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WIP: Add OpenPMD support#1050

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pgrete wants to merge 94 commits intodevelopparthenon-hpc-lab/parthenon:developfrom pgrete/pmd-outputparthenon-hpc-lab/parthenon:pgrete/pmd-outputCopy head branch name to clipboard

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Commits

Commits on Jan 8, 2024

• Add OpenPMD as external lib

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Commits on Jan 11, 2024

• Add OpenPMD skeleto

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• WIP more Open PMD

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Commits on Jan 12, 2024

• WIP OpenPMD use file id

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Commits on Feb 29, 2024

• Merge branch 'develop' into pgrete/pmd-output

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  108fc7a

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• Write blocks

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Commits on Mar 8, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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• Centralize getting var info for output

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• WIP openpmd, chunks don't work yet plus check dimensionality

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Commits on Mar 14, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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• Fix chunk extents

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Commits on Mar 15, 2024

• Write Attributes

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• Rename restart to restart_hdf5

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Commits on Mar 18, 2024

• WIP abstract RestartReader

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• WIP separating RestartReader

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Commits on Mar 19, 2024

• Make RestartReader abstract

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Commits on Mar 20, 2024

• Merge branch 'pgrete/refactor-restart' into pgrete/pmd-output

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  8bf955b

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• Add OpenPMD restart skeleton

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  e3ea8d7

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• WIP updating loc logic

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Commits on Apr 11, 2024

• Merge branch 'develop' into pgrete/pmd-output

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  788118c

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• Fix interface from recent changes in develop

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• Read and Write loc

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• Houston, we have a build

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Commits on Apr 12, 2024

• Added OpenPMD restart ReadBlocks

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  ae1f241

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• Fix loc level

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Commits on Apr 15, 2024

• Make Series persistent and fix rootlevel typo

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  e2b2bd1

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• WIP Read/Write Params

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• Make ReadParams private member

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Commits on Apr 18, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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  61306a0

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• Fix root level in output

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Commits on Apr 23, 2024

• Move to mesh per record standard for writing

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• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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  9fb9f68

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• Allow for 2D and 3D output. Fix single dataset reset.

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  684b7ab

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• Fix logical loc

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Commits on Apr 24, 2024

• Rename opmd files

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  03f80c7

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• Separate common calls to chunks and names

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  890fffe

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• Reuse shared chunk and name for restarts

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  04359d3

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• Add regression test

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  2b89659

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• Somewhat make restarts working

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Commits on Apr 26, 2024

• Fix order of arguments for correct flush

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• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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  6a3a80d

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• Fix handling of output variable names

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  28d725d

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• Fix reading chunks for sparsely populated output files

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Commits on Apr 29, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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Commits on May 3, 2024

• Dont tell anyone I spent days on this...

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• Temp disable dumping Views from device

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Commits on May 22, 2024

• Merge branch 'develop' into pgrete/pmd-output

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Commits on Jun 12, 2024

• Merge branch 'pgrete/fix-hasghost-restart' into pgrete/pmd-output

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• Dump deref cnt in opmd restart

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Commits on Jun 18, 2024

• Merge branch 'develop' into pgrete/pmd-output

  BenWibking

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• install openpmd in macOS CI

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Commits on Jun 21, 2024

• Merge branch 'develop' into pgrete/pmd-output

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Commits on Jun 25, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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  cd007d3

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• Remove extraneous popRegion

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Commits on Jul 11, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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  5324e00

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• Fix formatting

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  af4b966

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• Make format clang16 compatible

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Commits on Jul 12, 2024

• Fix default backend_config parsing

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• another attempt

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• Bump OpenPMD version

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Commits on Jul 25, 2024

• pmd: Write scalar particle data

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  0e3f758

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• Code dedup

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• Allow writing non-scalar particles

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• Make positions standard compliant

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  08d6b41

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• Allow for particles restarts (serial works)

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Commits on Jul 26, 2024

• Support particle restarts in parallel

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• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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Commits on Aug 6, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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• Add now prefix to pmd outputs

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Commits on Aug 7, 2024

• Make linter happy

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Commits on Sep 2, 2024

• Merge remote-tracking branch 'origin/develop' into pgrete/pmd-output

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  c0d7f11

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Commits on Sep 4, 2024

• Bump OPMD version and add delim

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Commits on Sep 26, 2024

• Merge branch 'develop' into pgrete/pmd-output

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• Change delim. Is this stupid?

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Commits on Oct 7, 2024

• Merge branch 'develop' into pgrete/pmd-output

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  d59d573

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• Make params IO test more flexible

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  3f95fc4

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• Add test case for opmd params IO

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  1141ff3

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• Reading/writing non-ParArray Params works

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  e6e4d0b

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Commits on Oct 8, 2024

• Allow writing ParArray and Views to Params

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  8230f94

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• Read ParArray/View from opmd raw

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  e64ae7e

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• Make basic parsing of Params work

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  b789711

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• Restore view from opmd params

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  466ecd2

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• Fix manual pararray reading

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• Make linter happy?

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  4c1c70f

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Commits on Oct 9, 2024

• Make restoring HostViews possible

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  8a1850b

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• Make reading host arrays work using the direct interface in the unit test

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  1f02ffa

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• Expands types for read/write to all vec

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  d6565c5

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• Remove debug info

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Commits on Oct 16, 2024

• Merge branch 'develop' into pgrete/pmd-output

  BenWibking

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Commits on Nov 9, 2024

• Merge branch 'develop' into pgrete/pmd-output

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  e67f589

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• Fix bc interface from PR 1177

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Commits on Nov 22, 2024

• Merge branch 'develop' into pgrete/pmd-output

  BenWibking

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Commits on Nov 29, 2024

• Merge branch 'develop' into pgrete/pmd-output

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  dfbcb27

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• Fix output numbering for triggered opmd outputs

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