How to constrain the computational resources used for Modeller?
I need to build a model with over 16,000 residues on Win10 which requires high demand for memory (maybe CPU as well). Can I set the maximum memory MODELLER uses, so that my PC will not freeze, and I can terminate the program without forcing the PC to restart? Thank you!
On 5/18/20 2:33 AM, ZHANG Cheng wrote: > I need to build a model with over 16,000 residues on Win10 which > requires high demand for memory (maybe CPU as well). Can I set the > maximum memory MODELLER uses, so that my PC will not freeze, and I can > terminate the program without forcing the PC to restart? Thank you!
Modeller needs memory to store the set of restraints, which will scale roughly as the square of the number of atoms in your system. Thus the only realistic way to constrain Modeller to use less memory is to model a smaller system. That being said I'm surprised you're running out of memory - Modeller's memory usage is generally quite modest and shouldn't be an issue on a typical modern 64-bit system (it was written in the 1990s when systems were much less powerful).
Ben Webb, Modeller Caretaker
Thank you Ben! My PC crashed when running the RosettaCM to model a structure of 16,000 residues. So I want to make sure the MODELLER does not have the memory issue. As you said, I will give it a try for the MODELLER.
------------------ Original ------------------ From: "Modeller Caretaker"<modeller-care@salilab.org>; Date: Tue, May 19, 2020 01:05 AM To: "ZHANG Cheng"<272699575@qq.com>;"modeller_usage"<modeller_usage@salilab.org>;
Subject: Re: [modeller_usage] How to constrain the computational resources used for Modeller?
On 5/18/20 2:33 AM, ZHANG Cheng wrote: > I need to build a model with over 16,000 residues on Win10 which > requires high demand for memory (maybe CPU as well). Can I set the > maximum memory MODELLER uses, so that my PC will not freeze, and I can > terminate the program without forcing the PC to restart? Thank you!
Modeller needs memory to store the set of restraints, which will scale roughly as the square of the number of atoms in your system. Thus the only realistic way to constrain Modeller to use less memory is to model a smaller system. That being said I'm surprised you're running out of memory - Modeller's memory usage is generally quite modest and shouldn't be an issue on a typical modern 64-bit system (it was written in the 1990s when systems were much less powerful).
Ben Webb, Modeller Caretaker
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Modeller Caretaker -
ZHANG Cheng