the state Department of Environmental Protection.

Overcrowding has become enough of a problem on the Attleboro line that Roberta DeDonato of North Easton said she will wait at Canton Junction for the less-crowded train from Stoughton, which uses the same stop.