The ABINIT Users Mailing List ( CLOSED )

[Marcin Kaczmarski <mkaczm@us.edu.pl>]

Hello,
> 
>        Abinit is the main program in our group. Recently, 
> an USD50,000 fund was granted to us to set up a small PC 
> cluster. We consulted with both Intel and AMD companies 
> here in Shanghai, China. They all suggested a PC cluster 
> structure of 15 computing nodes (each with 2 CPUs on 1 
> motherboard) + 1 server connected together by 16 Intel 
> 1000M ethernet cards. As we have no experiences, we would
> be very grateful to you if the following questions could
> be clarified before our purchasing:
> 
>     (1) Could abinit program be installed and run on the 
> linux cluster where 2 CPUs on 1 motherboard share the same 
> memory?
> 
>     (2) Which version of MPICH works best for this kind
> of cluster and abinit?
>
        Please try not to  use mpich library especially on linux clusters. Try
rather LAM MPI library, because lam has approximately two times lower
latency than mpich which is very important, while the bandwith remains
almost unchanged ( it is a little bit smaller for lam).
        Considering using gigabit ethernet for your cluster it may be risky to
do that with 2cpu machines. For well paralellized planewave dft codes it
it usually enough to use triple fast ethernet cards or gigabit card for
1 cpu machines, but for 2 cpu machines gigabit may be not enough.
Practically it is often impossible to get better bandwith than
300Mbits/sec while using giabit ethernet with 32-bits motherboards.If
you really  want to have 2 cpu machines I would recommend using
SCI-dolphinics cards or Myrinet. SCI cards are then at the same
price-level while comparing with gigabit ethernet with a reliable switch
(buy only that one which supports jumbo frames)
and SCI are far better solution, perhaps myricom , giganet and sci are
the best industrial solution at this moment in the world. Sorry if I
omitted other companies.

 
>     (3) Which CPU (Intel and AMD) works best for thisipset 
> cluster and abinit?   
>   
        I saw benchmarks from planewave dft calculations with athlon 1.4GHz 
and
Pentium 1.7Ghz . Athlon was approximately 10-15 % faster. Perhaps this
is beacouse of very quick double precision calculations that amd
processors can do (3DNow). BUt if you want to buy pentium iv xeon or
penitum iii fsb 100 xeon with big cache they will be better than athlon
xp, or even mp but you will pay even 5-25 times more for such intel
processor.

If you plann to buy amd cpu then DO NOT BUY other mainboard than TYAN.
There is only one reliable chipset for amd cpu - it is amd760mp/mpx and
TYAN company motherboards are the most reliable and there are severeal
number of amd cluster that work only with tyan and sci or myricom or
giganet cards. Never buy any mainboard with via chipset  - it is not
good for clusters.


Consider if it is not better to buy quad cpu motherboard, because the
communication is the weakest part of cluster. As I know there are only
quad cpu for intel processor.

Best Regards

Marcin Kaczmarski