Linux only displays two physical and four logical CPUs - IBM eServer xSeries 366

Resolving The Problem

Source

Retain tip: H183615

Symptom

Users with more than two processors installed in their IBM eServer xSeries 366 servers may notice that only two physical CPUs (or four logical CPUs if Hyperthreading is enabled) are visible when running Linux. This could be seen when using a system monitoring tool such as "top", or when using a hardware information or configuration
tool.
 

Affected configurations

The system may be any of the following IBM eServer xSeries servers:

• xSeries 366, type 8863, any model
• xSeries 366, type 8864, and model

The following operating systems are affected:

• Red Hat Enterprise Linux, version 3 for EM64T
• Red Hat Enterprise Linux, version 4 for EM64T
  
  
• SUSE Linux Enterprise Server 9 for EM64T

Note: This does not imply that the network operating system will work under all combinations of hardware and software.
 
Please see the compatibility page for more information:
 
http://www.ibm.com/servers/eserver/serverproven/compat/us/

Solution

Changes to the Linux kernel are required. These changes were submitted to the mainline kernel as well as to Red Hat and SuSE. Target releases are Red Hat Enterprise Linux (RHEL) 3 Update 5, RHEL 4 Update 1, and SuSE Linux Enterprise Server (SLES) 9 Service Pack 1.

Workaround

When prompted during system POST, press F1 to enter Setup. In the main menu, select Advanced Setup. In the following menu, select CPU Options.  
Highlight Clustering Technology and press the left or right arrow key until Special Mode is displayed.
 
Press Escape until you return to the main menu and select Save Settings, then Exit Setup.  

Additional information

The x86_64 Linux kernel (for AMD64 and EM64T processors) did not contain code to support a the mode of operation called "clustered mode" for each CPU's Local Advanced Programmable Interrupt Controller (APIC) until recently. This means that the kernels in current distributions (RHEL 3 Update 4, RHEL 4, SLES 9) also do not support it.
 
Due to advanced system design and capability, updated Linux kernels with code to support this clustered APIC mode are required for the xSeries 366 unless the Special Mode Setup option detailed in the workaround is enabled. This Special Mode simplifies the configuration of the Local APICs so that the current Linux kernels can initialize all CPUs. If you later update to a Linux kernel that supports clustered APIC mode, the Clustering Technology option in Setup can be toggled back to Logical, although this is not necessary.
 
To see if your updated kernel contains this support, you can perform the following steps:

1. To determine the identification for the currently running kernel, type uname -r at a command line. A kernel version string will be returned.
2. Type
   grep cluster_init_apic_ldr /boot/System.map-<version>
   where <version> is replaced with the kernel version string obtained in step 1.

If the command in step 2 prints something like:
 
ffffffff8011ba40 t cluster_init_apic_ldr0

then your kernel has the clustered APIC code (the hexadecimal address can very between kernels). If the command prints nothing, your kernel does not have the updates.