[gmx-users] Suggestion needed for new workstation

Martin Höfling martin.hoefling at gmx.de
Sun Aug 12 14:57:52 CEST 2007

Am Freitag, 10. August 2007 schrieb Erik Lindahl:

> >> RAM size shouldn't be an issue, except if you're simulating huge
> >> systems.
> >
> > RAM is essential for some analysis tools and if you want to do ab
> > initio
> > calculations.

Ok, i was mainly concerned about doing longer simulations, you're right with 
analysis and probably too with ab initio ;-)

> And remember that there are 8 cores in this machine, so with 8
> processes running in parallel I don't think 8Gb is excessively much.

This probably strongly depends on what you're doing. We have 4 way nodes with 
8G. Our simulations seldom use more than a few percent, so thinking about it 
befor can save you some money and ram can also be upgraded easily.

> However, if you priced it out at apple.com you should be aware that
> Apple charges a _lot_ for memory. FB-DIMMs are expensive, but you can
> often find mac-certified memory for half the price elsewhere (e.g.
> Kingston).

Personally, I never have seen an advantage in "original" ram, no matter if it 
is lenovo or apple or ... whatever. We upgraded our G5 workstation 
with "cheap" ram and many others are also running with it. Reliability might 
make a difference for critical infrastructure but "original" ram can fail 

> > Today: Dual Intel Woodcrest with 3GHz and Infiniband connection, i
> > don`t know

How pricy is infiniband interconnect per node? Is it in range for low end 
cluster systems already? Some years ago. The only "cheap" interconnect 
compared to rest of the hardware was Gigabit, which is probably the worst 
choice if you're doing inter-node calculations.

> > how clovertown architecture will scale with more than 2 nodes
> > (haven`t tested
> > it yet or seen any benchmark results)
> >
> > Later this year i would think about Penryn architecture from Intel.
> > Opteron
> > CPUs are nice, but if you are using mainly gromacs, buy Intel.
> I think the new Barcelona Opterons will be very interesting even if
> they are about the same speed as the Intel CPUs.
> First, they should be very competitively prices, and second the
> memory is standard cheap registered DDR2 (ECC), which matters a lot
> when you are buying ~8Gb per dual quad-core machine.

Not to forget the other hardware. Chipsets and so on are pricier on intel arch 

Best and thanks for the comments

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