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Memory Issues PyRosetta?

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Memory Issues PyRosetta?

I´m running a Pyrosetta script on a 300aa protein with 30 mutable residues a packmover and a fastrelax (3 iterations each) on EX-level 4. When I allocate Memory below 16G I often have uncommented script abortions or "bad alloc" failures. Above 16G that never occurs. Now 16G is a lot and a lot more I seemed to need with Rosetta, albeit, not with the exact same job config. Is there a rule of thump concerning memory usage in PyRosetta? Comparisons with rosetta? Does anybody else encountered memory problems?

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Sat, 2012-03-24 03:21

I assume when you say "ex level 4" you mean "ex1 ex2 ex3 ex4". Design on 30 residues with ex1, 2, 3, and 4 is going to use a TON of memory - 16 GB is higher than I'd predict, but not surprising. I don't know if there are any memory inefficiencies in PyRosetta relative to regular Rosetta w/r/t packing; I'd guess not.

Turning on the -linmem_ig functionality (flag is "-linmem_ig 20"; there's a PackerTask function call for it too) will fix your memory issue.

Sat, 2012-03-24 08:20