We recently installed a Dell Blade server cluster running Freesurfer v4.5 under CentOS 64-bit Linux, with each Blade server having two Intel Xeon E5405 quad core CPUs, running at 2.0 GHz, 2x6144 KB cache and 16 GB of RAM, with a swap file of size between 8-16 GB.
Using a single Blade server of this cluster, a single subject takes between 70 and 100 minutes to complete the Freesurfer autorecon1 stage, which seems overly long.
We also have another computer, running an older version of Freesurfer (v4.0.5) under Fedora 64-bit Linux. This computer is similar to a single Blade server - it has two Xeon X5482 quad core CPUs, running at 3.2 GHz, 2x6144 KB cache and also with 16 GB RAM with a swap file of 16 GB. This computer can complete autorecon1 stage in about 18 minutes.
The only real difference with this computer and the Blade computers that I aware of is the clock speed (3.2 vs 2.0 GHz, 1.6x faster), so the Dell Blade computers should be able to complete autorecon1 in no worse than about 30 minutes.
Does anyone have an idea as to why Freesurfer v4.5 is running so slow on our Dell Blade cluster? Has anyone found the newest version of Freesurfer (v4.5) slower than v4.0.5? Thanks in advance for your help.