Absolutely no issue here, but I noticed that a lot of long runs WU on my GTX285, take shorter to finish than the average ACEMD2: GPU molecular dynamics v6.16 (cuda31).
So in my case a long run, runs shorter than a "normal" WU. I guess I am not the only one.

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Greetings from TJ

It happened a few times to me also, due to normal WUs that have a low GPU load and thus are taking longer time then usual.

But mostly long runs are really longer then normal (ACEMD2) WUs.