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I am looking at building/buying myself a workstation for scientific computing. I will be doing molecular dynamics simulations that are memory intensive (data on a large number of particles and a million time steps or more) and require multiple instances of the same code running (to generate an ensemble). I am new to computing but my guess is I will be using C++ and learn to utilize the best memory handling practices. In terms of ensemble averaging, it appears to me I could either just run the code N times or maybe run N instances of the codes in simultaneously on N processors. At this point I don't have access to HPC resources and I am only trying to get a simple desktop (maybe 2 or 4 cores) but I want to learn to make this code parallel.

At this point I know very little about the code itself to make a more specific assessment of my needs. However, my question is what might be the very essential features I should keep in mind while buying a workstation. For example, things to keep in mind if eventually I want to transition to HPC, things to keep in mind if some amount of parallel processing needs to be done (or just having 2 or more cores in enough) etc.

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I can almost garentee we will need more information to give relevant answers. Do you have any idea what packages/libraries you will use? Or will you be rolling all of your own code (not recommended to say the least)? I recently spent close to 2 months speccing out a rackmount server for my own grad school career, and at the end of that time still ended up guessing on a lot of my requirements. Knowing what you need comes with experience with your code. – Godric Seer Jan 29 at 2:25
I fear you are asking for the silver bullet, ... Maybe the only general advice is to have an extra gpu dedicated to computation only. – Stefano M Jan 29 at 8:01
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Sankaran, perhaps you could rephrase the question to ask about what features of a new computer are the most relevant? As Godric mentioned, specifying the exact type of computations you are interested in doing and what type of software development you will be doing will be a help. Another really important question is whether you have access to HPC resources, because I usually recommend that people match hardware with their big machine whenever they can. – Aron Ahmadia Jan 29 at 11:26
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In addition to the points Godric Seer and @AronAhmadia made, I'm also concerned that answers to your question in its current form (which reads like a request for a shopping recommendation) will have a rather short half life, as hardware evolves quickly. Maybe it would be better to turn the question around: What are the computational bottlenecks and possibilities for parallelization in molecular dynamics (SIMD vs. multithread, memory bandwidth etc.)? The answers would tell you where to put your money. – Christian Clason Jan 29 at 12:58
Thanks Godric, Stefano, Aron, and Christian. I have tried to make the question more specific. Of course I do realize that this is a question with no specific answer. My only goal is to buy myself a decent starting machine so I can explore, something that will let eventually get the basics needed to transition to HPC. – Sankaran Jan 29 at 19:00

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