An update on my comment above: when doing heavy I/O from an external
drive (/dev/sdb) to a slow external flash key (/dev/sda), I can hear my
internal hard drive (/dev/sda) thrashing away constantly, even though
its light indicates no disk read/write operations. So something in the
kernel must be making it constantly seek, and this is affecting /dev/sda
access and hence desktop responsiveness.

The desktop is now much faster for applications that are already loaded,
but anything that has to access the disk still experiences long wait
times.

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Heavy Disk I/O harms desktop responsiveness
https://bugs.launchpad.net/bugs/131094
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