HP Compaq 6000 pro - Multi-processor issues?

First time linuxcnc user. Working on a machine rebuild and control refit. I've picked up an older HP box to attempt to use as a controller. I've not dug very deep yet, just playing with latency testing.

System is a core 2 quad 9500 with 4gb ram.

I've been all through the bios and some software settings. I can get around 50000 servo, 25000 base for jitter numbers with some load, glxgears, etc. Which I gather is all I really should care about. I gather that this is probably acceptable for a machine using mesa cards, but maybe not amazing. isolcpus=1 or 3 or 1,3 are necessary to avoid the numbers being fairly horrific, most other settings have limited/no effect. The machine doesn't appear to have any period issue as would present from SMI. Switching to an nvidia card running nouveau drivers (only card i had kicking around) instead of onboard doesn't really seem to change much, other than glxgears runs at beyond v-sync framerates (hurray?)

So I've tweaked further and the thing I've found that makes the biggest difference is in the bios disabling "multi-processor". When I do that /proc/cpuinfo shows only 1 cpu core instead of 4. It seems fast enough still to run a few glxgears and firefox etc. The best case numbers are around 10k servo/10k base, drifting towards 19k servo/12k base. These seem like fairly solid numbers.

What I don't really get is why disabling multi-processor is having such a large impact. Is there any negative to just running this way? Some alternative setting I should try?

Thanks for the feedback.

I fiddled with this machine some more. And i just wasn't happy with it. Although the numbers seemed ok with certain setups, it meant turning off a lot of stuff or spending hours and hours tweaking (many hours of which I had already invested).

So I went out and found an Intel reference board implementation on the local used market, a DQ67SQW with an i5-2400. What a difference. 11k/9k right off the Wheezy live CD with only the most bare bones sanity bios tweaks, and the bios is much more fully featured than the rather limited HP. The CPU is a bit faster, but for our purposes I think we can be fairly sure that really has nothing to do with the difference, both CPUs were plenty fast enough.

So my current recommendation to anyone reading this and looking for a machine. Find an intel reference board.

I will update this thread later with the bios and wheezy settings I settle on.

Well I fiddled with it some more. Still happy, but I haven't found any settings that really improved anything by a noticeable amount in either software or bios.

I've attached a plot and histogram screenshot. I'm open to suggestions, but may call it good enough soon and move on to ordering Mesa boards and mounting this machine in the control cabinet.