Re: Compiling 8Core macs

From: Christopher Hartshorn (
Date: Tue Nov 25 2008 - 15:28:51 CST

I have not received any replies as of yet. So, thank you for the
response. As far as benchmarks, I have done the following:
All 8 cores of the cluster nodes=14min/ps
On 8 core mac with:

The fastest is the +p4 option which I am not sure what that means
since I thought that the option designated the number of core/
processors to be utilized. I see the obvious trend from the +p2
option where +p4 is 2x faster, but I would expect anything >+p4 to be
faster (maybe not double, but definitely faster). Also, the AMD
cluster is still so much faster that it must be the that they (the Mac
Intel binaries) are compiled for totally different systems, but I
would suprised if the performance gain in compiling for 64bit vs 32
bit would be any more then 15% (not quite the 2X difference that there
is between the two). Finally, can I compile my own using the latest
XCode 3.x.x and the latest Intel Fortran compiler for Mac 11.x.x plus
the source of the latest Charmm++ build and the latest NAMD build? I
really am hoping to optimize the two MacPros I have because even a
savings of 5min/ps will save me weeks of time on this project.

Thank you,

On Nov 25, 2008, at 11:41 AM, Warner Yuen wrote:

> Hi Chris,
> Wondering if you have gotten any replies on this. I can only guess
> at the slowness of the Mac OS X version. First, it's only 32-bit, a
> 64-bit version would allow the application to access more registers
> on the the processor. Second, if you do build it with the Intel
> compilers, even at 32-bit, it should be faster than the binaries
> that you downloaded.
> Also, I have found that some applications just don't scale that well
> with all 8-cores running on the same box. Have you run benchmarks
> with 4 or 6 cores on the Mac Pro compared to the two cluster nodes
> with all 8 cores?
> Warner Yuen
> Scientific Computing
> Consulting Engineer
> Apple Computer
> email:
> Tel: 408.718.2859
> Fax: 408.715.0133
> On Nov 24, 2008, at 3:03 PM, Christopher Hartshorn wrote:
>> Hello everyone. I have a few questions as to optimizing NAMD to
>> current MacPro with dual 4-core Intel Xeons. First, off even
>> though there are 8 cores total in these machines, when I run NAMD
>> with:
>> charmrun ++local namd2 +p8
>> I get much slower (almost half speed) performance than if use a +p4
>> option (also if I use +p2 the speed is cut in half).
>> Next, is there any gains to be had from playing with charmrun
>> options like "++p n" or ++pe for the MacPro.
>> Next, in the optimization page I see that numprocs=numpatch+1
>> scaled to number of cores. If I have a 5x5x5 patch grid
>> (125=npatches) and I have 8cores would the optimized value be 128
>> because 125+1=126 then scaled to the next multiple of 8. And where
>> is this value set? Is this +p128? Or is this put into one of the +
>> +p options in charmrun?
>> Finally, I noticed that I can not set the +setcpuaffinity option
>> for charmrun which got me thinking that I do not have the latest
>> charmrun compiled. I have simply downloaded the binaries from the
>> NAMD website which were compiled over two years ago for 32bit
>> Intels. I have the latest Intel compilers, so would it be wise
>> just to get the latest source for Charmm++ and the bleeding-edge
>> NAMD and compile them myself.
>> What got me into this idea that I needed to optimize in the first
>> place is that I installed the binaries on the above computer as
>> well as on our cluster here at WSU. I get the following results
>> between the two computers on the exact same initial MDSim:
>> 2nodes of cluster (each node has 2x2core AMD 64bit opterons running
>> at 2.4GHz) total of 8cores=14min/ps
>> MacPro (main motherboard has 2x4core Intel 64bit Xeons running at
>> 2.83GHz) total of 8cores=31min/ps
>> Thus, the MacPro is considerable slower than the same number of
>> slower Opterons. Only difference would be compilers of the
>> respective binaries and some OSX overhead on the MacPro (which
>> could not possibly account for the massive difference between the
>> two). Any help and/or thoughts on this would be greatly
>> appreciated. Thank you in advance.
>> Christopher M Hartshorn
>> WSU

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