Version 7 (modified by andmirek, 6 months ago) (diff)

review

Name and subject of the action

Last edition: 11/26/20 17:08:09 by francesca

The PI is responsible to closely follow the progress of the action, and especially to contact NEMO project manager if the delay on preview (or review) are longer than the 2 weeks expected.

  1. Summary
  2. Preview
  3. Tests
  4. Review

Summary

Action MPI3 collective neighbours communications instead of point to point communications
PI(S) Silvia Mocavero and Italo Epicoco
Digest MPI-3 provides new neighbourhood collective operations that allow to perform halo exchange with a single MPI communication call.
Dependencies If any
Branch dev_r13296_HPC-07_mocavero_mpi3
Previewer(s) Mirek Andrejczuk
Reviewer(s) Mirek Andrejczuk
Ticket #2496

Description

This is the continuation of the work started in 2019 (HPC-12_Mocavero_mpi3).

MPI-3 provides new neighbourhood collective operations (i.e. MPI_Neighbor_allgather and MPI_Neighbor_alltoall) that allow to perform halo exchange with a single MPI communication call.

These collective communications have been integrated and tested on the NEMO code during 2019 in order to evaluate the code performance compared with the traditional point-to-point halo exchange currently implemented in NEMO. The first version of the implementation uses a cartesian topology, so it does not support 9-point stencil neither land domain exclusion and the north fold is handled as usual. The use of new collective communications has been tested on a representative kernel implementing the FCT advection scheme.

Preliminary tests show an improvement within a range of 18%-32% on the GYRE_PISCES configuration (with nn_GYRE=200), depending on the allocated number of cores. The output accuracy is preserved.

During 2020 we intend to integrate the graph topology to support the routines that use a 9-point stencil, the land domain exclusion and the north fold exchanges through MPI3 neighbourhood collective communications.

Implementation

Step 1: alignment of the dev_r13296_HPC-07_mocavero_mpi3 branch with the new trunk (after July merge party) (done)

Step 2: integration of graph topology to support halo exchange for both 5-points (when exchange with only north, south, east and west processes is enough to preserve data dependency) and 9-points stencil (when exchange with diagonal processes is needed) computation. Land domains exclusion is also handled due to the flexibility of graph topology. A parameter in lbc_lnk mpi3 routine call allows to choose between 5-points or 9-points exchange (done)

Step 3: add lbc_lnk mpi3 in traadv_fct.F90 (5-points stencil) and icedyn_rhg_evp.F90 (9-points stencil) files to perform comparability tests. Sette tests will be executed, also activating land domain exclusion

Step 4: perform performance tests to evaluate the gain in both 5-points and 9-points stencil (done)

Step 5: replacement of point-to-point communications with collective ones within the NEMO code. The choice between 5-points and 9-points exchange requires a data dependency analysis. The replacement will be performed in three steps:

step 5.1: all the lbc_lnk will be replaced with 9-points mpi3 exchange (a key_mpi3 will be introduced to preserve the old point-to-point exchange version to be used on architectures where MPI3 is not supported or it does not provide a performance gain) (done)
step 5.2: 5-points stencil exchange is introduced when data dependency is satisfied without diagonal exchange (in 2021)
step 5.3: key_mpi3 will be removed (when the ST will confirm that implementation is more performant)

Documentation updates

Using previous parts, define the main changes to be done in the NEMO literature (manuals, guide, web pages, …).

No need for changes in documentation.

Preview

Since the preview step must be completed before the PI starts the coding, the previewer(s) answers are expected to be completed within the two weeks after the PI has sent the request to the previewer(s).
Then an iterative process should take place between PI and previewer(s) in order to find a consensus

Possible bottlenecks:

  • the methodology
  • the flowchart and list of routines to be changed
  • the new list of variables wrt coding rules
  • the summary of updates in literature

Once an agreement has been reached, preview is ended and the PI can start the development into his branch.

Tests

Once the development is done, the PI should complete the tests section below and after ask the reviewers to start their review.

This part should contain the detailed results of SETTE tests (restartability and reproducibility for each of the reference configuration) and detailed results of restartability and reproducibility when the option is activated on specified configurations used for this test

Regular checks:

  • Can this change be shown to produce expected impact (option activated)?
  • Can this change be shown to have a null impact (option not activated)?
  • Results of the required bit comparability tests been run: are there no differences when activating the development?
  • If some differences appear, is reason for the change valid/understood?
  • If some differences appear, is the impact as expected on model configurations?
  • Is this change expected to preserve all diagnostics?
  • If no, is reason for the change valid/understood?
  • Are there significant changes in run time/memory?

Performance tests have been done on CMCC Zeus machine, by evaluating the improvement on the communication time of two representative routines, respectively implementing the 5-points and 9-points stencil. An improvement within the range of 15-31% is achieved on the GYRE_PISCES configuration depending on the number of allocated cores, when 5-points version is used. As we expected, 9-points stencil does not provide the same improvement. However, a modest gain is achieved.

Restartability and reproducibility tests for all the sette configurations are ok.

Review

Changes are OK. The documentation, however, should be modify to include new cpp key introduced in this development (including sette). The update of the documentation shouldn't stop this development to be merged with the trunk in 2020