Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

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Keivan
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Joined: Sat Apr 22, 2006 4:28 am

Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by Keivan »

Reading the book named "Introduction to Parallel Programming Concepts", I find this phrase
while L1 cache in a modern CPU is random access, access to the main memory
(DRAM) is fastest when sequential. Morever, on a PC access to cache is much, much faster than
access to main memory, even when main memory is on the same circuit board. Consequently,
a program developer should attempt to partition calculations into blocks of data that will fit
into cache. This is done automatically for some optimized libraries such as ATLAS, used for
linear algebra.
I want to know your opinion about this library? (If it is useful to improve, neurons cache efficacy further)

Also, I have decided to buy a new Multiprocessor workstation, to work on my neuron project. In that book, there is another phrase that say
For high-performance computing (HPC) applications, better performance has often been obtained
when SMT was disabled. It remains to be determined the efficiency of SMT on the Intel Core
i7 processor introduced at the end of 2008.
I have 2 options available -->
1) to buy a core i7 950, --> (High End CPU's benchmark) OR
2) buy a 2 xeon 5405 processors (Multiple CPU Systems benchmark)
both of them are in the same range of price. I want to know which one is recommended for neuron.
ted
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Re: Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by ted »

It is probably a mistake to focus on raw speed. Within a given price range, differences tend to be small and idiosyncratic, with different CPU architectures leading and lagging in different tests. Who knows which of these benchmarks is most like what you're actually going to do with your new machine?

If you're buying a box that is going to sit in a rack grinding out numbers, never to be attached to monitor or keyboard, then speed and memory are the determining factors. However, CPU speed isn't the only thing that affects overall performance; memory speed, bus speed, and hard drive speed and capacity are also important. And it is a mistake to skimp on memory if you plan to simulate large models or analyze the results of long simulations.

Graphics performance is important if you intend to use this new machine for interactive program development or data analysis. If you're using Linux, it may be helpful to know that nVidia has a history of better Linux support than Radeon.

"Balance in all things," as the Epicureans would say.
Keivan
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Joined: Sat Apr 22, 2006 4:28 am

Re: Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by Keivan »

Thank you ted for your recommendation.
If you're using Linux, it may be helpful to know that Nvidia has a history of better Linux support than Radeon.
Thank you I didn't know that. Also I like NVIDIA for its GPGPU technology. Maybe some day I made neuron faster using GPUs!!
If you're buying a box that is going to sit in a rack grinding out numbers, never to be attached to monitor or keyboard, then speed and memory are the determining factors. However, CPU speed isn't the only thing that affects overall performance; memory speed, bus speed, and hard drive speed and capacity are also important. And it is a mistake to skimp on memory if you plan to simulate large models or analyze the results of long simulations.
I don't want a fast machine in every aspect, the only important thing to me is the numerical simulation in the neuron. Let me expand my question.
I always assemble my computers myself. so there is no limitation in the VGA or HDD for me.
If I buy a xeon 5405 I would have 8 physical cores each one 2GHz in frequency, and (12MB of L2 cache per chip) * 2 available + DDR2 technology.
If I buy a Core i7 I would have 4 physical cores, with SMT would be 8 cores with higher frequency 3GHz and only 8mb of cache + DDR3 technology.
I really don't know, but, my models probably would have 100,000 stats (a complicated single cell model 10 times more complicated than poirazi 2003 CA1 model).
I didn't noticed a lot memory consumption in my model but when I activate cache effect on my model it become 100% faster.
In a 2 core laptop I have see about 30% improvement in speed.

It is a little bit complicated, I know. But, I really could not decide what to do. There is no benchmark available about numerical modeling in the net.
Before core i7 I was sure about xeon 5400 series but now I realy don't know. I thought the programmers may know which architecture is better for their software. Which one would be your choice?
ted
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Re: Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by ted »

This is too much of an "on the one hand this, but on the other hand that" situation for me to point you to either one. My prejudice favors the faster machine with 4 cores because (1) even though there are only 4 of them, there's more cache per core than in the 8 core machine, (2) they're faster than the cores in the 8 core machine, and (3) unless I'm mistaken, DDR3 is faster than DDR2. But it's just that--my personal prejudice.
Keivan
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Re: Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by Keivan »

thank you ted
ted
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Re: Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by ted »

Just don't blame me if it turns out to be the wrong choice!
Keivan
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Re: Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by Keivan »

I know ted. I just wanted to appreciate you because you give your time to me and think about my question and told me your idea. I am very happy there are such person like you and Hines to support us and help us progresses in our research with less pain.
------------------------------------------
PS: Neuron behaves strange sometimes. If you had time test this. Compile neuron with gcc-3 and gcc-4. Every one believe that the gcc-4 is a new compiler that works better and can make software faster than gcc-3, because of new technologies new vectorization method and also better support for new CPUs and SSE instructions. However, gcc-3-compiled-neuron is significantly faster than gcc-4-compiled one (I tested this in windows XP, because my ubuntu does not support g++-3). I don’t know why? But I am trying to understand.
I say this to make you sure that I know in the research field, there is no easy way sometimes.

PS: congradulations for the new website. I like that hippocampus banner.
ted
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Re: Your Opinion about ATLAS Library? +Xeon 5400 or Core i7?

Post by ted »

Glad to be of help.

I don't have much to say about compilers, except that I'm glad somebody else is providing support and development.

As far as the new web site is concerned, you may have noticed that we don't spend much time on artistic touches. But this drawing by Ramon y Cajal seemed just right for this purpose.
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