Question

Which plan more suitable for my work?

Posted September 26, 2019 338 views
DigitalOcean

My work is a molecular dynamics simulation of a large protein when I was running it at 1nanosecond (ns) of simulation by using (16 CPU) of CPU-optimized it took about 15 hours and resulted in 44GB, but now I want to run it at (50ns) so which plan will give a good result in a shorter time?

2 comments
  • Could the job be distributed across multiple machines? If so, Your account allows you to use 25 droplets max (more upon request) by default. I would suggest top that out with 25 32CPU machines.

  • Thank you for the replay, but do you know how to run many droplets and connect it with each other?
    I have this command to run the simulation:
    namd2 +p32 sim50ns.namd

    (P) for parallel and (32) the number of CPU

    Do I have to run this command in each droplet?

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1 answer

In order to run namd in a distributed manner you will need to use mpi which is managed by charm++

You can’t simply run namd on separate droplets, as that would not orchestrate the data, but instead just run the same process individually with no clustering benefit.

Unfortunately I haven’t used namd so I can’t be of more help, however you can check out this resource to help get you started:

https://scitas-data.epfl.ch/confluence/display/DOC/How+to+launch+NAMD

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