tips for customisiing a PC for scientific process

Posted on 2005-05-12
Last Modified: 2012-05-05
I have a software package consisiting of scientific process (i.e. CFD) and visualisation process for calculation results written in C and Java.  I would like to run this program in Linux on a PC customised for this specific purpose. I don't want unneccessary components for the customising project (e.g.  DVD player should be ruled out).

I want some advice on how to attain the best performance  from the PC.
for example, what are the significant points to construct the mothoerboard ?
processors(Intel or AMD), memory, bus type etc.

I don't know about the hardware.

Question by:bdp97126
    LVL 69

    Accepted Solution

    If scientific calculations are the main use, then cpu speed may be the most important factor.  You say you need to visualize the process - what software is being used to display it?  If it's OpenGL-based, you will want a video card that supports that.  At this point in time, I would say the socket 939 Athlon 64 cpus are the best for value and performance, and nForce3 chipset motherboards are best for supporting it.  I have an MSI K8N Neo2 Platinum motherboard teamed with an XFX 6600GT video card and it is a high performance machine that doesn't cost too much.  Since you are running Linux, you can take advantage of the 64-bit cpu now for applications.  Any further description you can give will be helpful in narrowing down the field.

    Author Comment


    the software is a CFD (computational Fuild dynamic) application, which was implemented in mainly Fotran and C.  
    a bunch of numerical process is involved.
    On the other hand, as a post-processing application, a Java 3D (OPEN-GL and VRML) application run to display the result in 3D virtual reality and animation. I would lile to make this program for multiple-users so that clients can use the application in their PC(MS Window) via Unix emualtor or soemthing(e.g. VNC).

    I understand that  the performance of PC (or server) is various even if the specification of CPU is same.
    Sometime slower CPU process is much faster than high-spec CPU.
    this overall performance is also dependent on the software, I guess.

    I hope this will be helpful for you to give me more tips.

    LVL 69

    Expert Comment

    The motherboard can be teamed up with a faster cpu if necessary, since socket 939 cpus go up to Athlon64 4000.  The Athlon64's have extraordinary memory bandwidth.  Do you know what currently works to your satisfaction with this application?  For example, some financial options calculations take several minutes to calculate, even with a modern cpu, and I'm sure fluid dynamics calculations also depend on how many nodes you are using in a simulation.

    The display performance will also depend on how many points you are trying to show.  OpenGL-specific cards can be very expensive, up to a thousand dollars, but lower-end models are available if top-of-the-line performance is not necessary.  Again, if you have a current benchmark that is satisfactory, that would helpful.  Keep in mind also that overlays can be difficult to show on multiple displays, much like DVD movies can only be shown on one screen (the software uses an overlay).
    LVL 13

    Expert Comment

    Just a comment on "DVD Player should be ruled out".  I presume that you need an optical drive to load things (including the OS) into the computer.  You may need a burner to get things out of the computer.  CD and DVD drives are both "optical drives".  In my view, the best optical drive made right now happens to be the Pioneer "09" series, a DVD burner, and it's under $60.  It does everything .... burns every form of writeable CD and DVD, and reads everything (every form of CD and DVD).  Whether you need DVD or not, why you would spend even $30 to get "just" a CD-ROM drive would escape me.  There is no "overhead cost" to having the extra capabilities if you don't use it.

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