Hello,
Question about eking out maximum machine performance: Is there a performance advantage (or alternatively penalty) for running twice as many FreeSurfer jobs (simultaneously) as physical CPUs on a Linux machine with HyperThreading enabled CPUs? That is, say you have two physical cores with HyperThreading -- the Linux OS treats this as four logical processors. However, given that Freesurfer is very 'execute' intensive is there any advantage to be gained by running 4 rather than 2 FS jobs simultaneously? Or will the total time per brain with 4 simultaneous jobs be (on average) just twice as long?
thanks, Mike H.
Mike,
I can't say I have benchmarked this myself, but I am guessing there would be only a small performance advantage, as memory access would be the bottleneck. I don't know if each HyperThreaded CPU has its own memory cache.
Nick
On Sat, 2007-10-13 at 21:43 -0500, Michael Harms wrote:
Hello,
Question about eking out maximum machine performance: Is there a performance advantage (or alternatively penalty) for running twice as many FreeSurfer jobs (simultaneously) as physical CPUs on a Linux machine with HyperThreading enabled CPUs? That is, say you have two physical cores with HyperThreading -- the Linux OS treats this as four logical processors. However, given that Freesurfer is very 'execute' intensive is there any advantage to be gained by running 4 rather than 2 FS jobs simultaneously? Or will the total time per brain with 4 simultaneous jobs be (on average) just twice as long?
thanks, Mike H.
Mike, I have the two 3 GHz processor quad core mac pro with 12 gb of RAM. I can run 7 freesurfers simultaneously and they all finish in about 24-28 hours with FS version 4.x If I only run 7, I have no problem doing word processing, email, etc. during the recons.
Brian
On 10/14/07 2:36 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Mike,
I can't say I have benchmarked this myself, but I am guessing there would be only a small performance advantage, as memory access would be the bottleneck. I don't know if each HyperThreaded CPU has its own memory cache.
Nick
On Sat, 2007-10-13 at 21:43 -0500, Michael Harms wrote:
Hello,
Question about eking out maximum machine performance: Is there a performance advantage (or alternatively penalty) for running twice as many FreeSurfer jobs (simultaneously) as physical CPUs on a Linux machine with HyperThreading enabled CPUs? That is, say you have two physical cores with HyperThreading -- the Linux OS treats this as four logical processors. However, given that Freesurfer is very 'execute' intensive is there any advantage to be gained by running 4 rather than 2 FS jobs simultaneously? Or will the total time per brain with 4 simultaneous jobs be (on average) just twice as long?
thanks, Mike H.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Brian,
With 2 quad core you have 8 processors. So you can run 8 tasks simultaneously (only memory is shared.) Notice that each recon-all will need 1GB memory. So for 8 cores you need 8GB Ram at least.
From the FAQ
"Q: How can I reduce the time of recon-all in a group of patients? A: FreeSurfer run its process in a non-parallel environment, so you won't have benefit from a dual core machine for a single case analysis. However if you have many cases you can start two FreeSurfer recon-all process in the same machine and theoretically you can reduce by half the time to analyze your group of cases. A similar procedure can also be used in quad-core environment. Note that to take benefit of a multi-core environment you need to use a SMP kernel in your OS."
One Hyperthread core doesn't act as 2 processors. "The advantages of Hyper-Threading are listed as: improved support for multi-threaded code, allowing multiple threads to run simultaneously, improved reaction and response time." Since FreeSurfer is single threaded AFAIK you usually won't get much benefit from running two process in HT.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Brian C. Schweinsburg, Ph.D. Sent: domingo, 14 de outubro de 2007 21:09 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] hyperthreading
Mike, I have the two 3 GHz processor quad core mac pro with 12 gb of RAM. I can run 7 freesurfers simultaneously and they all finish in about 24-28 hours with FS version 4.x If I only run 7, I have no problem doing word processing, email, etc. during the recons.
Brian
On 10/14/07 2:36 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Mike,
I can't say I have benchmarked this myself, but I am guessing there would be only a small performance advantage, as memory access would be the bottleneck. I don't know if each HyperThreaded CPU has its own memory cache.
Nick
On Sat, 2007-10-13 at 21:43 -0500, Michael Harms wrote:
Hello,
Question about eking out maximum machine performance: Is there a performance advantage (or alternatively penalty) for running twice as many FreeSurfer jobs (simultaneously) as physical CPUs on a Linux machine with HyperThreading enabled CPUs? That is, say you have two physical cores with HyperThreading -- the Linux OS treats this as four logical processors. However, given that Freesurfer is very 'execute' intensive is there any advantage to be gained by running 4 rather than 2 FS jobs simultaneously? Or will the total time per brain with 4 simultaneous jobs be (on average) just twice as long?
thanks, Mike H.
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@nmr.mgh.harvard.edu
-
Brian C. Schweinsburg, Ph.D. -
Michael Harms -
Nick Schmansky -
Pedro Paulo Oliveira Jr