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Issue created by Paul Bauer@acmnpvMaintainer

Provide Context (e.g. to runner code) to manage client and runtime environment - Redmine #2587

gmxapi milestone 5 as described in #2585

Proposal:

Instead of relying on a global variable for ProgramContext, explicitly require client code to pass a context object to library code. This allows a context to be configured differently depending on the use case of the client code, as well as to capture details of the computing environment that could be better abstracted.

This issue covers restructuring of GROMACS to support an expanded role of client-managed “context”. Specific enhancements are deferred to downstream issues to be linked from here.

Near term goals of the expanded role for the Context include

  • Support run-time extensibility of MD code, such as by providing a source of factory functions from which MD module implementation code can be retrieved.
  • ownership of highest level communicator(s) and source of simulation-level communicators
  • Translation of ANSI C signals to GROMACS signalling facilities
  • Handling of logging and status messaging

Longer term goals include

  • Negotiating allocation of computing resources
  • I/O abstractions and filesystem-decoupling
  • Interfaces for workflow-level check-pointing

Completion:

This issue requires that code like gmx::Mdrunner (and the call stack below) receive the context from the client code. A context implementation should not require global variables, and as much as possible globals should be removed from the current ProgramContext.

Provisions for runtime extensibility:

  • Library-facing Context interface provides factory functions for, e.g.
    • MDModules
    • Communications
    • Logger
    • Messenger
    • Reference data
    • I/O
  • Simple C API allows registering resource providers named in simple hierarchical schema.

(from redmine: issue id 2587, created on 2018-07-24 by eirrgang)

Move mdrun mainFunction to client code.

supports gmxapi milestone 4, described at #2605

API clients need to be able to initialize and run MD simulations with
calls from separate code blocks or even translation units. Also, we
need clear distinctions between a pre-launch master Mdrunner and the
non-master Mdrunner threads.

In this change:

* Insert a Builder on which to develop the distinction between user
  interface and implementation code. User interface is handled in
  Director code, while the Builder and code further down the mdrun call
  stack should be user interface agnostic (i.e. not CLI-centric).
* Introduces a Context object to hold some resources. (see milestone 5
  and issue #2587)
* Prepare for more stateful Mdrunner objects, documenting resources in
  need of clearer management, describing future use cases and possible
  implementation details.
* Make Mdrunner non-copyable and not constructable by clients. Worker
  threads can initialize a new Mdrunner from the master instance with
  cloneOnSpawnedThread.
* Clarify parameter setting for spawned Mdrunner threads.
* Begin to encapsulate filename options available to client code from
  the actual client code.
* Remove extraneous variables `nfile` and `fnm`.

Later changes will:

* Separate Mdrunner into Launcher and Worker at mdrunner() call so that
  tMPI runner does not look reentrant.
* Hide data and clarify ownership / modernize memory management /
  clarify the subjects of the Builder `add` operations.
* Clarify separation of user interface from API parameters.
* Flesh out SimulationContext and related classes.

Refs #2605

Change-Id: I1db1d34b07ec0f8ba5f246ab763c74ad9eafe8f3
  • Revision 7a90bcdb by Eric Irrgang on 2018-10-03T15:27:37Z:
Add gmxapi::Context.

The Context holds the details necessary to launch work in a given
environment. A runtime session is launched using the configured details
of a Context implementation and the object bindings configured by the
user (managed by the Context).

Part of a sequence of changes introducing gmxapi classes System,
Context, Session, and Workflow.

Supports gmxapi milestone 5

Refs: #2587

Change-Id: I75baed9b5c856f284bc2c2370ef284319e95f13e
  • Revision e39949c7 by Mark Abraham on 2019-10-01T05:24:02Z:
Removed dependency on commrec of mdrun setup

Changes no functionality.

Setup is now parameterized directly on MPI_COMM_WORLD, which we will
want later for letting library-based callers pass in an
MPI_Communicator. This permits commrec to be initialized later, once
the threads have been spawned for the thread-MPI ranks.

The initialization of multi-simulations moves from LegacyMdrunOptions
to SimulationContext, which is more appropriate for
ensemble-parallelism established directly by the user.

Before the decision about the duty of a rank, there is no difference
between MASTER(cr) and SIMMASTER(cr), so several calls to macros
taking a t_commrec pointer are replaced by booleans. Introduced
findIsSimulationMasterRank to compute that value. This eliminates
early use of t_commrec that has necessitated other hacks and
workarounds.

Removed redundant check for replica exchange when the number of multi
simulations is less than two, because gmx_multisim_t constructor
already prohibits that.

Resolves several TODO items and improves modularity, too.

Refs #2587, #2605, #3081

Change-Id: I48bd3b713bc181b5c1e4cbcd648706a9f00eab96