Multithreading on different platforms about openmm HOT 3 OPEN

I don't quite understand what you're doing. What is dummy_context for? And what does "GPU" mean? There's no platform with that name.

The CPU platform is internally parallelized, and by default uses all available cores. If you want to run many simulations in parallel with it, you should set the "Threads" property to limit how many threads each one uses.

I assume from the name that this is a tiny system, just three alanines in vacuum? Running on a GPU, the time will be entirely dominated by kernel launch overhead. There may be little or no benefit to running multiple simulations in parallel in that case.

What hardware are you running on? GPUs in general aren't very good at running multiple jobs in parallel. Some are better than others.

openmmtools.integrators.LangevinIntegrator is not a good choice. Use openmm.LangevinMiddleIntegrator instead. It is much faster.

The first few steps of any simulation may take much longer than later ones as it compiles kernels and does other initialization work. You shouldn't start timing until you've completed about 10 steps or so on each context. In addition, just because step() returns that doesn't mean the GPU has finished. The CPU and GPU can run asynchronously at the same time. To make sure it really has finished, you need to transfer data back from the GPU to the CPU, for example by calling getState().

Here is how the benchmarking script times a simulation:

It runs some initial steps to make sure everything is initialized, then calls getState() to make sure those initial steps have completed, then takes the intended number of steps, and then calls getState() again to block until they have finished.

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By 'GPU' I mean 'CUDA' sorry for the confusion. The dummy context was created simply because I am pretty new to openmm and have problems when I try to define a platform properly :(, sorry again for the confusion. Thank you for all you suggestions. I was not aware at all the problems and all of them are very helpful!

What hardware are you running on?

I am running on a single Nvidia GeForce GTX TITAN Z and 96 cpu cores with 1 thread each.

The CPU platform is internally parallelized, and by default uses all available cores. If you want to run many simulations in parallel with it, you should set the "Threads" property to limit how many threads each one uses.

If this is the case, in what circumstances can I gain benefits by running multithread on CPU? Or would it be better for me just to use all the available cores for a single simulation and start another when it is done?

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If this is the case, in what circumstances can I gain benefits by running multithread on CPU?

When simulating very small systems, it might be faster to run multiple simulations each using a fraction of the cores. However you do it, make sure the total number of threads between all simulations doesn't exceed the number of cores.

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