I've been trying to get help on this particular issue for a few days in a few different threads. As I learn more, I post again. This time I'm posting under a new, more general title. The previous thread is here.
Here is my setup: two computers on my home LAN, fairly new Gigabyte motherboards with AMD 6-core CPU's, both running Ubuntu 11.10 x86/64. The two machines are not identical, but highly similar. My router is a Linksys WRT54G with the most recent firmware.
The symptom: peer-to-peer connections between the two machines stall and restart in a semi-regular pattern; about two minutes up, then about two minutes down. I have a graphic representation of my findings posted here. I first noticed this when I set up an ssh connection between the two machines. However, even plain-old ping times out. The graphs show the behavior of the pings when I am not logged in using ssh.
When I do use ssh, and I execute commands, timeouts can be induced to occur more quickly. Executing a du command produces about 10 kB of output from my slave machine. If I try to execute a du over ssh from my master machine, it will almost certainly hang up somewhere in the middle -- only to resume again, 1-2 minutes later, if I wait.
If I'm logged on to the slave machine from the console when one of these remote timeouts occurs, I can still use the slave machine normally. The system as a whole is not stalled in the least. I see no CPU loading, no change in memory use, no network traffic.
The ping timeouts go away if my slave machine is booted into Windows 7. I can ping it continuously then. I didn't drop a single ping in over a half-hour.
I tried reversing the master and slave machines. The same behavior is observed in the reverse direction.
This would suggest that the problem is specific to the Linux implementation, and that the problem is something that my slave machine is doing. All of my hardware is apparently working. However, turning off the Linux firewall on the slave machine with a sudo ufw disable command does not affect the behavior.
Does anyone have a clue what might be causing this? Thanks!