Budget Server for Molecular Dynamics

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BaSuP

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Hi, I wonder if guys you can help me setup a decent server that is capable calculating molecular dynamics calculations pretty well. So here is the problem:

I used Gromacs (software that does these kinds of simulations) to run a water+ion+protein system with about 70k atoms on a 24 core server (not sure what kind of CPUs) and it was able to simulate about 10 ns of the 70k water+ion+protein system in a about a day's worth of time.

For these kinds of simulations to yield biologically relevant data, I need to run the system for about at least a microsecond. That means that I need to run the simulation for about 100 day on that 24 core system. It is not worth it.

Now the Gromacs team have written code that can make use of Nvidia's GPU together with CPUs. See this presentation if you are interested.

To give you an idea of how much this speeds up these simulation, I have run the same 70k water+ion+protein system on my desktop with a Xeon 1230v2 chip and an evga 660ti GPU and it yielded about 25 ns per day. But this is still not enough.

So I am thinking of applying for a research grant that allows for purchases of assets as I would like to train post-graduate students (still looking for them :p) on these desktop servers.

I was thinking of the following build:
CPU: 2x Intel Xeon™ E5-2630 - 2.30GHz Six Core (12 Thread), Socket 2011, 15MB L3 Cache
GPU: 4x GIGABYTE GV-N760OC-2GD, GTX760
MB: Asus Z9PE-D8 WS LGA2011 (Dual Xeon)
RAM: 2GB per core so --> 3x Kingston KVR13E9K3/24I ValueRam 3x8GB DDR3-1333 1.5V CL9 ECC

It comes in at R37500 and should do membrane proteins with 120k atoms at about 100ns per day, so a ten day simulation would be worth it. If I can get closer to about R30K it would be great (perhaps a cheaper GPU such as a 660ti? or cheaper RAM?)

Any suggestions would be great. Thanks :).
 
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RAM won't make a huge dip in the price,your CPU and graphics cards are contributing the most. Are there any benchmarks to show the Xeon's compared to i7 chips for these sims?
 
PsyWulf said:
RAM won't make a huge dip in the price,your CPU and graphics cards are contributing the most. Are there any benchmarks to show the Xeon's compared to i7 chips for these sims?
Click to expand...
Xeons with the same amount of cores as I7's perform in the same range as their I7 counterparts. For example, if you look at this graph here: http://www.cpubenchmark.net/high_end_cpus.html

Then a Xeon 1270 v3 would perform more or less the same when compared to an Intel I7 4470K.

The reason I opted for the above build is that the Xeon E5 range allows for dual CPUs on a motherboard and gives 12 cores+hyperthreading (i.e. 24 threads). Unfortunately the I7s can't be used in dual CPU builds (as far as I understand anyway, I hope I am wrong :p).
 
Have you considered getting server farms to do it for you? Amazon offers it as a service, and you pay in CPU time (per hour).
 
froot said:
Have you considered getting server farms to do it for you? Amazon offers it as a service, and you pay in CPU time (per hour).
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First time I have heard of it. Thanks, I'll have a look.
 
Thank you very much, I think I will try this! A quick look around there and it appears that the EC2 service is what I am looking for right?
 
BaSuP said:
Xeons with the same amount of cores as I7's perform in the same range as their I7 counterparts. For example, if you look at this graph here: http://www.cpubenchmark.net/high_end_cpus.html

Then a Xeon 1270 v3 would perform more or less the same when compared to an Intel I7 4470K.

The reason I opted for the above build is that the Xeon E5 range allows for dual CPUs on a motherboard and gives 12 cores+hyperthreading (i.e. 24 threads). Unfortunately the I7s can't be used in dual CPU builds (as far as I understand anyway, I hope I am wrong :p).
Click to expand...

Was thinking drop the dual CPU setup and go single with more graphics cards,might give you more bang for bucks

But the AWS option would be quite handy
 
Does it have to be nvidia gpus? amd gpus have more processing power than nvidia which was evident in bitcoin mining rigs.
Is the software compatible with asics? those things make gpu acceleration look like a left hand thrower.
 
Rocket-Boy said:
Does it have to be nvidia gpus? amd gpus have more processing power than nvidia which was evident in bitcoin mining rigs.
Is the software compatible with asics? those things make gpu acceleration look like a left hand thrower.
Click to expand...
Unfortunately not at the moment. The software was written to make use of Nvidia's Cuda development. I think in the future open-source software such as OpenMM will be developed so that AMD GPUs can be used.
 
Has anybody had some experience with the Amazon services?
 
After you used your planned setup for the simulation, wouldn't it make a great gaming PC? :whistle:
 
creeper said:
After you used your planned setup for the simulation, wouldn't it make a great gaming PC? :whistle:
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Haha, I would imagine so.

I decided to try the chpc option and so far they have been very helpful. They have a GPU cluster, imagine that and gaming... :D.
 
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