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H2300JF/S2600JF - Horrible Performance After BIOS Upgrade


I have an Intel Server Systems H2300JF chassis with three Intel S2600JF server trays installed. Each of the servers has two Intel E5-2690's. I'm running debian 6 (squeeze) with a 2.6.32-5-amd64 kernel. The original BIOS was version 01.01.1002 since there were several updates since the original, I thought it would be wise to upgrade. So I upgraded one of the servers to 01.03.0002. After a while but eventually I noticed that the performance of my application was cut in half. Here is a simple integer benchmark I found that illustrates the issue:

echo '2^2^20' | time bc > /dev/null

On a server with the old BIOS, I get:

$ echo '2^2^20' | time bc > /dev/null

3.55user 0.00system 0:03.56elapsed 99%CPU (0avgtext+0avgdata 9104maxresident)k

0inputs+0outputs (0major+785minor)pagefaults 0swaps

On the server with the new BIOS, I get:

$ echo '2^2^20' | time bc > /dev/null

8.57user 0.00system 0:08.59elapsed 99%CPU (0avgtext+0avgdata 9088maxresident)k

If I reboot, and run again, the first run will be around 3.5 but subsequent runs are around 8.5 sec. I should mention that I have the server set to "performance" in the bios.

Thinking it might be a hardware issue, I upgraded a second tray to the same 01.03.0002 bios and it exhibits the same behavior so I am pretty sure the bios change is causing the performance issue. Now I have two servers messed up.

I've tried all the other bios version on the downloads site - even the one from October 1. Version 01.03.0002 does not seem to have the performance issue but mess up my 10G NIC. The performance issue seems to start with BIOS 01.02.0004. I notice that the release notes mention say:

'Update new processor microcode and onboard device option roms'

Could this be the issue?

Would a newer kernel possibly solve the problem?

Unfortunately, remotely updating the bios has not gone well so each change is a trip to the data center. Going to head there tomorrow to try putting the 01.06.0001 version on and try with a couple other Linux flavors.

If anyone has any other advice, I'd appreciate it. -- Bud

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Load up Ubuntu 12.04 with a 3.2 kernel and things seem to be running normal performance wise. -- Bud