Hi,
I'm looking for a high performance computing environment for genetic analysis.
As far as I understood, as well Opterons as Xeons can only address 4GB of main
memory per core. Is this right?
Looking for alternate platfoms, I came across the IBM Power 520 Express
(http://www-03.ibm.com/systems/power/hardware/520/), which is capable of
addressing up to 16GB as a single core system.
Furthermore, it runs linux, and should therefore be able to compile and run
common gentic analysis software such as plink
(http://pngu.mgh.harvard.edu/~purcell/plink/) or birdsuite
(http://www.broad.mit.edu/mpg/birdsuite/).
Did anyone ever try this before?
Recommedations, please!
Thx,
Chris

Mon, 30 Jun 2008 10:35:59 +0000, Chris:

> Hi,
> I'm looking for a high performance computing environment for genetic
> analysis. As far as I understood, as well Opterons as Xeons can only
> address 4GB of main memory per core. Is this right?
Deadly wrong.
address sizes : 36 bits physical, 48 bits virtual

Do your math and discover you could address 64G of ram per processor.
(and 256TB of total memory)

Of course you have to use a 64bit os if you're not asking for troubles.

Mon, 30 Jun 2008 10:35:59 +0000, Chris:

> Hi,
> I'm looking for a high performance computing environment for genetic
> analysis. As far as I understood, as well Opterons as Xeons can only
> address 4GB of main memory per core. Is this right?
Deadly wrong
address sizes : 36 bits physical, 48 bits virtual


i.e. 64GB ram (256TB of total memory).

Mon, 30 Jun 2008 10:35:59 +0000, Chris:

> Hi,
> I'm looking for a high performance computing environment for genetic
> analysis. As far as I understood, as well Opterons as Xeons can only
> address 4GB of main memory per core. Is this right?
Deadly wrong
address sizes : 36 bits physical, 48 bits virtual


i.e. 64GB ram (256TB of total memory).

On Mon, 30 Jun 2008 10:35:59 UTC in comp.os.linux.hardware, Chris
<me@privacy.net> wrote:

> As far as I understood, as well Opterons as Xeons can only address 4GB of main
> memory per core. Is this right?

No.

--
Trevor Hemsley, Brighton, UK
Trevor dot Hemsley at ntlworld dot com

Jim <Jim@j.eu> wrote:
> Mon, 30 Jun 2008 10:35:59 +0000, Chris:
>
>> Hi,
>> I'm looking for a high performance computing environment for genetic
>> analysis. As far as I understood, as well Opterons as Xeons can only
>> address 4GB of main memory per core. Is this right?
> Deadly wrong
> address sizes : 36 bits physical, 48 bits virtual
>
>
> i.e. 64GB ram (256TB of total memory).
Thanks.
So, to get a single-core Xeon 32GB Ram system, which hardware is needed?
Most mainboards applicable do not support that much Ram.
Is it reasonable at all?
How is the performance compared to an Opteron for single core apps?
Thx,
Chris

In article <g4acuf$291d$1@gwdu112.gwdg.de>, Chris <me@privacy.net> wrote:
> I'm looking for a high performance computing environment for genetic analysis.
> As far as I understood, as well Opterons as Xeons can only address 4GB of main
> memory per core. Is this right?

Hm, even the 64-bit chips? I would've thought they'd be able to address
2^64 B (16 EiB) per core. Not so?

--
"Never go off on tangents, which are lines that intersect a curve at
only one point and were discovered by Euclid, who lived in the 6th
century, which was an era dominated by the Goths, who lived in what we
now know as Poland." - from Nov. 1998 issue of Infosystems Executive.

Chris <me@privacy.net> writes:
>Jim <Jim@j.eu> wrote:
>> address sizes : 36 bits physical, 48 bits virtual
>>
>>
>> i.e. 64GB ram (256TB of total memory).

I am pretty sure today's Xeons support more than 64GB. Certainly
there are motherboards that support 128GB of physical RAM.

>Thanks.
>So, to get a single-core Xeon 32GB Ram system, which hardware is needed?
>Most mainboards applicable do not support that much Ram.

There are quite a number of Xeon motherboards that support 32GB and
more. They are typically dual-socket boards, but you can run it with
only one socket equipped. I think nowadays you can but only dual- and
quad-core Xeons, but maybe you can get a single-core Xeon that fits on
the second-hand market.

>Is it reasonable at all?

Doing it with a single-core Xeon is not reasonable (they are based on
the Pentium 4, if you can get them at all). I suggest getting a
dual-core Xeon 51xx or 52xx (i.e., Core 2 Duo-based), which tend to be
faster (even for single-threaded applications) and consume less power.

>How is the performance compared to an Opteron for single core apps?

The fastest of the Xeons mentioned above are faster than the fastest
Opterons on most single-threaded applications. Also, if you want
32GB, it may be cheaper to equip both sockets of a dual-core board to
get two additional memory channels than to try to do it with one
Opteron (and forget about single-socket Opteron boards, they don't
have enough memory slots).

- anton
--
M. Anton Ertl Some things have to be seen to be believed
anton@mips.complang.tuwien.ac.at Most things have to be believed to be seen
http://www.complang.tuwien.ac.at/anton/home.html

Chris wrote:
> Hi,
> I'm looking for a high performance computing environment for genetic analysis.
> As far as I understood, as well Opterons as Xeons can only address 4GB of main
> memory per core. Is this right?

No, Opterons are able to address upto 1TB of memory, no matter how many
cores, and something like 256TB of memory spread across multiple sockets
(rather than cores). Xeons are dependent on their chipset memory
controller, and their limitations. Depending on the chipset, Xeons
should also be able to address upto 1TB of memory, and more spread
across independent chipsets (rather than shared chipsets).

This is also dependent on current RAM manufacturing technology. If the
RAM itself can't be made dense enough, then you're probably limited in
the amount of memory just based on that.

Yousuf Khan

Mon, 30 Jun 2008 16:15:13 +0000, Anton Ertl:

> Chris <me@privacy.net> writes:
>>Jim <Jim@j.eu> wrote:
>>> address sizes : 36 bits physical, 48 bits virtual
>>>
>>>
>>> i.e. 64GB ram (256TB of total memory).
>
> I am pretty sure today's Xeons support more than 64GB. Certainly there
> are motherboards that support 128GB of physical RAM.

Show me address sizes and I'll tell you.