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I have a strange memory issue: I've been running out of free memory for months now, which I thought was OK, since I use the Creative Suite apps and Xcode regularly, all of them is quite memory intensive.

But somehow the situation seems to be getting worse. Today I logged off to free up some RAM, then when logged back in, all the 4 GB of my RAM was used. (I've uploaded the list to here)

I exported the processes, and added the memory usage, but they add up to 684 MB only.
("All Processes" is selected in Activity Monitor)

How could I check which process is using up the memory in the system?

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Was your RAM marked as used or inactive? See info about inactive memory here: – Nathan Greenstein May 14 '11 at 21:12
@Nathan Thank you, that mostly explains it. 1.14 GB was marked as inactive. – Antal May 14 '11 at 21:26
up vote 2 down vote accepted

Most of the difference was marked probably memory marked as inactive. Any app can still use this memory, so it's not marked as used by some process.
For more info about inactive memory, see this thread.

Wired memory usually makes up a much smaller portion. This is memory used by the OS; it isn't available to your apps.

For more info, see the Apple article Reading System Memory Usage in Activity Monitor.

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