Re: [phenixbb] Memory and CPU usage

Hi Jon, you can find the answer without wasting time on guesswork... Take a few extreme cases from PDB (big model, many reflections, tricky space group), and run them from the command line: phenix.refine model.pdb data.mtz ordered_solvent=true --show-process-info The log file should contain memory usage throughout the run. Look for the max memory intake in the last record (towards the end of log file). This will give you an idea about how much memory you may need. Pavel On 7/22/12 4:31 AM, Jon Agirre wrote:

Dear Nat and Pavel,

thank you so much for your explanations. Assuming that the 8 in Nat's formula provides conversion to bytes, it is not such a big RAM requirement. I guess most virus structures should be approachable with an 8GB machine.

About the CPU, I think I'm going to invest in a quad-core. I feel quite comfortable in command line and I don't have fear paralelizing existing code.

Thanks again,

Jon

2012/7/21 Pavel Afonine mailto:[email protected]>

But the resolution_factor is inconsistent - for the FFT structure factors calculation (which is unavoidable), we are definitely using 1/3 (I assume for speed reasons). For most of the other optional tasks like rotamer correction and filling missing F-obs, it's 1/4.

Yes, we use 1/3 for structure factors and gradients calculations, and 1/4 in map calculation if the map is going to be used for things like water picking, real-space refinement, etc. This is intentional.

Pavel

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