From the Telegraph, UK
Tensions between Gen McChrystal and the White House were disclosed in an unflattering article in the magazine.
Gen McChrystal has now been forced to issue an apology for the comments.
"I extend my sincerest apology for this profile," Gen McChrystal said in a statement issued hours after the article was released.
"It was a mistake reflecting poor judgment and should never happened."
Gen McChrystal, a former special operations chief, usually speaks cautiously in public and has enjoyed mostly sympathetic US media coverage since he took over the Nato-led force last year. But the article appears to catch him and his staff in unguarded moments.
"Throughout my career, I have lived by the principles of personal honour and professional integrity. What is reflected in this article falls far short of that standard.
"I have enormous respect and admiration for President Obama and his national security team."
In the profile, McChrystal jokes sarcastically about preparing to answer a question referring to the Vice President, Joe Biden, known as a sceptic of the commander's war strategy.
"Are you asking about Vice President Biden?" Gen McChrystal says with a laugh. "Who's that?" the article quotes him as saying.
"Biden?' suggests a top adviser. 'Did you say: Bite Me?"
Gen McChrystal tells the magazine that he felt "betrayed" by the US ambassador to Kabul, Karl Eikenberry, in a White House debate over war strategy last year.
Referring to a leaked internal memo from Eikenberry that questioned Gen McChrystal's request for more troops, the commander suggested the ambassador had tried to protect himself for history's sake.
"I like Karl, I've known him for years, but they'd never said anything like that to us before," he said.
"Here's one that covers his flank for the history books. Now if we fail, they can say, 'I told you so.'"
Eikenberry, himself a former commander in Afghanistan, had written to the White House saying Afghan President Hamid Karzai was an unreliable partner and that a surge of troops could draw the United States into a open-ended quagmire.
The article revisits the friction between the White House and the military last fall as Mr Obama debated whether to grant Gen McChrystal's request for tens of thousands of reinforcements.
Although Mr Obama in the end granted most of what Gen McChrystal asked for, the strategy review was a difficult time, the general tells the magazine.
"I found that time painful," Gen McChrystal said. "I was selling an unsellable position."
An unnamed adviser to Gen McChrystal alleges the general came away unimpressed after a meeting with Mr Obama in the Oval Office a year ago.
"It was a 10-minute photo op," the general's adviser said.
"Obama clearly didn't know anything about him, who he was ... he didn't seem very engaged. The boss was pretty disappointed," he said.
The profile, titled The Runaway General, argues that Gen McChrystal has pushed through his vision of how to fight the war, sidelining White House and State Department heavyweights along the way.
His aides are portrayed as intensely loyal to Gen McChrystal while dismissive of the White House and those who question their commander's approach.
One aide calls the national security adviser, Jim Jones, a retired general, a "clown" who is "stuck in 1985."
One unnamed senior military official speculates that yet another surge of US forces could be requested "if we see success here."
But his own troops voice doubts about the war and new rules limiting the use of force at a meeting with Gen McChrystal at a combat outpost near Kandahar city, according to the magazine.
One sergeant tells him: "Sir, some of the guys here, sir, think we're losing, sir."
Gen McChrystal complains about a dinner with an unnamed French minister during a visit to France in April.
In a hotel room in Paris getting ready for a dinner with the French official, Gen McChrystal says: "How'd I get screwed into going to this dinner?"
He also derides the hard-charging top US envoy to the region, Richard Holbrooke.
"Oh, not another email from Holbrooke," Gen McChrystal said, looking at his messages on a mobile phone. "I don't even want to open it."
