RE: Linear speedup of NONMEM on quad-core CPUs?
I've actually run this experiment (not on a quad-core, but, on a four
cpu cluster). I have no reason to believe the quad-core would behave
differently than the cluster assuming appropriate software on the
quad-core.
N = n cpu's
O = observed run-time in minutes for multiple identical runs
D = observed decrease in runtime with n cpu's
T = theoretical decrease in runtime with n cpu's
N O D T
1 159 - 0
2 79 80 80
3 53 106 106
4 40 119 119
The equations for the reduction in processing time were also derived and
presented at AAPS in 2003, "Use of a Linux Cluster with PDx-Pop and
NONMEM V to Streamline Population Analysis", W. Bachman and W. Knebel.
Quoted reply history
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED]
On Behalf Of Steve Chapel
Sent: Monday, March 12, 2007 11:31 AM
To: [email protected]
Subject: Re: [NMusers] Linear speedup of NONMEM on quad-core CPUs?
That's really not my question. My question was about speedup of multiple
NONMEM runs, not one NONMEM run. Let me rephrase the question.
Let's say I have eight NONMEM jobs to run each week. Each NONMEM job
takes eight hours to run. I go to a computer and start one NONMEM job,
and when it is finished, I start another, and so on. After eight hours,
all eight NONMEM jobs are run.
The next week, I get a great idea. Instead of using one computer, I can
use eight computers. I start all eight NONMEM jobs at the same time, and
after only one hour they are all done. I have achieved eightfold
(linear) speedup in running eight jobs by using eight computers.
The next week, I make a further realization. The computers I was running
the NONMEM jobs are dual-core, so I need to use only four computers. I
start two NONMEM jobs on each of the four computers, and after one hour
all the jobs are done. The benefit is that this week I needed only four
computers to be available.
It might occur to me that all I really need is one computer with two
quad-core processors. I could start all eight NONMEM jobs simultaneously
on just one computer. The question is, has anyone actually tried this?
Does it run all eight NONMEM jobs in the same time it would take to run
one NONMEM jobs? In other words, has going from one core to eight cores
enabled an eightfold (linear) speedup in running eight NONMEM jobs? If
not, how much speedup might I expect from an eight-core computer?
-- Steve
Brian M. Sadler wrote:
> Steve,
>
> I have just set up NONMEM 6 on a 4GB Core(2) Quad system running XP64.
I
> don't yet have benchmarks, but I have noted activity on all four CPU
using
> the "/Qparallel" option with the Intel Fortran Compiler. I look
forward to
> hearing of others' experiences.
>
> Cheers... Brian
>
>
> -----Original Message-----
> From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On
> Behalf Of Steve Chapel
> Sent: Friday, March 09, 2007 12:08 PM
> To: [email protected]
> Subject: [NMusers] Linear speedup of NONMEM on quad-core CPUs?
>
> A few years ago there was a post about benchmarking results for NONMEM
> on a dual-core CPU
( http://huxley.phor.com/nonmem/nm/99nov212005.html).
> Given the relatively recent release of Xeon quad-core processors I
> wanted to know if anybody has compared NONMEM runs on a machine with
two
> dual-core processors to NONMEM runs on a quad-core CPU, or even NONMEM
> runs on a computer with two quad-core CPUs. Has anyone confirmed that
> having four or eight cores provides linear speedup of running four or
> eight NONMEM jobs? Alternatively, if anyone has confirmed that the
> speedup is not linear, what is the approximate speedup, and what was
> model number of the CPU(s)?
>
> If a similar topic has been discussed recently (in January or
February)
> on this mailing list, could someone please re-post the information? I
> just joined in March 2007, and the archives seem to contain no
messages
> from 2007.
>
> Thanks,
> Steve
>
>
>
>
>
_______________________________________________________________________________________________________________________________________