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Building a Desktop Number Cruncher



 
 
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  #1  
Old September 28th 07, 04:43 AM posted to alt.comp.hardware
Tom
external usenet poster
 
Posts: 6
Default Building a Desktop Number Cruncher

I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?

http://computershopper.com/reviews/a...erboard-review

The above motherboard accepts up to 8 gigabytes (4 x 2) of DDR3 memory
at up to 1,600 MHz.

Considering Vista Ultimate 64-bit is able to support up to 128GB of
memory ...

http://www.crucial.com/kb/answer.aspx?qid=4251

.... what motherboard/memory card combinations should I consider that
could go beyond the above motherboard's 8 gig limit?

I am currently looking at Intel Quad CPU's ... but understand that for
pure number crunching tasks there are other issues (i.e. L2 cache)
that enter into the performance calculation. Perhaps I should consider
an AMD configuration?

A dream set-up would be a multibladed server with lots of cores
working independently ... but for now a quad core desktop would really
be stretching my available funds. The ultimate would some research
super computer!!

Looking into DDR3 memory modules and latency issues

http://www.kingston.com/hyperx/products/ddr3_faq.asp
---------------------------------
Below is from above site:

Q. What latencies will standard DDR3 DIMMs support?

A. JEDEC DDR3 specifications define standard DDR3 CAS Latencies of 7,
9, and 10:
-1066MHz DDR3: CAS 7 (7-7-7)
-1333MHz DDR3: CAS 9 (9-9-9)
-1600MHz DDR3: CAS 10 (10-10-10)

----------------------------------

Seems the higher latency chews up a lot of the higher speed
performance?

Any advice for building a good number cruncher will be much
appreciated.

I will greatly value the input from those with 64-bit experience.

Currently I am stuck in the single core, 32-bit realm and am looking
for the fast lane.

GiGa-Thanks !!
  #2  
Old September 28th 07, 05:18 AM posted to alt.comp.hardware
CBFalconer
external usenet poster
 
Posts: 919
Default Building a Desktop Number Cruncher

Tom wrote:

I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?

http://computershopper.com/reviews/a...erboard-review

The above motherboard accepts up to 8 gigabytes (4 x 2) of DDR3 memory
at up to 1,600 MHz.

Considering Vista Ultimate 64-bit is able to support up to 128GB of
memory ...


Don't even consider Vista. Linux will give you more performance,
be totally transparent, and you can have complete source if you
wish. It also costs much less. Nor will it call home and expose
all your secrets. Best of all is the EULA.

--
Chuck F (cbfalconer at maineline dot net)
Available for consulting/temporary embedded and systems.
http://cbfalconer.home.att.net



--
Posted via a free Usenet account from http://www.teranews.com

  #3  
Old September 28th 07, 07:00 AM posted to alt.comp.hardware
Tom
external usenet poster
 
Posts: 6
Default Building a Desktop Number Cruncher

On Fri, 28 Sep 2007 00:18:12 -0400, CBFalconer
wrote:

Tom wrote:

I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?

http://computershopper.com/reviews/a...erboard-review

The above motherboard accepts up to 8 gigabytes (4 x 2) of DDR3 memory
at up to 1,600 MHz.

Considering Vista Ultimate 64-bit is able to support up to 128GB of
memory ...


Don't even consider Vista. Linux will give you more performance,
be totally transparent, and you can have complete source if you
wish. It also costs much less. Nor will it call home and expose
all your secrets. Best of all is the EULA.

--
Chuck F (cbfalconer at maineline dot net)
Available for consulting/temporary embedded and systems.
http://cbfalconer.home.att.net



Thanks Chuck --

I have begun researching Linux 64 bit. First article I found dated
back to 2003 ... so there must be a LOT for me to catch up on! I have
never used Linux ... but I keep hearing the phrases of those who do.
Perhaps I should take the plunge. I'd much prefer stability, security,
and performance over aero effects and phone home hassles. The only
hesitation is my total ignorance of Linux. I guess everything would be
new from word processor, spreadsheet, C/C++ IDE, etc. That's a big
bite to take ... but it does look appealing.

Thanks again for the advise.

-- Tom

  #4  
Old September 28th 07, 07:28 AM posted to alt.comp.hardware
kony
external usenet poster
 
Posts: 7,416
Default Building a Desktop Number Cruncher

On Thu, 27 Sep 2007 22:43:50 -0500, Tom
wrote:

I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?


First, you should determine which processor architecture
performs best at your particular App. Until you know this,
you can't know if a particular board is the best choice
since it will only support one of several CPU possibilities.

For some uses, including general PC use, a Core2Duo is the
best median-priced option, but when talking about a special
purpose build, Core2Duo may not be the right choice. In
some cases, even the dreaded Pentium4 is a better band for
the buck, but are you looking for best band for buck or best
performance, IOW, what is more important the price or
performance if you had to pick one, and what is the budget
ceiling?


http://computershopper.com/reviews/a...erboard-review

The above motherboard accepts up to 8 gigabytes (4 x 2) of DDR3 memory
at up to 1,600 MHz.


Ok, but how much memory do you *need* for your special
purpose? Beyond a certain point, adding more memory than is
needed just raises cost and/or requires slower memory
timings that will degrade the performance of the application
by a few percent.



Considering Vista Ultimate 64-bit is able to support up to 128GB of
memory ...

http://www.crucial.com/kb/answer.aspx?qid=4251

... what motherboard/memory card combinations should I consider that
could go beyond the above motherboard's 8 gig limit?


Number crunching seldom needs these large amounts of memory.
Would you be surprised if the typical number cruncher didn't
even need 128MB with WinXP? However, I don't know your
particular application, that will certainly matter.



I am currently looking at Intel Quad CPU's ...


Why? Is your app quad core optimized? Most number cruncher
apps aren't even dual core optimized. Generally
(historically) someone looking for good number crunchig
would want to determine if floating point performance is
important, what L2 cache size their working code fits
within, and within these limitations, pick the highest IPC
core and highest clockspeed core possible. When doing a
specific thing, the generalized web review benchmarks fly
out the window. It really matters a lot what the specifics
are of your particular task.


but understand that for
pure number crunching tasks there are other issues (i.e. L2 cache)
that enter into the performance calculation. Perhaps I should consider
an AMD configuration?


You should seek benchmarks of your specific app, or find a
roughly equivalent task keeping in mind issues of floating
point significance (or not), cache size, clockspeed, etc...
then seek benchmarks for that equivalent app on different
CPU designs.



A dream set-up would be a multibladed server with lots of cores
working independently ...



Really? Can your code accomplish this? If it can't, some
kind of exotic cooling to run fewer cores and insane speeds
would be more effective.



but for now a quad core desktop would really
be stretching my available funds. The ultimate would some research
super computer!!


Maybe, maybe not. Some tasks depend more on a fast memory
bus, and to make use of parallel processing you would
require code written to do it. IOW, on some supercomputers,
some apps will run slower than on a modern purpose-optimized
desktop.



Looking into DDR3 memory modules and latency issues

http://www.kingston.com/hyperx/products/ddr3_faq.asp
---------------------------------
Below is from above site:

Q. What latencies will standard DDR3 DIMMs support?

A. JEDEC DDR3 specifications define standard DDR3 CAS Latencies of 7,
9, and 10:
-1066MHz DDR3: CAS 7 (7-7-7)
-1333MHz DDR3: CAS 9 (9-9-9)
-1600MHz DDR3: CAS 10 (10-10-10)

----------------------------------

Seems the higher latency chews up a lot of the higher speed
performance?


I am starting to suspect your post is some kind of
kid's-dream, that you are not serious about really building
a system. You write about PC parts then DDR3 and
supercomputers. If you can divide the work like that, how
about just building separate budget-effective systems.
Three $1,000 systems will have higher performance than one
$3,000 system if you can do this.




Any advice for building a good number cruncher will be much
appreciated.

I will greatly value the input from those with 64-bit experience.


Why? Do you see a benefit from a 64 bit system? Your post
is far too light on details of your applications
optimizations and requirements.


Currently I am stuck in the single core, 32-bit realm and am looking
for the fast lane.


If you have no reason to believe these more exotic things
will help, a 32bit single core may actually be the highest
performing solution. It depends entirely on exactly what
you're trying to do, down to the last detail. I'm not
trying to discourage an elaborate cutting edge system but so
far, no details have suggested a gain from these things.
  #5  
Old September 28th 07, 07:32 AM posted to alt.comp.hardware
CBFalconer
external usenet poster
 
Posts: 919
Default Building a Desktop Number Cruncher

Tom wrote:
CBFalconer wrote:
Tom wrote:

I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?

http://computershopper.com/reviews/a...erboard-review

The above motherboard accepts up to 8 gigabytes (4 x 2) of DDR3 memory
at up to 1,600 MHz.

Considering Vista Ultimate 64-bit is able to support up to 128GB of
memory ...


Don't even consider Vista. Linux will give you more performance,
be totally transparent, and you can have complete source if you
wish. It also costs much less. Nor will it call home and expose
all your secrets. Best of all is the EULA.


I have begun researching Linux 64 bit. First article I found dated
back to 2003 ... so there must be a LOT for me to catch up on! I have
never used Linux ... but I keep hearing the phrases of those who do.
Perhaps I should take the plunge. I'd much prefer stability, security,
and performance over aero effects and phone home hassles. The only
hesitation is my total ignorance of Linux. I guess everything would be
new from word processor, spreadsheet, C/C++ IDE, etc. That's a big
bite to take ... but it does look appealing.


Just go to ubuntu.com and order the (free) cdrom.

--
Chuck F (cbfalconer at maineline dot net)
Available for consulting/temporary embedded and systems.
http://cbfalconer.home.att.net



--
Posted via a free Usenet account from http://www.teranews.com

  #6  
Old September 28th 07, 10:27 AM posted to alt.comp.hardware
GT
external usenet poster
 
Posts: 889
Default Building a Desktop Number Cruncher

"Tom" wrote in message
...
I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?


Before answering any of the other points in your post. Is the number
crunching software multithreaded? If it is written in C, then I would
suspect not, so multiple cores etc is a waste of time!


  #7  
Old September 28th 07, 10:28 AM posted to alt.comp.hardware
GT
external usenet poster
 
Posts: 889
Default Building a Desktop Number Cruncher

"CBFalconer" wrote in message
...
Tom wrote:
CBFalconer wrote:
Tom wrote:

I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?

http://computershopper.com/reviews/a...erboard-review

The above motherboard accepts up to 8 gigabytes (4 x 2) of DDR3 memory
at up to 1,600 MHz.

Considering Vista Ultimate 64-bit is able to support up to 128GB of
memory ...

Don't even consider Vista. Linux will give you more performance,
be totally transparent, and you can have complete source if you
wish. It also costs much less. Nor will it call home and expose
all your secrets. Best of all is the EULA.


I have begun researching Linux 64 bit. First article I found dated
back to 2003 ... so there must be a LOT for me to catch up on! I have
never used Linux ... but I keep hearing the phrases of those who do.
Perhaps I should take the plunge. I'd much prefer stability, security,
and performance over aero effects and phone home hassles. The only
hesitation is my total ignorance of Linux. I guess everything would be
new from word processor, spreadsheet, C/C++ IDE, etc. That's a big
bite to take ... but it does look appealing.


Just go to ubuntu.com and order the (free) cdrom.


Will that OS run a windows based application?


  #8  
Old September 28th 07, 04:13 PM posted to alt.comp.hardware
Pecos[_2_]
external usenet poster
 
Posts: 49
Default Building a Desktop Number Cruncher

Tom wrote in
:

I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.


snip

I will greatly value the input from those with 64-bit experience.

Currently I am stuck in the single core, 32-bit realm and am looking
for the fast lane.

GiGa-Thanks !!


Giga Hellos Tom,

I have used XP x64 and Vista 64 bit and I like them a lot but there are
some issues that you should consider before you go that route.

Not all hardware has drivers for the 64 bit versions but since you are
talking about building from scratch, you can eliminate those problems up-
front with some research. You would still have to worry though about
drivers for printers, modems, scanners, etc that you already own.

Next you need to find out if the applications that you want to run will
work in the 64 bit version.

Forget 16 bit programs - they won't run at all.

32 bit programs for the most part will run, but verify first. Programs
like firewalls, anti-virus and some games are the most problematic.

64 bit programs will run of course, but are still few and far between.

Since you don't need Aero, XP x64 would probably be a better choice for
you. If you have the right drivers, it is very stable and fast. I don't
know this for a fact, but I suspect XP x64 would run most number
crunching apps faster than Vista 64 bit.

You can still order or download a free trial version of XP x64 at:
http://www.microsoft.com/windowsxp/6...cts/trial.mspx

Try it and see if it works for you. You have 120 days to test it before
it goes into 60 days of 'limited functionality mode'.

As you say, the 64 bit operating systems break the 4 GB barrier, but if
you only need two GB to do your number crunching, 32 bit will suffice.
The 64 bit versions *are* recommended for people just like you who will
be working with large amounts of data like audio/video editing and large
data file manipulation. You didn't mention just how much data you will
be crunching.

You should also consider a RAID 0 or RAID 0 + RAID 1 setup in addition to
a standalone hard drive if you want speed. Your hard drive will be a
real bottleneck when working with large data files. The RAID 0 volume
space is perfect for fast temporary data manipulation. Again, this
depends on just how big these data files of yours are.

--
Alan "Pecos" Norton
  #9  
Old September 28th 07, 06:42 PM posted to alt.comp.hardware
Tom
external usenet poster
 
Posts: 6
Default Building a Desktop Number Cruncher

On Fri, 28 Sep 2007 10:27:30 +0100, "GT"
wrote:

"Tom" wrote in message
.. .
I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?


Before answering any of the other points in your post. Is the number
crunching software multithreaded? If it is written in C, then I would
suspect not, so multiple cores etc is a waste of time!


Yes, it is multi-threaded. The reason I mentioned the program type was
so that others would realize I was not building a gaming rig or
running a canned application that required a specific operating
system. BTW ... my current favorite book on this topic is Sybex's "C#
Network Programming" by Richard Blum. Even though it is based on C#
and not C++.

The program uses double precision predominately. Thus it takes two
clock cycles to move a single value. I have zero 64 bit experience,
but simply moving values in one clock cycle should drastically improve
the speed.

To run a single thread requires about 0.7 gig of ram including the
full buffering of raw data. A single 2.4 GHz machine requires about 10
hours per window year. Thus a 4 year moving and dynamically optimized
window requires 40 hours each time you move the window.

I'm wanting to build a 4 core system in the $2,000 to $3,500 range and
make smart choices on operating system and components. My guess is
that such a system can reduce my current machine's topology 40 hour
run times down to about 4 hours.

Do I need more than 8 gig of ram for a 4 core system when running my
topology program? No.

I do not know if there is a time penalty for allowing each thread on
each core to share the same buffered raw data. If there is a time
penalty ... each core could independently buffer the same data.
Certainly the number of threads and cores directly impacts the
performance of topology type work. Two gigs of ram would be sufficient
for four threads if no data buffer sharing penalty exists.

My question about addressing up to 128 gig with a 64 bit operating
system is not just a hardware curiosity issue. In the future I want to
run multiple instances of my program in real time data acquisition
mode. Each instance will need approximately 0.3 gig of ram. I could
easily need to run 40+ instances simultaneously and thus will exceed
the typical motherboard 8 gig limit.

I am now becoming very interested in Linux. However, I do also have a
Vista Ultimate question for those with this experience.

- Can you easily dual boot Vista Ultimate? I'd like to boot in 64 bit
mode for running my topology program and in 32 bit mode to run various
canned applications that I already own. I'm betting someone in here
knows the slickest way to boot in Vista 32, Vista 64, Linux, etc.
Using Partition Magic and renaming the partitions seems clunky ... but
I have never done it. Maybe a Boot Magic program? Any suggestions
along these lines folks?

Thanks again for any help received.

-- Tom
  #10  
Old September 28th 07, 06:56 PM posted to alt.comp.hardware
[email protected]
external usenet poster
 
Posts: 466
Default Building a Desktop Number Cruncher

Tom wrote:
On Fri, 28 Sep 2007 10:27:30 +0100, "GT"
wrote:
"Tom" wrote in message
.. .


I want to build a good desk top number cruncher. Primary usage is a C
based program that performs the mathmatical calculations used to map
out a topology of various parameters. I do not need high end graphics.

Is a motherboard such as the ASUS P5K3 Delux a good choice?


Before answering any of the other points in your post. Is the number
crunching software multithreaded? If it is written in C, then I would
suspect not, so multiple cores etc is a waste of time!


Yes, it is multi-threaded. The reason I mentioned the program type was
so that others would realize I was not building a gaming rig or
running a canned application that required a specific operating
system. BTW ... my current favorite book on this topic is Sybex's "C#
Network Programming" by Richard Blum. Even though it is based on C#
and not C++.

The program uses double precision predominately. Thus it takes two
clock cycles to move a single value. I have zero 64 bit experience,
but simply moving values in one clock cycle should drastically improve
the speed.

To run a single thread requires about 0.7 gig of ram including the
full buffering of raw data. A single 2.4 GHz machine requires about 10
hours per window year. Thus a 4 year moving and dynamically optimized
window requires 40 hours each time you move the window.

I'm wanting to build a 4 core system in the $2,000 to $3,500 range and
make smart choices on operating system and components. My guess is
that such a system can reduce my current machine's topology 40 hour
run times down to about 4 hours.

Do I need more than 8 gig of ram for a 4 core system when running my
topology program? No.

I do not know if there is a time penalty for allowing each thread on
each core to share the same buffered raw data. If there is a time
penalty ... each core could independently buffer the same data.
Certainly the number of threads and cores directly impacts the
performance of topology type work. Two gigs of ram would be sufficient
for four threads if no data buffer sharing penalty exists.

My question about addressing up to 128 gig with a 64 bit operating
system is not just a hardware curiosity issue. In the future I want to
run multiple instances of my program in real time data acquisition
mode. Each instance will need approximately 0.3 gig of ram. I could
easily need to run 40+ instances simultaneously and thus will exceed
the typical motherboard 8 gig limit.

I am now becoming very interested in Linux. However, I do also have a
Vista Ultimate question for those with this experience.

- Can you easily dual boot Vista Ultimate? I'd like to boot in 64 bit
mode for running my topology program and in 32 bit mode to run various
canned applications that I already own. I'm betting someone in here
knows the slickest way to boot in Vista 32, Vista 64, Linux, etc.
Using Partition Magic and renaming the partitions seems clunky ... but
I have never done it. Maybe a Boot Magic program? Any suggestions
along these lines folks?

Thanks again for any help received.

-- Tom


If youre only interested in running an application, there is no need
for all the extra guff in vista, it would merely consume useful
resources and slow things down.

A single program will see more resources and run a bit better under
win if you use winsolo.


NT

 




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