You're writing a ton of data to disk, and this causes the X
server to have long freezes.
Probably the X server is waiting on a disk read, which is
blocked behind all the writes. This is worsened by the
VM's tendency to evict useful data in favour of caching
large read/write data.
You'll find that the -aa VM will improve the page replacement
decisions, so the X server won't have to read random
pages as often. This should help a bit. The patch at
http://www.zip.com.au/~akpm/linux/patches/2.4/2.4.18-pre1/read-latency2.patch
will decrease the time which the remaining reads take.
This should help a lot.
We're getting there, albeit a bit slowly.
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