Code

Merge MPI into Taal#285

Code

Merged

sloede merged 119 commits intotrixi-framework:devtrixi-framework/Trixi.jl:devfrom ranocha:hr/merge_MPI_devranocha/Trixi.jl:hr/merge_MPI_devCopy head branch name to clipboardNov 3, 2020

Commits

Commits on Sep 4, 2020

• Add MPI as a dependency

  sloede

  committed
  d0e85da

  Copy full SHA for d0e85da

• Create parallel mesh struct

  sloede

  committed
  fb633ac

  Copy full SHA for fb633ac

• Add "domain_ids" to parallel mesh and comment out duplicate methods

  sloede

  committed
  8f81b0b

  Copy full SHA for 8f81b0b

• Add some very basic parallelization methods

  sloede

  committed
  8b7c9b4

  Copy full SHA for 8b7c9b4

• Initialize MPI (if not yet done) at the beginning of run

  sloede

  committed
  3151f4b

  Copy full SHA for 3151f4b

• Create mesh with parallel tree if running in parallel

  sloede

  committed
  98c0339

  Copy full SHA for 98c0339

• Serialize startup message

  sloede

  committed
  177c559

  Copy full SHA for 177c559

• Read in parameters in parallel

  sloede

  committed
  f82d34d

  Copy full SHA for f82d34d

• Safe-guard non-parallelized code paths

  sloede

  committed
  4bb6914

  Copy full SHA for 4bb6914

Commits on Sep 5, 2020

• Partition mesh statically by leaf cell count

  sloede

  committed
  6d6eba7

  Copy full SHA for 6d6eba7

• Use OffsetArrays to store data by domain id with 0-based indices

  sloede

  committed
  82751ba

  Copy full SHA for 82751ba

Commits on Sep 7, 2020

• Add initial setup for MPI exchange in Dg2D

  sloede

  committed
  05abed5

  Copy full SHA for 05abed5

• Move MPI-related methods to parallel.jl

  sloede

  committed
  6d8792a

  Copy full SHA for 6d8792a

• Sort interface by global interface id

  sloede

  committed
  aaffd56

  Copy full SHA for aaffd56

• First working parallel DG computations on 2 domains (L2/Linf values and EOC tests for scalar advection and compressible Euler are matching)

  sloede

  committed
  641c15a

  Copy full SHA for 641c15a

• Add total and serial performance index

  sloede

  committed
  1ca6441

  Copy full SHA for 1ca6441

• Move init_mpi() to its proper place

  sloede

  committed
  a271e53

  Copy full SHA for a271e53

Commits on Sep 8, 2020

• Fix parallel output

  sloede

  committed
  0c75f91

  Copy full SHA for 0c75f91

• Merge branch 'master' into msl/mpi_parallel

  sloede

  committed
  c7e0216

  Copy full SHA for c7e0216

Commits on Sep 9, 2020

• Merge branch 'master' into msl/mpi_parallel

  sloede

  committed
  374bd19

  Copy full SHA for 374bd19

• Calculate total number of elements and local offset

  sloede

  committed
  a0bb098

  Copy full SHA for a0bb098

• Fix L2/Linf error calculation for MPI

  sloede

  committed
  623041a

  Copy full SHA for 623041a

• MVector -> SVector for center_level_0

  sloede

  committed
  9a3b277

  Copy full SHA for 9a3b277

• Add MeshType to Dg2D/Dg3D parameters

  sloede

  committed
  3566b47

  Copy full SHA for 3566b47

• Remove mesh from Dg2D struct again

  sloede

  committed
  f7d2463

  Copy full SHA for f7d2463

Commits on Sep 10, 2020

• Also clean up Dg3D constructor

  sloede

  committed
  d8212ca

  Copy full SHA for d8212ca

• Store n_elements_by_domain in solver for MPI Gatherv/Scatterv operations

  sloede

  committed
  baf999d

  Copy full SHA for baf999d

• Writing restart files in parallel works (it seems)

  sloede

  committed
  67d2c73

  Copy full SHA for 67d2c73

Commits on Sep 19, 2020

• Merge branch 'master' into msl/mpi_parallel

  sloede

  committed
  198779e

  Copy full SHA for 198779e

• Fix errors from previous merge

  sloede

  committed
  5533451

  Copy full SHA for 5533451

Commits on Sep 21, 2020

• Initialize global MPI state in __init__()

  sloede

  committed
  da2c11c

  Copy full SHA for da2c11c

• Make parse_parameters_file MPI-aware

  sloede

  committed
  00aee1c

  Copy full SHA for 00aee1c

• Use MPI.COMM_WORLD directly

  sloede

  committed
  affacfb

  Copy full SHA for affacfb

Commits on Sep 22, 2020

• Make save_xxx_file MPI-aware (parallel noet yet fully working)

  sloede

  committed
  10f94a8

  Copy full SHA for 10f94a8

• Merge branch 'master' into msl/mpi_parallel

  sloede

  committed
  43ec9bf

  Copy full SHA for 43ec9bf

• Merge branch 'master' into msl/mpi_parallel

  sloede

  committed
  3d82fcd

  Copy full SHA for 3d82fcd

• save_restart_file and save_solution_file work in parallel

  sloede

  committed
  527fe01

  Copy full SHA for 527fe01

Commits on Sep 23, 2020

• Fix that only root actually creates output files

  sloede

  committed
  757e2a2

  Copy full SHA for 757e2a2

Commits on Sep 24, 2020

• Simplify MPI code

  sloede

  committed
  6263538

  Copy full SHA for 6263538

Commits on Sep 25, 2020

• Parallel restarting works

  sloede

  committed
  9f56ff6

  Copy full SHA for 9f56ff6

• added parallel versions of analyze_solution, calc_error_norms, and integrate

  sloede

  committed
  d8e44f3

  Copy full SHA for d8e44f3

• Rename 'domain'/'domain_id'/'n_domains' -> 'rank'/'mpi_rank'/'n_mpi_ranks'

  sloede

  committed
  ac3c87b

  Copy full SHA for ac3c87b

Commits on Sep 26, 2020

• Collect all MPI initialization in init_mpi()

  sloede

  committed
  6444e9f

  Copy full SHA for 6444e9f

• Fix several parallel I/O issues

  sloede

  committed
  d79cadf

  Copy full SHA for d79cadf

• Move partition! to parallel.jl

  sloede

  committed
  5d3dbce

  Copy full SHA for 5d3dbce

• Fix several MPI calls

  sloede

  committed
  f06da84

  Copy full SHA for f06da84

• Parallel output fix

  sloede

  committed
  d43f3d4

  Copy full SHA for d43f3d4

• If MPI is already initialized, query for sufficient threading support

  sloede

  committed
  db34d04

  Copy full SHA for db34d04

• Split calc_dt in serial and parallel version

  sloede

  committed
  2ecc439

  Copy full SHA for 2ecc439

Commits on Sep 27, 2020

• Fix AMR & allow shock capturing without smoothing in parallel

  sloede

  committed
  bcc4801

  Copy full SHA for bcc4801

• Hopefully fix 3D simulation

  sloede

  committed
  3ce35b7

  Copy full SHA for 3ce35b7

• Add first documentation on how to run Trixi in parallel

  sloede

  committed
  8b1084c

  Copy full SHA for 8b1084c

Commits on Sep 28, 2020

• using MPI -> import MPI

  sloede

  committed
  40874dd

  Copy full SHA for 40874dd

• Simplify type hierarchy

  sloede

  committed
  ccc7056

  Copy full SHA for ccc7056

• Reduce code duplication in generate_mesh

  Show description for f69d3f8
  

  sloede

  and

  ranocha

  authored
  f69d3f8

  Copy full SHA for f69d3f8

• Rename Tree -> SerialTree and move all generic tree functions to AbstractTree

  sloede

  committed
  cc29ac4

  Copy full SHA for cc29ac4

• Refactor get_restart_mesh_filename

  sloede

  committed
  786cc74

  Copy full SHA for 786cc74

• Add MIME"text/plain" to multi-line Base.show methods

  sloede

  committed
  1fa802f

  Copy full SHA for 1fa802f

• Avoid constructing another Val(false)

  Show description for 223b081
  

  sloede

  and

  ranocha

  authored
  223b081

  Copy full SHA for 223b081

• Further improve potential for overlapping communication & computation

  sloede

  committed
  3c392ca

  Copy full SHA for 3c392ca

• Update docs/src/parallelization.md

  Show description for d635cbd
  

  sloede

  and

  ranocha

  authored
  d635cbd

  Copy full SHA for d635cbd

• Remove unused and non-canonical overload

  sloede

  committed
  b84fe79

  Copy full SHA for b84fe79

Commits on Oct 1, 2020

• Add 1D tests to Travis

  sloede

  committed
  b1f1057

  Copy full SHA for b1f1057

Commits on Oct 2, 2020

• Merge branch 'master' into msl/mpi_parallel

  sloede

  committed
  99f360f

  Copy full SHA for 99f360f

• Adapt 1D solver to new mesh type infrastructur

  sloede

  committed
  33dc1b0

  Copy full SHA for 33dc1b0

• Ensure correct return values (l2, linf) on all ranks

  sloede

  committed
  04537ba

  Copy full SHA for 04537ba

• First attempt at MPI-parallel Trixi tests

  sloede

  committed
  2b54b04

  Copy full SHA for 2b54b04

Commits on Oct 3, 2020

• Enable parallel 2D tests in Travis

  sloede

  committed
  d91a7ff

  Copy full SHA for d91a7ff

• Fix AMR for 1D (hopefully)

  sloede

  committed
  18a65d4

  Copy full SHA for 18a65d4

• Update manual tests

  sloede

  committed
  11e3d5b

  Copy full SHA for 11e3d5b

Commits on Oct 4, 2020

• Disable module precompilation for MPI tests

  sloede

  committed
  4fd5569

  Copy full SHA for 4fd5569

• Remove test for non-existent ndims method

  sloede

  committed
  68d10e1

  Copy full SHA for 68d10e1

Commits on Oct 6, 2020

• Update linear_scalar_advection.jl

  

  Felipe

  authored and

  Felipe

  committed
  527df5b

  Copy full SHA for 527df5b

Commits on Oct 8, 2020

• changes to linear_scalar_advection

  Show description for a753069
  

  Felipe

  authored and

  Felipe

  committed
  a753069

  Copy full SHA for a753069

Commits on Oct 9, 2020

• Disable MHD test in parallel since calc_mpi_interface_flux is not yet implemented for non-conservative terms

  sloede

  committed
  7eb678c

  Copy full SHA for 7eb678c

• Remove wololo

  sloede

  committed
  98468a3

  Copy full SHA for 98468a3

• Restrict MPI ranks to 2 or 3 for testing

  sloede

  committed
  2c021ba

  Copy full SHA for 2c021ba

• Improve coverage on show for mortar container

  sloede

  committed
  a2ea737

  Copy full SHA for a2ea737

• Improve TreeMesh coverage

  sloede

  committed
  4d43e51

  Copy full SHA for 4d43e51

• Remove unused methods

  sloede

  committed
  bd3874f

  Copy full SHA for bd3874f

• Improve coverage for show of ParallelTree

  sloede

  committed
  fa329ce

  Copy full SHA for fa329ce

• Add parallel restart test

  sloede

  committed
  e5f9a31

  Copy full SHA for e5f9a31

• Test for reset_data_structures! for ParallelTree

  sloede

  committed
  f296a8f

  Copy full SHA for f296a8f

• Comment AMR-specific I/O for parallel cse

  sloede

  committed
  f754fb8

  Copy full SHA for f754fb8

Commits on Oct 11, 2020

• Add additional tests and comment out unused methods for MPI + MHD and MPI + Euler-gravity

  sloede

  committed
  346239a

  Copy full SHA for 346239a

• Fix integrate and calc_error_norms for MPI

  sloede

  committed
  73c02a5

  Copy full SHA for 73c02a5

• Fix calc_error_norms for MPI/non-2D runs

  sloede

  committed
  166f06d

  Copy full SHA for 166f06d

• Sort Travis jobs by descending run time (such that longer-running jobs start first)

  sloede

  committed
  e8ce36c

  Copy full SHA for e8ce36c

• Prefix MPI-related methods with mpi_

  sloede

  committed
  a7011af

  Copy full SHA for a7011af

Commits on Oct 12, 2020

• Update .gitignore

  FelipeSantillan

  authored
  7e39697

  Copy full SHA for 7e39697

• linear_scalar_advection,jl

  Show description for d5b5a88
  

  Felipe

  authored and

  Felipe

  committed
  d5b5a88

  Copy full SHA for d5b5a88

• Merge pull request trixi-framework#167 from trixi-framework/msl/mpi_parallel

  Show description for 83923d9
  sloede

  authored
  83923d9

  Copy full SHA for 83923d9

Commits on Oct 13, 2020

• CompatHelper: add new compat entry for "MPI" at version "0.15"

  github-actions[bot]

  committed
  6ecaea9

  Copy full SHA for 6ecaea9

• CompatHelper: add new compat entry for "OffsetArrays" at version "1.3"

  github-actions[bot]

  committed
  1498be8

  Copy full SHA for 1498be8

• CompatHelper: add new compat entry for "MPI" at version "0.15" for package test

  github-actions[bot]

  committed
  8542152

  Copy full SHA for 8542152

• Merge pull request trixi-framework#220 from trixi-framework/compathelper/new_version/2020-10-13-00-07-36-552-678425944

  Show description for 8b83011
  ranocha

  authored
  8b83011

  Copy full SHA for 8b83011

• Merge pull request trixi-framework#222 from trixi-framework/compathelper/new_version/2020-10-13-00-08-02-102-1597678616

  Show description for 77e1668
  ranocha

  authored
  77e1668

  Copy full SHA for 77e1668

• Merge branch 'master' into compathelper/new_version/2020-10-13-00-07-47-919-3480444568

  ranocha

  authored
  ccd295c

  Copy full SHA for ccd295c

• Merge pull request trixi-framework#221 from trixi-framework/compathelper/new_version/2020-10-13-00-07-47-919-3480444568

  Show description for 256ff44
  ranocha

  authored
  256ff44

  Copy full SHA for 256ff44

Commits on Oct 16, 2020

• Merge branch 'master' of https://github.com/FelipeSantillan/Trixi.jl

  

  Felipe

  authored and

  Felipe

  committed
  432a0ac

  Copy full SHA for 432a0ac

Commits on Oct 20, 2020

• Update linear_scalar_advection.jl

  

  Felipe

  authored and

  Felipe

  committed
  b62be6d

  Copy full SHA for b62be6d

Commits on Oct 21, 2020

• Update linear_scalar_advection.jl

  

  Felipe

  authored and

  Felipe

  committed
  ccfcf6d

  Copy full SHA for ccfcf6d

Commits on Oct 22, 2020

• update to linear_scalar_advection.jl

  

  Felipe

  authored and

  Felipe

  committed
  b8fb9b6

  Copy full SHA for b8fb9b6

Commits on Oct 25, 2020

• copy list of authors when building docs

  ranocha

  committed
  7c62951

  Copy full SHA for 7c62951

Commits on Oct 26, 2020

• Merge pull request trixi-framework#201 from FelipeSantillan/master

  Show description for 30bbeb9
  sloede

  authored
  30bbeb9

  Copy full SHA for 30bbeb9

• Merge pull request trixi-framework#250 from trixi-framework/hr/author_list

  Show description for 31bde79
  ranocha

  authored
  31bde79

  Copy full SHA for 31bde79

• Update docs to include 3D features of Trixi2Img

  efaulhaber

  committed
  898a3c2

  Copy full SHA for 898a3c2

• Improve documentation of Trixi2Img

  efaulhaber

  committed
  e593d1a

  Copy full SHA for e593d1a

• Fix "yz-plane" in docs

  efaulhaber

  committed
  7aacefe

  Copy full SHA for 7aacefe

• Merge pull request trixi-framework#251 from erik-f/trixi2img-docs

  Show description for 357d98c
  sloede

  authored
  357d98c

  Copy full SHA for 357d98c

Commits on Oct 30, 2020

• Ensure final time step size dt is not nearly zero

  sloede

  committed
  c4353a4

  Copy full SHA for c4353a4

• Update failing testcase

  sloede

  committed
  226ff2a

  Copy full SHA for 226ff2a

• Update failing testcase

  sloede

  committed
  a5fbff2

  Copy full SHA for a5fbff2

• Merge pull request trixi-framework#273 from trixi-framework/msl/no-zero-size-final-dt

  Show description for b5c2d07
  sloede

  authored
  b5c2d07

  Copy full SHA for b5c2d07

Commits on Oct 31, 2020

• Update TagBot.yml

  Show description for 7ff51cb
  ranocha

  authored
  7ff51cb

  Copy full SHA for 7ff51cb

Commits on Nov 1, 2020

• update TagBot.yml [ci skip]

  ranocha

  authored
  1d8401f

  Copy full SHA for 1d8401f

Commits on Nov 3, 2020

• Merge branch 'master' into hr/merge_MPI_dev

  ranocha

  committed
  8abfb4c

  Copy full SHA for 8abfb4c

• fix additional merge conflicts

  ranocha

  committed
  efd3fe8

  Copy full SHA for efd3fe8

• fix additional merge conflicts

  ranocha

  committed
  081575c

  Copy full SHA for 081575c