McLaren protege Magnussen beat Force India race driver Paul di Resta to the top spot by 0.172 seconds, with Antonio Felix da Costa next best among the rookies in third for Red Bull.
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Magnussen acknowledged that the nature of F1 testing made head-to-head pace comparisons difficult, but reckoned there was nothing deceptive about his performance.
"It's always nice to see yourself in P1, but in a Formula 1 test we don't know what fuel people are running, so it's hard to compare yourself to people," he said.
"But we have a pretty good idea of whether it was a good day or not - and I think it was a good day.
"We didn't run a qualifying trim. I'm sure no one did. But you don't know if someone ran 60 kilos or 40 kilos, you don't know where exactly everyone is.
AUTOSPORT's guide to the F1 young drivers
"But you get an idea if it's good, and we're happy."
The Formula Renault 3.5 title contender said he could not judge whether McLaren had made a step forward during the test.
"It's not easy for me to tell because I've never driven this car before," said Magnussen, who is a regular in the team's simulator and tried the 2012 McLaren in last year's Abu Dhabi young driver test.
"I cannot say if we've made big improvements with aero or tyres or whatever. We do the test, I give the feedback, and they analyse it."
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