I’m running Ubuntu Server 9.04 64bit on an ASRock A780LM with an AMD Athlon 64 X2 BE and 4GB of RAM. I was seeing the lines at the top in my messages file as well. I was also seeing some I/O errors on the console just after the boot process started, but I wasn’t able to capture them or find them in other logs.

I just added the iommu=noaperture option to my boot line in grub and now I don’t see the I/O errors at boot up and /var/log/messages is clean. I did capture the “free -m” output before and after, but the system had been up several days when I captured the before and I’m not sure what else may have been consuming memory. Anyway here is the output before adding the iommu=noaperture option:
$ free -m
total used free shared buffers cached
Mem: 3650 582 3067 0 141 235
-/+ buffers/cache: 205 3444
Swap: 10695 0 10695

And here is the after:
$ free -m
total used free shared buffers cached
Mem: 3650 400 3249 0 8 169
-/+ buffers/cache: 221 3428
Swap: 10695 0 10695