I have this system based on the Intel D510MO motherboard, which is basically an Atom D510 (dual-core HT Atom w/built-in GPU), an Intel NM10 chipset, and a Realtek Gigabit LAN controller. It's entirely passively cooled. I noticed almost immediately that there was a kind of very, very soft noise that corresponded with graphics operations, sort of the noise you'd get if you had a sheet of flat paper and slid something really light across it — but more electronic than that. I wrote it off as observation error and/or disk activity triggered by the graphics operation (although the latter seemed like a lot of unnecessary disk activity).
It isn't.
I got curious enough that I finally did a few controlled experiments, and here's what I've determined:
It isn't the HDD. For one thing, the sounds the HDD makes (when seeking, when reading or writing, when just sitting there spinning) is different. For another, I used sudo hdparm -y /dev/sda (I'm using Ubuntu 10.04 LTS) to temporarily put the disk on standby while making sure that non-disk graphics op was happening in a loop. The disk spun down, but the other sound continued, corresponding perfectly with the timing of the graphics op. (Then the disk spun up again, but it takes long enough that I could rule out the HDD.)
It isn't the monitor; I ensured the two were well physically-separated and the sound was definitely coming from the main box.
It isn't something else in the room; the sound is coming from the box.
It isn't cross-talk to an audio circuit coming out the speakers. (It doesn't have any speakers.)
It isn't my mouse (e.g., when I'm trying to make graphics ops happen); the sound happens if I set up a recurring operation and don't use the mouse at all, or if I lift the mouse off the table slightly (but enough that the laser still registers movement).
It isn't the voices in my head; they never whisper like that.
Other observations:
It doesn't seem to matter what the graphics operation is; anything that changes what's on the screen seems to do it. I get the sound when moving the mouse over the Chromium tab bar (which makes the tab backgrounds change); I get it when a web page has a counter on it that changes the text on the page: I get it when dragging window contents around.
The sound is very, very slightly louder if the graphics op is larger, like scrolling a text area when writing a question on superuser.com, than for smaller operations like the tick counter on the web page. But it's very slight.
It's fairly loud (and of good duration) when the op involves color changes to substantial surface areas. For instance, when asking a question here on superuser and you move the cursor between the question box and the tag box, and the help to the right fades out, changes, and fades back in. (Yet another example related to the web browser, so let me say: I hear it when operations completely unrelated to the web browser as well.)
It doesn't sound like arcing or anything like that (I'd've shut off the machine Right Quick Like if it did).
Moving windows does it. Scrolling windows (by and large) doesn't.
I have the feeling I've heard this sort of thing before, when all system fans were on low and such, with other systems — but (again) written it off as observational error. For all the world it's like I'm hearing the CPU working (as opposed to the GPU; note the window scroll thing above) or data being transferred somewhere, but that just seems...unlikely.
So what am I hearing?
This may seem like a very localized question, but perhaps other silent PC enthusiasts may be interested as well...
