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WIP: Ensemble read to 2.9 #3988

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Closed

WIP: Ensemble read to 2.9 #3988

wants to merge 122 commits into from

Commits on Feb 14, 2023

  1. ci: migrate to almalinux, cuda base image

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  2. Merge pull request ornladios#3484 from vicentebolea/update-almalinux-… 

    …images

ci: migrate to almalinux, cuda base image
    @vicentebolea
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  3. Merge pull request ornladios#3482 from pnorbert/iotest-sst-mpi 

    Make adios_iotest work with SST again: add CurrentStep() to SstWriter…
    @pnorbert @vicentebolea
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  4. Merge release_29

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Commits on Feb 17, 2023

  1. Merge pull request ornladios#3489 from pnorbert/fix-matlab-build-29 

    Fix Matlab build which depends on the C bindings not the C++ bindings.
    @pnorbert @vicentebolea
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  2. Merge release_29

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  3. ci: update kokkos to 3.7

    @vicentebolea
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  4. Merge pull request ornladios#3490 from vicentebolea/update-kokkos-ver… 

    …sion-ci

ci: update kokkos to 3.7
    @vicentebolea
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Commits on Feb 21, 2023

  1. Merge pull request ornladios#3446 from anagainaru/gpu-reorg-kokkos 

    Kokkos backend in ADIOS2
    @anagainaru @vicentebolea
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  2. Merge release_29

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  3. codeowners: added code owners file

    @vicentebolea
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  4. Merge pull request ornladios#3496 from vicentebolea/add-codeowners-file 

    codeowners: added code owners file
    @vicentebolea
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  5. Merge pull request ornladios#3495 from anagainaru/kokkos-doc 

    Update the documentation for the GPU backend
    @anagainaru @vicentebolea
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  6. Merge release_29

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  7. Merge pull request ornladios#3498 from vicentebolea/remove-kokkosview… 

    …-example

kokkos,cmake: remove kokkosview example
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  8. Merge release_29

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Commits on Feb 22, 2023

  1. Merge pull request ornladios#3494 from eisenhauer/Deprecated 

    Remove deprecated bindings for release
    @pnorbert @vicentebolea
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  2. Merge release_29

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  3. Merge pull request ornladios#3500 from vicentebolea/remove-kokkos-cud… 

    …a-warnings

ci,kokkos,cuda: remove warnings
    @vicentebolea
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  4. Merge release_29

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  5. Merge pull request ornladios#3501 from vicentebolea/stop-installing-e… 

    …mpty-dirs

cmake: do not install empty sst dirs
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  6. Merge release_29

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Commits on Feb 24, 2023

  1. Merge pull request ornladios#3502 from vicentebolea/fix-external-ci-t… 

    …ests

Workaround for lammps and Scorpion to have a green CI
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  2. Merge release_29

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Commits on Feb 28, 2023

  1. Merge pull request ornladios#3506 from mathrack/patch-2 

    Update fortran.rst
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  2. Merge release_29

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Commits on Mar 1, 2023

  1. Hdf5 vol support requires latest hdf5 1.14

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  2. Updated according to the most recent VOL interface in HDF5 1.14

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Commits on Mar 2, 2023

  1. Merge pull request ornladios#3517 from anagainaru/set-cuda-architecture 

    Set the CMAKE GPU architectures to what is used for Kokkos
    @anagainaru @vicentebolea
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  2. Merge release_29

    @vicentebolea
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  3. removed comments and minor fixes

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  4. clang-format

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  5. Merge branch 'master' into h5vol_update

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  6. Merge pull request ornladios#3516 from guj/h5vol_update 

    Hdf5 vol support will require latest hdf5 1.14
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Commits on Mar 10, 2023

  1. Merge pull request ornladios#3522 from eisenhauer/FortranBind 

    Add adios2_mode_readRandomAccess to fortran bindings
    @pnorbert @vicentebolea
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  2. Merge release_29

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Commits on Mar 14, 2023

  1. Merge pull request ornladios#3427 from caitlinross/update-docs-readme 

    update docs/README.md for using conda env
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  2. Merge release_29

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  3. Bump cryptography from 38.0.2 to 39.0.1 in /docs 

    Bumps [cryptography](https://github.com/pyca/cryptography) from 38.0.2 to 39.0.1.
- [Release notes](https://github.com/pyca/cryptography/releases)
- [Changelog](https://github.com/pyca/cryptography/blob/main/CHANGELOG.rst)
- [Commits](pyca/cryptography@38.0.2...39.0.1)

---
updated-dependencies:
- dependency-name: cryptography
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
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  4. Bump numpy from 1.21.6 to 1.22.0 in /docs 

    Bumps [numpy](https://github.com/numpy/numpy) from 1.21.6 to 1.22.0.
- [Release notes](https://github.com/numpy/numpy/releases)
- [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst)
- [Commits](numpy/numpy@v1.21.6...v1.22.0)

---
updated-dependencies:
- dependency-name: numpy
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
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  5. Merge pull request ornladios#3535 from ornladios/dependabot/pip/docs/… 

    …numpy-1.22.0

Bump numpy from 1.21.6 to 1.22.0 in /docs
    @vicentebolea
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  6. Merge pull request ornladios#3534 from ornladios/dependabot/pip/docs/… 

    …cryptography-39.0.1

Bump cryptography from 38.0.2 to 39.0.1 in /docs
    @vicentebolea
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  7. fixup! Merge pull request ornladios#3534 from ornladios/dependabot/pi… 

    …p/docs/cryptography-39.0.1
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Commits on Mar 20, 2023

  1. Merge pull request ornladios#3542 from anagainaru/warpx-bug-null-blocks 

    Fix bug when writing null blocks
    @anagainaru @vicentebolea
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  2. Merge release_29

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  3. Merge pull request ornladios#3519 from dmitry-ganyushin/b3503-dataman… 

    …-1D-python-arrays-fin

Fix for the issue 3503.
    @dmitry-ganyushin @vicentebolea
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  4. Merge release_29

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Commits on Mar 21, 2023

  1. ci,xl: added p9 xl build, removed p9 smpi build

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Commits on Mar 22, 2023

  1. Merge pull request ornladios#3537 from vicentebolea/enable-linux-emu-… 

    …builds

Enable Linux Emulation build (Power8, IBM XL)
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Commits on Mar 24, 2023

  1. Merge pull request ornladios#3557 from dmitry-ganyushin/group-API-cle… 

    …anup

Refactoring and clean-up group API
    @eisenhauer @vicentebolea
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  2. Merge release_29

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  3. Setting notifications for the GPU files

    @anagainaru
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  4. Merge pull request ornladios#3561 from anagainaru/code-owner-gpu 

    Setting code owners for the GPU files
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Commits on Mar 28, 2023

  1. Merge pull request ornladios#3562 from eisenhauer/LaterShapeCollection 

    Collect Shape at EndStep (and restore DataWrite test)
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  2. Merge release_29

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  3. Merge pull request ornladios#3560 from anagainaru/kokkos-scratch-mem-bug 

    Bug fix for the Kokkos backend used with a Kokkos application
    @anagainaru @vicentebolea
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  4. Merge release_29

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Commits on Mar 29, 2023

  1. Merge pull request ornladios#3567 from anagainaru/zfp-cuda-backend 

    Throw an error when unsupported parameters are used with the ZFP CUDA backend
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  2. Merge release_29

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Commits on Mar 30, 2023

  1. Merge pull request ornladios#3568 from vicentebolea/bump-release-version 

    Bump version to v2.9.0
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  2. Merge release_29

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Commits on Mar 31, 2023

  1. Allowing ADIOS2 to receive Kokkos::View with HIP backend

    @anagainaru
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  2. Merge pull request ornladios#3571 from anagainaru/hip-adios-view 

    Allowing Put/Get to receive Kokkos Views with HIP backend
    @anagainaru
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Commits on Apr 4, 2023

  1. Prototype DAOS engine

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  2. Merge pull request ornladios#3576 from eisenhauer/DAOSEngine 

    Prototype DAOS engine
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Commits on Apr 7, 2023

  1. CODEOWNERS: update codeowner file

    @vicentebolea
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  2. Merge pull request ornladios#3581 from vicentebolea/edit-codeowners 

    CODEOWNERS: update codeowner file
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  3. shellcheck: add shellcheck ci check

    @vicentebolea
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Commits on Apr 8, 2023

  1. Merge pull request ornladios#3582 from vicentebolea/add-shellcheck-ci 

    shellcheck: add shellcheck ci check
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  2. Scripts for building ADIOS2 with CUDA support

    @anagainaru
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  3. Scripts for building ADIOS2 with Kokkos support

    @anagainaru
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  4. Ignoring warning SC2191 in shellcheck

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  5. Merge pull request ornladios#3579 from anagainaru/build-scripts-gpu-a… 

    …ware

Build scripts for ADIOS2 with CUDA and Kokkos backend
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Commits on Apr 10, 2023

  1. emu,ppc64le: disable tests

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  2. Merge pull request ornladios#3583 from vicentebolea/disable-emu-tests 

    Disable emu tests
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Commits on Apr 11, 2023

  1. cmake: set correct soname

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  2. Merge pull request ornladios#3585 from vicentebolea/fix-soname 

    cmake: set correct soname
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Commits on Apr 17, 2023

  1. Move ChangingShape.Multiblock to standalone test and add various comp… 

    …ressors to it if they are available (blosc, mgard, zfp).

Tests: Engine.BP.*/BPChangingShapeWithinStep.MultiBlock/*.
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  2. Merge pull request ornladios#3577 from pnorbert/test-changing-shape-b… 

    …losc2

TestBPChangingShapeWithinStep without and with various compressors
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Commits on Apr 21, 2023

  1. add release files

    @vicentebolea
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  2. Merge pull request ornladios#3570 from vicentebolea/add-release-files 

    add release files
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Commits on Apr 25, 2023

  1. Heat Transfer Example: MPI Datatype 

    Replace the `MPI_REAL8` datatype, which is optional in the MPI
standard and not always available, with `MPI_DOUBLE`. The latter
is always available and corresponds to the data sent around.
    @ax3l
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Commits on Apr 27, 2023

  1. Merge pull request ornladios#3571 from anagainaru/hip-adios-view 

    Allowing Put/Get to receive Kokkos Views with HIP backend

(cherry picked from commit f102c60)
    @anagainaru @vicentebolea
    anagainaru authored and vicentebolea committed Apr 27, 2023
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  2. Merge branch 'release_29' 

    * release_29:
  Merge pull request ornladios#3571 from anagainaru/hip-adios-view
    @vicentebolea
    vicentebolea committed Apr 27, 2023
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Commits on Apr 28, 2023

  1. Merge pull request ornladios#3593 from ax3l/fix-mpireal8-example 

    Heat Transfer Example: MPI Datatype
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    vicentebolea authored Apr 28, 2023
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Commits on May 3, 2023

  1. Merge pull request ornladios#3591 from eisenhauer/BP5MemSel 

    Implement BP5 (and BP4) reader-side memory selection, do testing
    @eisenhauer @vicentebolea
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  2. Merge release_29

    @vicentebolea
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Commits on May 9, 2023

  1. test,install: paramaterize adios2_DIR

    @vicentebolea
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Commits on May 10, 2023

  1. BP5: fixes memory error with IBM XL

    @vicentebolea
    vicentebolea committed May 10, 2023
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Commits on May 11, 2023

  1. Merge pull request ornladios#3586 from vicentebolea/fix-test-post-ins… 

    …tall

test,install: paramaterize adios2_DIR
    @vicentebolea
    vicentebolea authored May 11, 2023
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  2. Merge pull request ornladios#3605 from anagainaru/hip-specific-func 

    Adding missing HIP specific functionality
    @anagainaru @vicentebolea
    anagainaru authored and vicentebolea committed May 11, 2023
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  3. Merge release_29

    @vicentebolea
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  4. ci,ascent: enable ascent builds

    @vicentebolea
    vicentebolea committed May 11, 2023
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Commits on May 12, 2023

  1. Merge pull request ornladios#3610 from vicentebolea/enable-olcf-build 

    ci,ascent: enable ascent builds
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    vicentebolea authored May 12, 2023
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Commits on May 17, 2023

  1. ci: use nvcc_wrapper in adiosKokkos

    @vicentebolea
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  2. Using g++ for all ADIOS2 builds

    @anagainaru
    anagainaru committed May 17, 2023
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  3. Merge pull request ornladios#3623 from vicentebolea/kokkos-use-nvcc-w… 

    …rapper

ci: use nvcc_wrapper in adiosKokkos
    @vicentebolea
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  4. Making our Kokkos backend agnostic to Kokkos specific memory space

    @anagainaru
    anagainaru committed May 17, 2023
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  5. Remove support for long double from GPU metadata

    @anagainaru
    anagainaru committed May 17, 2023
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  6. Add SYCL specific functions 

    Co-authored-by: Daniel Arndt <[email protected]>
    @anagainaru @masterleinad
    anagainaru and masterleinad committed May 17, 2023
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  7. Add script to build ADIOS with Kokkos/SYCL backend on Polaris

    @anagainaru
    anagainaru committed May 17, 2023
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Commits on May 18, 2023

  1. Merge pull request ornladios#3621 from anagainaru/sycl-backend 

    Adding SYCL support to the Kokkos backend
    @anagainaru
    anagainaru authored May 18, 2023
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Commits on May 22, 2023

  1. CI,windows: change MSMPI URL

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    vicentebolea committed May 22, 2023
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Commits on May 23, 2023

  1. Bump requests from 2.28.1 to 2.31.0 in /docs 

    Bumps [requests](https://github.com/psf/requests) from 2.28.1 to 2.31.0.
- [Release notes](https://github.com/psf/requests/releases)
- [Changelog](https://github.com/psf/requests/blob/main/HISTORY.md)
- [Commits](psf/requests@v2.28.1...v2.31.0)

---
updated-dependencies:
- dependency-name: requests
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <[email protected]>
    @dependabot
    dependabot[bot] authored May 23, 2023
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Commits on May 24, 2023

  1. Merge pull request ornladios#3628 from ornladios/dependabot/pip/docs/… 

    …requests-2.31.0

Bump requests from 2.28.1 to 2.31.0 in /docs
    @vicentebolea
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  2. Merge pull request ornladios#3627 from vicentebolea/fix-windows-msmpi… 

    …-flaky-installation

Fix flaky MSMPI installation in windows builds
    @vicentebolea
    vicentebolea authored May 24, 2023
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Commits on May 25, 2023

  1. docs: update whatsnew

    @vicentebolea
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  2. Merge pull request ornladios#3634 from vicentebolea/change-whatsnew 

    docs: update whatsnew
    @vicentebolea
    vicentebolea authored May 25, 2023
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  3. ci,olcf,crusher: enable Crusher CI

    @vicentebolea
    vicentebolea committed May 25, 2023
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  4. Merge pull request ornladios#3620 from vicentebolea/add-olcf-crusher-ci 

    ci,olcf,crusher: enable Crusher CI
    @vicentebolea
    vicentebolea authored May 25, 2023
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  5. ci,crusher: minor tweaks

    @vicentebolea
    vicentebolea committed May 25, 2023
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  6. Merge pull request ornladios#3635 from vicentebolea/tweaks-crusher-build 

    ci,crusher: minor tweaks
    @vicentebolea
    vicentebolea authored May 25, 2023
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  7. Ascent,CI: do not report sync script build

    @vicentebolea
    vicentebolea committed May 25, 2023
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  8. Merge pull request ornladios#3637 from vicentebolea/tweak-ascent-build 

    Ascent,CI: do not report sync script build
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    vicentebolea authored May 25, 2023
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Commits on May 26, 2023

  1. Revert "Ascent,CI: do not report sync script build" 

    This reverts commit f4f7d24.
    @vicentebolea
    vicentebolea committed May 26, 2023
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  2. fixed ornladios#3638

    @guj
    guj committed May 26, 2023
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Commits on May 29, 2023

  1. Merge pull request ornladios#3640 from guj/bugfix 

    replaced uint with size_t
    @guj
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  2. crusher,ci: set unique env per pipeline

    @vicentebolea
    vicentebolea committed May 29, 2023
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  3. Merge pull request ornladios#3644 from vicentebolea/tweaks_crusher_ci 

    crusher,ci: set unique env per pipeline
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    vicentebolea authored May 29, 2023
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Commits on May 30, 2023

  1. Update documentation for GPU-aware functionality

    @anagainaru
    anagainaru committed May 30, 2023
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  2. Merge pull request ornladios#3639 from anagainaru/sycl_documentation 

    Update documentation for the GPU-aware functionality
    @vicentebolea
    vicentebolea authored May 30, 2023
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Commits on Nov 9, 2023

  1. * Add a new functionality to an Engine, to serialize metadata in memo… 

    …ry after Open(ReadRandomAccess), to send over to another programs that can then use this metadata to open the same dataset with an accelerated function (using metadata from memory instead of retrieving from disk). BP4 and BP5 engine supports this new function.

  Program 1:  reader = io.Open(fname, adios2::Mode::ReadRandomAccess);
              char *md;
              size_t mdsize;
              reader.GetMetadata(&md, &mdsize);
  Program 2:  reader = io.Open(fname, md, mdsize);

* Added Transport::CurrentPos() to get the current seek position
    @pnorbert
    pnorbert committed Nov 9, 2023
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