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.
We are having the same issue after upgrade to FreeSurfer 4.5. It takes more than 1.5 hrs for the jobs that used to complete in less than 30 minutes.
Alex Zaitsev
Chris Hyatt wrote:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
are all the steps taking longer, or are some binaries longer than others
On Thu, 15 Oct 2009, Alexander Zaitsev (CNI) wrote:
We are having the same issue after upgrade to FreeSurfer 4.5. It takes more than 1.5 hrs for the jobs that used to complete in less than 30 minutes.
Alex Zaitsev
Chris Hyatt wrote:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, -autorecon1 and -autorecon2 are taking longer. (on a cluster)
Also, atlas registration takes 2 hrs instead of 20 minutes on one of our local machines. Though I have to verify the version (use that machine via web services) - will do it on Monday
Alex
Bruce Fischl wrote:
are all the steps taking longer, or are some binaries longer than others
On Thu, 15 Oct 2009, Alexander Zaitsev (CNI) wrote:
We are having the same issue after upgrade to FreeSurfer 4.5. It takes more than 1.5 hrs for the jobs that used to complete in less than 30 minutes.
Alex Zaitsev
Chris Hyatt wrote:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
when testing (retesting) the -autorecon1 stage, be sure to include the -clean-lta (or -clean) flag. during the skull strip stage, an alignment to an atlas is computed, which takes quite a bit of time (40-60 minutes). if -autorecon1 is rerun, and the .lta file produced by a prior run is detected, then it will skip the alignment computation. this can explain why it may seem to run quicker.
nick
On Thu, 2009-10-15 at 23:34 -0400, Alexander Zaitsev (CNI) wrote:
We are having the same issue after upgrade to FreeSurfer 4.5. It takes more than 1.5 hrs for the jobs that used to complete in less than 30 minutes.
Alex Zaitsev
Chris Hyatt wrote:
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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick,
during the skull strip stage, an alignment to an atlas is computed, which takes quite a bit of time (40-60 minutes).
Just so you know, this isn't included in the approximate timings in the help for recon-all, which seem to suggest that autorecon1 should be more like 15 minutes in total: -<no>motioncor < 5 min -<no>nuintensitycor 3 min -<no>talairach 4 min -<no>normalization 3 min -<no>skullstrip 1 min
Cheers, Ged
freesurfer@nmr.mgh.harvard.edu
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Alexander Zaitsev (CNI) -
Bruce Fischl -
Chris Hyatt -
DRC SPM -
Nick Schmansky