Hi everyone,
Just a few questions about running amber14 on HPC.
1. HPC-CPUs
I would like to simulate a protein-ligand complex that is treated
solvent explicitly (regular MD). Up to how many cores it is sensible to
use? For example, if I run it on 1000 cores, will it be faster than run
it on 800 cores?
This HPC is new so they ask about the libraries required by Amber. I
mentioned: gz, bz2, netcdf, xorg, fftw3 (guessing that g++, gcc and
gfortran should be there). Any I forgot?
And also, they ask about the maximum amount of memory per core
during MD runs. No idea. I chose netcdf as the I/O strategy, am I
right?
2. HPC-GPUs
Same question goes here : up to how many GPUs in parallel? Do I have to
use p2p in a multi-GPU node? Can you run 2 nodes in parallel?
3. And ... just out of pure curiosity: has anyone used Xeon Phi
Co-processors for running MD? Any results? Are they able to run energy
calculations? Get it to work seems a bit of 'mission impossible'...
Cheers,
Sofia V.
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Received on Thu Sep 10 2015 - 12:30:03 PDT
