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Name and subject of the action
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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.
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
No need for changes in documentation.
Preview
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Tests
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
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