Open
Conversation
Begin 0.0.6 development cycle
We call gmx::initialize() in the import code and gmx::finalize() on the destruction of an object stored as a module variable. This means that if we want mpi4py to manage MPI initialization and deinitialization, we need to import it before importing gmx. To do: we need to pass a communicator to GROMACS without initializing or finalizing MPI. We should probably do that when sessions are launched in a context. We should probably store a "current context" as a module member variable, and we could tie MPI initialization and deinitialization to that with the caveat that, once created, the first context to initialize MPI needs to be the last one to use it. To support all of this, we need to make substantial updates to GROMACS to use a received subcommunicator instead of MPI_COMM_WORLD. For the moment, we should be able to use MPI_COMM_WORLD if we prohibit running jobs whose workflow width does not match the MPI width. We can't use ensembles, though, until we manage the communicator. Mark's suggestion the quickest band-aid is to override the definition of MPI_COMM_WORLD and manage a global variable in basenetwork.h.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
work in progress
development toward issue #50