I have a computer with one CPU (Intel Xeon Gold 6134 Octa-Core 3.20 GHz Processor) and GPU (Nvidia RTX 2070).
I want to perform temperature replica exchange Molecular Dynamics on this machine, so I installed Gromacs. However, I found that it needs MPI and multiple CPUs more than the number of replicas.
I found Amber and NAMD treat GPU better than Gromacs, but I cannot figure out whether they can run REMD on a single CPU because in their manual they use MPI as an example.
Hey,
depending on you system size and the resulting performance, you can try to simply oversubscribe your CPU. So for example if you need 32 replicas, just start 32 processes. This should work independently of the MD engine.
Performance shouldn't be worse then for example doing the replica MD in serial rather than parallel. Also, if the machine gets too unresponsive, consider leaving one core empty by using core bindings.
Btw. how many atoms does your system have and how many replicas you need? Whats your temperature span?
Bests
Norman Geist
Thank you for the answer.
I want to perform coarse-grained simulation (one bead per one atom) of the multiple proteins with implicit solvent following this interaction following this instruction.
https://github.com/ZhangGroup-MITChemistry/MOFF/blob/main/Example/HP1alpha_monomer/README.md
So the number of atoms is 200 * 10-100(the number of proteins) = 2000 - 20000, and the temperature span is 300, 320, 340, 360, 380, and 400K.
Thats six replica, and you have 8 cores, so you don't even need to oversubscribe.
I thought the number of jobs gmx_mpi could assign depends on the number of processors, not cores. Therefore I tried to run the replica-exchange simulation by other programs.
So what I should do is just installing gmx_mpi and performing REMD using 6 cores of one CPU for 6 replicas?
Yes, that's kind of a wording problem. In the computing word, a CPU often refers to a core while a socket would refer to the "one" piece of hardware normally refered to as a CPU ;)
- Badges
- Science topic