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Merged
merged 44 commits into from
Sep 17, 2024
Merged

LAMMPS with GPU support #9244

merged 44 commits into from
Sep 17, 2024

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@jmeziere
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@jmeziere jmeziere commented Aug 12, 2024

Similar to cufinufft, I'd like to create a GPU version of the LAMMPS wrapper.

Similar to cufinufft, it would be difficult to maintain both versions simultaneously in one package, as discussed briefly here.

This is my first foray into adding to Yggdrasil, so any suggestions are appreciated. I'm also pretty motivated to get this done, so I'll be able to put some time into it to fix it.

@giordano giordano requested a review from vchuravy August 12, 2024 20:02
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vchuravy commented Aug 13, 2024

Similar to cufinufft, it would be difficult to maintain both versions simultaneously in one package, as discussed briefly here.

I don't quite agree with that, for me it is more complicated to have to jll and to keep them in sync and how to explain to people which one they need to use.

@jmeziere
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jmeziere commented Aug 13, 2024

That makes sense. Do you think that it would be better to have cuda support on some and mpi on the others or mix them. I'm worried about there being too many possible machine that it must compile for. Or is this not an issue?

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vchuravy commented Aug 15, 2024

Currently we do not have CUDA aware MPIs in Yggdrasil, but we could go there.
Right now #9185 is a bigger issue since we thought we shipped MPI enabled LAMMPS builds xD.

@jmeziere
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jmeziere commented Aug 22, 2024

@vchuravy Sorry for the delay. I had a paper to submit, but I should be able to spend more time now.

Is this approach better? Just have the CUDA portion added to the end.

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jmeziere commented Sep 6, 2024

@vchuravy I have fixed up the cuda portions, but I haven't quite figured out how to combine both mpi and cuda.

@giordano Do you know how to compile for both cuda and mpi simultaneously? I tried following the Extrae build, but it didn't seem to work.

jmeziere and others added 18 commits September 6, 2024 11:20
@jmeziere
fix cuda and mpi platform
47fe0e7
@jmeziere
Merge branch 'master' into master
a685d68
@jmeziere
change settings for non-cuda and non-mpi
37c0036
@jmeziere
Merge branch 'master' of github.com:byu-cxi/Yggdrasil
a4bbad6
@jmeziere
try string
a56a3a3
@jmeziere
change env var
3914fa8
@jmeziere
use full target
022f65c
@jmeziere
actually add gpu package
814eaa5
@jmeziere
remove ADD_CUDA
5aa2457
@jmeziere
Add cuda path
5efd7b5
@jmeziere
link cuda libs
981bdea
@jmeziere
change CUDA_PATH to CUDA_HOME
ad8c334
@jmeziere
add soft link
919ce89
@jmeziere
add nvcc to path
0e693f9
@jmeziere
set cmake prefix
3e17898
@jmeziere
attempt to fix cmake prefix
3163a3d
@jmeziere
include nvcc info
9274811
@jmeziere
Squashed commit of the following:
8f8f47f 
commit 9274811
Author: jmeziere <jmeziere@gmail.com>
Date:   Sat Sep 7 01:52:46 2024 -0600

    include nvcc info

commit 3163a3d
Author: jmeziere <jmeziere@gmail.com>
Date:   Sat Sep 7 01:30:52 2024 -0600

    attempt to fix cmake prefix

commit 3e17898
Author: jmeziere <jmeziere@gmail.com>
Date:   Sat Sep 7 01:09:09 2024 -0600

    set cmake prefix

commit 0e693f9
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 21:11:05 2024 -0600

    add nvcc to path

commit 919ce89
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 17:55:47 2024 -0600

    add soft link

commit ad8c334
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 16:41:17 2024 -0600

    change CUDA_PATH to CUDA_HOME

commit 981bdea
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 15:44:05 2024 -0600

    link cuda libs

commit 5efd7b5
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 15:16:05 2024 -0600

    Add cuda path

commit 5aa2457
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 14:32:26 2024 -0600

    remove ADD_CUDA

commit 814eaa5
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 14:27:45 2024 -0600

    actually add gpu package

commit 022f65c
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 13:53:35 2024 -0600

    use full target

commit 3914fa8
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 13:46:02 2024 -0600

    change env var

commit a56a3a3
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 13:31:24 2024 -0600

    try string

commit a4bbad6
Merge: 37c0036 a685d68
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 13:05:41 2024 -0600

    Merge branch 'master' of github.com:byu-cxi/Yggdrasil

commit 37c0036
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 13:04:35 2024 -0600

    change settings for non-cuda and non-mpi

commit a685d68
Merge: 47fe0e7 6ae3f38
Author: Jason Meziere <mez16003@byui.edu>
Date:   Fri Sep 6 12:39:48 2024 -0600

    Merge branch 'master' into master

commit 47fe0e7
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 11:20:41 2024 -0600

    fix cuda and mpi platform

commit 6ae3f38
Author: Maximilian Hübl <89022871+mxhbl@users.noreply.github.com>
Date:   Fri Sep 6 18:30:56 2024 +0200

    nauty: bump version to 2.8.9, add TLSlibs (#9367)

commit ccf00b0
Author: jmeziere <jmeziere@gmail.com>
Date:   Fri Sep 6 09:49:54 2024 -0600

    add full cuda and mpi platforms

commit f6abae6
Author: Hans Schoenemann <hannes@mathematik.uni-kl.de>
Date:   Fri Sep 6 14:54:18 2024 +0200

    [Singular] singular library fixes: primary decomposition (#9381)

commit 1fb6812
Author: Hans Schoenemann <hannes@mathematik.uni-kl.de>
Date:   Fri Sep 6 13:36:11 2024 +0200

    [libsingular_julia] for Singular_jll 404.000.503 (#9380)

commit 44db844
Author: Hans Schoenemann <hannes@mathematik.uni-kl.de>
Date:   Fri Sep 6 11:45:30 2024 +0200

    [Singular] fix exit calls of childs (#9378)

commit 5b5107a
Author: Brian Klahn <bdklahn@users.noreply.github.com>
Date:   Thu Sep 5 18:15:57 2024 -0400

    add arm64 to quarto (#9375)

    * add arm64 to quarto

    * quarto add arm
    looks like the builder might implicitly require a Darwin version
    Maybe it defaults to 20 (latest one?). Let's try that.

commit 93063e5
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Thu Sep 5 16:15:37 2024 -0600

    [aws_c_auth] Update to 0.7.28 (#9376)

    Co-authored-by: github-actions <github-actions@github.com>

commit e2b68ca
Author: Jaakko Ruohio <jaakkor2@users.noreply.github.com>
Date:   Fri Sep 6 01:14:55 2024 +0300

    [gmsh] update to 4.13.1, compat for OCCT_jll (#9346)

commit 016428c
Author: Brian Klahn <bdklahn@users.noreply.github.com>
Date:   Thu Sep 5 12:47:28 2024 -0400

    bump quarto to v1.5.57 (#9372)

commit 787af53
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Thu Sep 5 05:41:13 2024 -0400

    OpenSSL: New version 3.0.15 (#9368)

commit 2afdb4d
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Thu Sep 5 03:40:11 2024 -0600

    [aws_c_s3] Update to version 0.6.5 (#9369)

    Co-authored-by: github-actions <github-actions@github.com>

commit 02d5184
Author: William Moses <gh@wsmoses.com>
Date:   Wed Sep 4 22:48:24 2024 -0500

    Update build_tarballs.jl (#9370)

commit c8b7a8c
Author: Jeremiah <4462211+jeremiahpslewis@users.noreply.github.com>
Date:   Wed Sep 4 13:17:09 2024 +0200

    [OpenSpiel] Version bump for compat (#9366)

commit c67a249
Author: Joroks <32484985+Joroks@users.noreply.github.com>
Date:   Wed Sep 4 10:12:28 2024 +0200

    [LAMMPS] Update LAMMPS to stable_29Aug2024 (#9360)

    * Update LAMMPS to newest release

    * Try solve compile issues on MacOS

commit 3876022
Author: Max Horn <max@quendi.de>
Date:   Wed Sep 4 03:00:17 2024 +0200

    [GAP_pkg_juliainterface] update for Julia 1.12.0-DEV (#9364)

commit f5e0f7c
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Tue Sep 3 19:01:20 2024 -0500

    [proxTV] Recompile with -O3 and include headers in the JLL (#9365)

commit 45b7014
Author: Jeremiah <4462211+jeremiahpslewis@users.noreply.github.com>
Date:   Wed Sep 4 01:08:59 2024 +0200

    [OpenSpiel] use more recent libcxxwrap_julia version (#9356)

commit b999104
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Tue Sep 3 16:19:38 2024 -0600

    [aws_c_auth] Update to 0.7.27 (#9362)

    Co-authored-by: github-actions <github-actions@github.com>

commit a44003c
Author: Max Horn <max@quendi.de>
Date:   Wed Sep 4 00:14:52 2024 +0200

    [GAP] workaround GC issue, update libjulia (#9363)

    Also restore GAC_LDFLAGS to what now hopefully really is a sane default.

commit f9f5c70
Author: enzyme-ci-bot[bot] <78882869+enzyme-ci-bot[bot]@users.noreply.github.com>
Date:   Tue Sep 3 21:32:59 2024 +0000

    Upgrade enzyme to refs/tags/v0.0.148 (#9361)

    * Upgrade enzyme to refs/tags/v0.0.148

    * Update build_tarballs.jl

    ---------

    Co-authored-by: wsmoses <1260124+wsmoses@users.noreply.github.com>
    Co-authored-by: William Moses <gh@wsmoses.com>

commit 5555a9d
Author: Laslo Hunhold <hunhold@uni-koeln.de>
Date:   Tue Sep 3 20:56:27 2024 +0200

    [libtakum] Update to v0.2.2 (#9357)

    Signed-off-by: Laslo Hunhold <hunhold@uni-koeln.de>

commit bb8ec62
Author: Mikael Slevinsky <Richard.Slevinsky@umanitoba.ca>
Date:   Tue Sep 3 13:17:41 2024 -0500

    [FastTransforms] update to v0.6.3 (#9359)

    * [FastTransforms] update to v0.6.3

    * switch to GitSource

    * srcdir changes because using GitSource instead of ArchiveSource tag

    * add new symbols used by fmm_source.c

commit 273a9c9
Author: James Wrigley <JamesWrigley@users.noreply.github.com>
Date:   Tue Sep 3 20:16:53 2024 +0200

    [CImGuiPack] Update for ImGui 1.91.0 (#9255)

    * [CImGuiPack] Update for ImGui 1.91.0

    * fixup! [CImGuiPack] Update for ImGui 1.91.0

    * fixup! [CImGuiPack] Update for ImGui 1.91.0

    * fixup! [CImGuiPack] Update for ImGui 1.91.0

commit 8ae7cc4
Author: Joroks <32484985+Joroks@users.noreply.github.com>
Date:   Tue Sep 3 17:59:18 2024 +0200

    [LAMMPS] disable MPI on Windows (#9358)

    * Fix the build option for LAMMPS to actually enable MPI

    * Update build_tarballs.jl

    * disable MPI on Windows

commit 0fca019
Author: Max Horn <max@quendi.de>
Date:   Tue Sep 3 13:58:50 2024 +0200

    Update libjulia 1.12.0-DEV to latest master (#9331)

    There were several breaking kernel API changes

    Also update 1.11 to 1.11.0-rc3

    Co-authored-by: Benjamin Lorenz <lorenz@math.tu-berlin.de>

commit 334fe02
Author: Hans Schoenemann <hannes@mathematik.uni-kl.de>
Date:   Tue Sep 3 10:50:45 2024 +0200

    [Singular] update to 4.4.0-5 (#9333)

commit b014250
Author: enzyme-ci-bot[bot] <78882869+enzyme-ci-bot[bot]@users.noreply.github.com>
Date:   Tue Sep 3 07:50:31 2024 +0000

    Upgrade enzyme to refs/tags/v0.0.147 (#9354)

    Co-authored-by: wsmoses <1260124+wsmoses@users.noreply.github.com>

commit 59c9489
Author: William Moses <gh@wsmoses.com>
Date:   Tue Sep 3 01:11:48 2024 -0500

    Update build_tarballs.jl (#9355)

commit 62b6940
Author: William Moses <gh@wsmoses.com>
Date:   Mon Sep 2 21:13:35 2024 -0500

    Reactant: now with libdl (#9353)

commit a0f4512
Author: William Moses <gh@wsmoses.com>
Date:   Mon Sep 2 19:08:42 2024 -0500

    Reactant: fix syntax error (#9352)

commit 778da9e
Author: Joroks <32484985+Joroks@users.noreply.github.com>
Date:   Mon Sep 2 22:09:27 2024 +0200

    Fix the build option for LAMMPS to actually enable MPI (new attempt) (#9339)

    * Fix the build option for LAMMPS to actually enable MPI

    * Update build_tarballs.jl

commit 5dfab57
Author: William Moses <gh@wsmoses.com>
Date:   Mon Sep 2 14:30:09 2024 -0500

    Reactant: cuda round 4? (#9351)

    Don't export libcuda

commit a224f0f
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Mon Sep 2 14:16:01 2024 +0100

    [LibUV] Backport another bugfix (#9350)

    Ref: libuv/libuv#4525.

commit 08c88f1
Author: Marius Meyer <Marius.meyer@uni-paderborn.de>
Date:   Mon Sep 2 15:13:17 2024 +0200

    Add build scripts for XRT (#9290)

    * Add build scripts for XRT

    * Refactoring and use of atomic_patch

    * Adding comments

    * Clean up using line

    * Update patch for the use with atomic_patch

    * Rearrange linux patch

    * Add windows patches

    * Patch RapidJSON dependency

    * Apply patches for mingw support

    * Fix cxx flags

    * Fix include upper case

    * Use ocl_icd bindings for windows

    * Add compat for libcurl

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    * Apply suggestions from code review

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    * Further patching for windows version

    * Use rapidjson package

    * Sort patches by os

    * Patch library configs

    * Fix xdp link

    * Further library import and export fixes for mingw

    * Add missing library

    * also patch alveo core

    * Fix XDP exports and xrt_core dependencies

    * Remove dependency to libffi

    * Copy over relevant libraries

    * Fix symbol for xdp_core library

    * Fix XRT install path

    * Prevent overwrite of install prefix

    ---------

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

commit 0f83020
Author: Divyansh Goyal <divital2004@gmail.com>
Date:   Mon Sep 2 18:41:19 2024 +0530

    ITKIOWrapper-v1.0.0 Added getDirection function (#9348)

    Co-authored-by: hurtbadly <divita2004@gmail.com>

commit 9d6d94a
Author: Marco Matthies <71844+marcom@users.noreply.github.com>
Date:   Mon Sep 2 15:10:57 2024 +0200

    [Cares] Update to v1.33.1 (#9349)

commit 2040d25
Author: William Moses <gh@wsmoses.com>
Date:   Mon Sep 2 03:21:27 2024 -0500

    Reactant: Don't use hermetic libcuda.so and dont debug linux (#9347)

    * Don't use hermetic libcuda.so and dont debug linux

    * fix plat

    * fix cuda

    * Bump version to avoid registration questions

    * runtime dep

commit b1ebadb
Author: William Moses <gh@wsmoses.com>
Date:   Sun Sep 1 19:38:33 2024 -0500

    Reactant: try debug build for linux (#9344)

    * Reactant: try debug build for linux

    * Update build_tarballs.jl

    * Update build_tarballs.jl

commit c49ca33
Author: William Moses <gh@wsmoses.com>
Date:   Sun Sep 1 12:28:50 2024 -0500

    Reactant: try fixing varname (#9343)

commit ff00ace
Author: enzyme-ci-bot[bot] <78882869+enzyme-ci-bot[bot]@users.noreply.github.com>
Date:   Sun Sep 1 10:49:05 2024 -0500

    Upgrade enzyme to refs/tags/v0.0.146 (#9342)

    Co-authored-by: wsmoses <1260124+wsmoses@users.noreply.github.com>

commit ba118b7
Author: Divyansh Goyal <divital2004@gmail.com>
Date:   Sun Sep 1 18:23:49 2024 +0530

    [ITKIOWrapper-v1.0.0] fixed  @wrapmodule error (#9340)

    * Update itklib.cpp

    * Update CMakeLists.txt

commit bc44d4c
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Sat Aug 31 23:13:13 2024 -0400

    [MUMPS_seq] Also compile MUMPS with 64-bit integer (#9341)

commit 2b8d0e1
Author: William Moses <gh@wsmoses.com>
Date:   Sat Aug 31 17:26:45 2024 -0500

    Reactant build without cuda fancy toys (#9338)

    * Reactant build without cuda fancy toys

    * Update build_tarballs.jl

    * Update build_tarballs.jl

commit 8120932
Author: William Moses <gh@wsmoses.com>
Date:   Sat Aug 31 09:46:44 2024 -0500

    Reactant: hermetic build, part 2 (#9330)

    * Restore file

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * fix

    * crosstool cuda

    * fixup

    * Update build_tarballs.jl

    * fix

    * fix

    * fix

    * fix

    * xla fix

    * clean

    * add license

    * cuda libs

    * cuda libs

    * cuda libs

    * cuda libs

commit ae9c13f
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Sat Aug 31 14:41:50 2024 +0200

    [LibUV] Includes a couple of backports from our fork (#9337)

    This includes

    * JuliaLang/libuv#38, backport of
      libuv/libuv#4521
    * JuliaLang/libuv#39, backport of
      libuv/libuv#4278

commit b17a65e
Author: Nicolas Riel <50235786+NicolasRiel@users.noreply.github.com>
Date:   Fri Aug 30 22:56:40 2024 +0200

    MAGEMin v1.5.2 (#9336)

commit 9476386
Author: James Wrigley <JamesWrigley@users.noreply.github.com>
Date:   Fri Aug 30 19:06:39 2024 +0200

    [libssh] Update to 0.11.1 (#9332)

    Compilation on GCC <5 has been fixed upstream.

commit dfc6fb9
Author: Boris Kaus <61824822+boriskaus@users.noreply.github.com>
Date:   Fri Aug 30 19:06:24 2024 +0200

    [PETSc] 3.20.5 (#9291)

    * add build for 3.20.5

    * simplufy buildscript

    * misspelled patch name

    * update patch

    * missing lines in the patch

    * test whether we can activate libgfortran3 on more systems with this version of PETSc

    * full build

    * deactivate libgfortran3 & mpitrampoline

    * Remove unused compat statements

    * missing bracket

    * simplify build script

    * fix merge issues

commit 6f6732e
Author: Tim Besard <tim.besard@gmail.com>
Date:   Fri Aug 30 16:35:10 2024 +0200

    pocl: Use wrapper scripts for JLL binaries. (#9322)

commit 84c1061
Author: Dominique <dominique.orban@gmail.com>
Date:   Thu Aug 29 18:15:36 2024 -0400

    proxTV: version 3.3.0 (#9329)

    * proxTV: version 3.3.0

    * Update P/proxTV/build_tarballs.jl

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    ---------

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

commit ca08b45
Author: Cody Tapscott <84105208+topolarity@users.noreply.github.com>
Date:   Thu Aug 29 16:05:45 2024 -0400

    [IntelOpenMP] Make artifacts lazy (#9319)

    * [IntelOpenMP] Make artifacts lazy

    * [IntelOpenMP] Upgrade to v2024.2.1

    Switch to PyPI for pre-compiled binaries.

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    ---------

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

commit f470d86
Author: William Moses <gh@wsmoses.com>
Date:   Thu Aug 29 00:27:58 2024 -0500

    Reactant: try hermetic cuda build (#9298)

    * Reactant: try removing new lld

    * Reactant: try hermetic cuda build

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * more bazel funtimes

    * no imm

    * no imm

    * no imm

    * no imm

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

    * Update build_tarballs.jl

commit 9438f80
Author: ArseniyKholod <119304909+ArseniyKholod@users.noreply.github.com>
Date:   Wed Aug 28 19:32:39 2024 +0300

    [openfhe_julia] update to version v0.3.4 (#9326)

commit 14d5872
Author: Jacob Quinn <quinn.jacobd@gmail.com>
Date:   Wed Aug 28 10:05:43 2024 -0600

    [aws_c_io] Update to 0.14.18 (#9327)

    Co-authored-by: github-actions <github-actions@github.com>

commit f4fde92
Author: Jacob Quinn <quinn.jacobd@gmail.com>
Date:   Wed Aug 28 10:05:36 2024 -0600

    [aws_lc] Update to 1.34.2 (#9328)

    Co-authored-by: github-actions <github-actions@github.com>

commit eb37a01
Author: Alexander Wietek <alexander.wietek@gmail.com>
Date:   Tue Aug 27 22:23:21 2024 +0200

    [XDiag] fix v0.2.2 (#9324)

    * [XDiag] bump 0.2.2

    * [XDiag] fix v0.2.2

    ---------

    Co-authored-by: Alexander Wietek <awietek@pks.mpg.de>

commit 562c581
Author: Jeremiah <4462211+jeremiahpslewis@users.noreply.github.com>
Date:   Tue Aug 27 21:58:39 2024 +0200

    [nghttp2] Bump to v1.63.0 (#9320)

commit 0a1b958
Author: Marek Kaluba <kalmar@amu.edu.pl>
Date:   Tue Aug 27 21:58:13 2024 +0200

    SCS: update to version 3.2.7 (#9317)

commit ca44cd1
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Tue Aug 27 11:33:26 2024 -0400

    [CUTEst] Upgrade to v2.2.5 (#9323)

commit 60235b3
Author: Jaakko Ruohio <jaakkor2@users.noreply.github.com>
Date:   Mon Aug 26 23:24:47 2024 +0300

    [OCCT] Update to version 7.7.2 (#9305)

    * [OCCT] Update to version 7.8.1

    * Let's see if v7.6.2 compiles

    * Test v7.7.2

commit 59b4f37
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Mon Aug 26 12:24:49 2024 -0400

    [CUTEst] Upgrade to v2.2.4 (#9316)

commit d75ad6b
Author: Nicolas Riel <50235786+NicolasRiel@users.noreply.github.com>
Date:   Mon Aug 26 14:15:27 2024 +0200

    MAGEMin v1.5.1 (#9314)

commit 4596dcc
Author: Marius Meyer <Marius.meyer@uni-paderborn.de>
Date:   Mon Aug 26 13:25:38 2024 +0200

    Add rapidjson v1.1.0 (#9272)

    * Add build script for rapidjson

    * Use current master branch for building instead of outdated release

    * Clean up script and change make up version

commit 40705c4
Author: Boris Kaus <61824822+boriskaus@users.noreply.github.com>
Date:   Mon Aug 26 12:44:31 2024 +0200

    new version of LaMEM build vs PETSc 3.19.6 (#9313)

commit 49a67a6
Author: Boris Kaus <61824822+boriskaus@users.noreply.github.com>
Date:   Sun Aug 25 20:39:56 2024 +0200

    [PETSc] version 3.19.6 (#6594)

    * petsc 3.19.0

    * updated for 3.19

    * use libblastrampoline; update mumps

    * update to 3.19.6

    * add HDF5

    * update BLAS name on windows

    * updates

    * static compilation of superlu_dist and mumps on linux

    * update

    * temporary reduce number of builds to save CPU time

    * update for mpitrampoline

    * fixes

    * deactivate MUMPS static compilation on non-cooperating systems

    * activate a few more libgfortran cases

    * exclude the remaining failing systems; activate build for complex and single libraries as well

    * cleanup script; deactivate last remaining failing system

    * simplify filtering

    * simplify build

    * deactivate libgfortran3 on mpitrampoline systems

    * retrigger build

    * Update build_tarballs.jl

    Remove unnecessary compat

    * Update P/PETSc/build_tarballs.jl

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    ---------

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

commit 9669e5c
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Sun Aug 25 00:34:46 2024 +0200

    [FFMPEG] Upgrade to v6.1.2 (#9310)

    Upgrade also some of the dependencies.

commit 8618591
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Sun Aug 25 00:09:50 2024 +0200

    [Opus] Rebuild, to remove Pkg dependency (#9311)

commit adf6266
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Sat Aug 24 23:38:55 2024 +0200

    [x264] Upgrade to a newer commit and change versioning scheme (#9309)

commit e670c14
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Sat Aug 24 16:15:41 2024 -0400

    [CUTEst] Upgrade to v2.2.3 (#9306)

    * [CUTEst] Upgrade to v2.2.3

    * Quadruple precision is not supported by ARM platforms

commit a698c75
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Sat Aug 24 17:33:45 2024 +0200

    [x265] Upgrade to v3.6 (#9308)

commit 0ca5e5d
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Sat Aug 24 17:14:11 2024 +0200

    [libfdk_aac] Upgrade to v2.0.3 (#9307)

commit dad8ca3
Author: Jared Wahlstrand <jwahlstrand@gmail.com>
Date:   Fri Aug 23 18:13:43 2024 -0400

    [Pango] rebuild for HarfBuzz update (#9302)

    * [Pango] rebuild for HarfBuzz update

    * use fake version

commit 4f73f9c
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Fri Aug 23 16:04:30 2024 -0600

    [aws_c_cal] Update to 0.7.4 (#9304)

    Co-authored-by: github-actions <github-actions@github.com>

commit 7ff6a90
Author: Jared Wahlstrand <jwahlstrand@gmail.com>
Date:   Fri Aug 23 17:57:52 2024 -0400

    [libass] update to 0.15.2 (#9303)

    and bump HarfBuzz compat

commit b8c393c
Author: Jared Wahlstrand <jwahlstrand@gmail.com>
Date:   Fri Aug 23 16:35:28 2024 -0400

    [Harfbuzz] update to 8.3.1 (#8392)

    * update Harfbuzz to 8.3.1

    * touch build_tarballs.jl

    * bypass broken check for CoreText on MacOS

commit e6787d9
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Fri Aug 23 14:12:34 2024 -0600

    [aws_c_auth] Update to version 0.7.26 (#9301)

    Co-authored-by: github-actions <github-actions@github.com>

commit dff058f
Author: Marius Meyer <Marius.meyer@uni-paderborn.de>
Date:   Fri Aug 23 10:43:10 2024 +0200

    Add OpenCL ICD v2.3.2 (#9270)

    Co-authored-by: Tim Besard <tim.besard@gmail.com>

commit 38b214d
Author: Alexander Wietek <alexander.wietek@gmail.com>
Date:   Fri Aug 23 09:58:09 2024 +0200

    [XDiag] bump 0.2.2 (#9289)

    Co-authored-by: Alexander Wietek <awietek@pks.mpg.de>

commit be9d4c0
Author: Jared Wahlstrand <jwahlstrand@gmail.com>
Date:   Thu Aug 22 13:22:21 2024 -0400

    [Pango] update to 1.54.0 (#9299)

    * bump to 1.54

    * use older FriBidi

commit dec1396
Author: Jared Wahlstrand <jwahlstrand@gmail.com>
Date:   Thu Aug 22 13:20:00 2024 -0400

    [GTK4] update to 4.14.5 (#9297)

commit c8b9a4a
Author: Tim Besard <tim.besard@gmail.com>
Date:   Thu Aug 22 16:37:01 2024 +0200

    LLVM: Bump LLVMExtra. (#9296)

commit 4120f1e
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Wed Aug 21 13:56:51 2024 -0600

    [aws_lc] Update to 1.34.0 (#9293)

    Co-authored-by: github-actions <github-actions@github.com>

commit 583896b
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Wed Aug 21 11:15:19 2024 -0600

    [aws_c_compression] Update to 0.2.19 (#9292)

    Co-authored-by: github-actions <github-actions@github.com>

commit 94b0365
Author: enzyme-ci-bot[bot] <78882869+enzyme-ci-bot[bot]@users.noreply.github.com>
Date:   Wed Aug 21 06:54:28 2024 +0000

    Upgrade enzyme to refs/tags/v0.0.145 (#9288)

    Co-authored-by: wsmoses <1260124+wsmoses@users.noreply.github.com>

commit bf12739
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Wed Aug 21 01:45:43 2024 -0400

    [CUTEst] Upgrade to v2.2.2 (#9156)

    * [CUTEst] Upgrade to v2.2.2

commit c347dd2
Author: André Guedes <andre.guedes@relational.ai>
Date:   Tue Aug 20 19:36:34 2024 -0300

    Upgrade object_store_ffi to v0.8.0 (#9287)

commit 554c476
Author: Philip Tellis <philip.tellis@gmail.com>
Date:   Tue Aug 20 15:57:18 2024 -0400

    Bump XML2 to 2.13.3 (#9286)

    * Bump XML2 to 2.13.3

    2.13.1 -> 2.13.3

    * Update sha256 sum for libxml2

commit 5e941b4
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Tue Aug 20 13:34:50 2024 -0600

    [s2n_tls] Update to 1.5.1 (#9285)

    Co-authored-by: github-actions <github-actions@github.com>

commit 7faddc5
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Tue Aug 20 12:27:38 2024 -0400

    Rclone: New version 1.67.0 (#9282)

    * Rclone: New version 1.67.0

    * Rclone: Clean up

commit 11b10c4
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Mon Aug 19 00:54:04 2024 -0400

    [SIFDecode] Recompile to have a shared library (#9280)

commit 05e7972
Author: Marius Meyer <Marius.meyer@uni-paderborn.de>
Date:   Sat Aug 17 22:12:35 2024 +0200

    Add Systemtap v4.6 (#9269)

    * Add Systemtap build script

    * Add linebreak to end of file

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    ---------

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

commit 13f7a59
Author: Rik Huijzer <github@huijzer.xyz>
Date:   Sat Aug 17 22:02:38 2024 +0200

    [pandoc_crossref] Update to 0.3.17.1c (#9279)

commit 11ee768
Author: Rik Huijzer <github@huijzer.xyz>
Date:   Sat Aug 17 21:31:13 2024 +0200

    [pandoc] Update to 3.3 (#9278)

commit d004386
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Sat Aug 17 14:34:08 2024 -0400

    [SIFDecode] Upgrade to v2.6.0 (#9277)

commit fbc0803
Author: Marius Meyer <Marius.meyer@uni-paderborn.de>
Date:   Sat Aug 17 17:32:56 2024 +0200

    Add ELFIO v3.12 (#9271)

    * Add build script for ELFIO

    * Add line breka at end of file

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    * Update E/ELFIO/build_tarballs.jl

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

    ---------

    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

commit 73115a7
Author: Alexander Wietek <alexander.wietek@gmail.com>
Date:   Sat Aug 17 10:52:05 2024 +0200

    [XDiag] trying to fix a problem with OpenMP on apple-aarch64 (#9265)

    Co-authored-by: Alexander Wietek <awietek@pks.mpg.de>
    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>
    Co-authored-by: Mosè Giordano <765740+giordano@users.noreply.github.com>

commit 2a5e608
Author: Jeremiah <4462211+jeremiahpslewis@users.noreply.github.com>
Date:   Sat Aug 17 01:54:09 2024 +0200

    [GDAL] bump 3.9.2 (#9273)

commit 4341b0e
Author: Thomas Vetter <80452158+thomvet@users.noreply.github.com>
Date:   Sat Aug 17 01:53:16 2024 +0200

    [open62541] v1.4.4 (#9274)

    * [open62541] update to version 1.4.4

commit b01a95f
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Fri Aug 16 17:52:46 2024 -0600

    [aws_c_http] Update to 0.8.8 (#9275)

    Co-authored-by: github-actions <github-actions@github.com>

commit 644ae37
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Fri Aug 16 17:52:36 2024 -0600

    [aws_c_event_stream] Update to 0.4.3 (#9276)

    Co-authored-by: github-actions <github-actions@github.com>

commit 2297685
Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Date:   Fri Aug 16 00:44:03 2024 +0200

    [CI] Update manifest (#9268)

    Notable changes:
    * JuliaPackaging/BinaryBuilder.jl@d9ba50f...8aadff4
    * JuliaPackaging/BinaryBuilderBase.jl@bfac3a4...8c16d55

    Co-authored-by: giordano <giordano@users.noreply.github.com>

commit fcd4dbe
Author: Erik Schnetter <schnetter@gmail.com>
Date:   Thu Aug 15 18:39:52 2024 -0400

    Blosc2: New version 2.15.1 (#9264)

commit 5b78a42
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Fri Aug 16 00:39:17 2024 +0200

    [RootFs/Go] Update to v1.23.0 (#9267)

    Co-authored-by: Luke Amdor <luke.amdor@juliahub.com>

commit b07c244
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Thu Aug 15 21:53:38 2024 +0200

    [LLVMOpenMP] Upgrade to v17.0.6 (#9266)

commit 6258bc4
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Thu Aug 15 16:12:38 2024 +0200

    [OpenBLAS] Backport new threading buffer patch (#9263)

commit 39e5a9a
Author: Mosè Giordano <765740+giordano@users.noreply.github.com>
Date:   Thu Aug 15 08:35:12 2024 +0200

    [OpenBLAS] Backport patch to fix init of threading memory buffers (#9262)

commit 38bb8bc
Author: Leandro Martínez <31046348+lmiq@users.noreply.github.com>
Date:   Wed Aug 14 15:05:49 2024 -0300

    Update Packmol to 20.15.1 (#9261)

commit 43c4d4b
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Wed Aug 14 11:48:57 2024 -0400

    [SIFDecode] Upgrade to v2.5.1 (#9260)

commit 6c58fe1
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Tue Aug 13 20:28:44 2024 -0600

    [aws_c_common] Update to 0.9.27 (#9259)

    Co-authored-by: github-actions <github-actions@github.com>

commit 0fbb7ce
Author: Frankie Robertson <frankier@users.noreply.github.com>
Date:   Wed Aug 14 05:26:07 2024 +0300

    Add the same DuckDB extensions as Python (#9251)

commit d9f43ee
Author: Viral B. Shah <virals@gmail.com>
Date:   Tue Aug 13 22:25:30 2024 -0400

    [Rmath-julia] Update to 0.5.0 (#9257)

    * [Rmath] Update to 0.5.0

commit 809e483
Author: Brendan Harris <brendanjohnharris@gmail.com>
Date:   Wed Aug 14 06:23:22 2024 +1000

    New recipe: catchaMouse16-v0.1.0 (#9151)

    * New recipe: catchaMouse16-v0.1.0

    * Exclude windows

    * Change compiler to generic 'cc'

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    * Change to command substitutions

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    * Set make job count

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    * Specify GSL_jll version (~2.7.2)

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    * Use install instead of cp

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    * Use make install target and lower Julia compat to LTS

    * Standardize output name

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    * Use command substitutions

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    * Use c11 to avoid warnings

    * Use gcc for apple (?)

    * Remove windows again

    * Hopeful fix for macos and windows

    * Enable all platforms

    * Extra flags for macos fix

    * Add extra flags in right place

    * Clean up makefile

    * Add headerpad flag

    * Headerpad flag for all machines

    * Fix src file finding

    * Update C/catchaMouse16/build_tarballs.jl

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

    ---------

    Co-authored-by: Mosè Giordano <giordano@users.noreply.github.com>

commit 9cebb84
Author: Alexis Montoison <35051714+amontoison@users.noreply.github.com>
Date:   Tue Aug 13 14:14:28 2024 -0400

    Add a recipe for SIFDecode (#9256)

    * Add a recipe for SIFDecode

    * Don't compile with libgfortran3

commit 5308e5b
Author: enzyme-ci-bot[bot] <78882869+enzyme-ci-bot[bot]@users.noreply.github.com>
Date:   Tue Aug 13 14:58:01 2024 +0000

    Upgrade enzyme to refs/tags/v0.0.144 (#9249)

    Co-authored-by: wsmoses <1260124+wsmoses@users.noreply.github.com>

commit d886cb3
Author: Benjamin Lorenz <benlorenz@users.noreply.github.com>
Date:   Tue Aug 13 16:27:48 2024 +0200

    [polymake_oscarnumber] version 0.3.1 (#9254)

commit f5da6c0
Author: Benjamin Lorenz <benlorenz@users.noreply.github.com>
Date:   Tue Aug 13 14:36:53 2024 +0200

    [libpolymake_julia] version 0.12.1, simplify workaround for lld issue (#9253)

commit 127f6dc
Author: Frankie Robertson <frankier@users.noreply.github.com>
Date:   Tue Aug 13 13:45:51 2024 +0300

    [DuckDB] Add in DuckDB shell to match SQLite (#9250)

commit c1528a9
Author: William Moses <gh@wsmoses.com>
Date:   Mon Aug 12 18:25:34 2024 -0700

    Reactant dbg (#9245)

    * Reactant dbg

    * now try

    * fix

    * Update build_tarballs.jl

    * Update build_tarballs.jl

commit 55cd286
Author: quinnj2 <karbarcca2@gmail.com>
Date:   Mon Aug 12 17:07:38 2024 -0600

    [aws_c_common] Update to 0.9.26 (#9247)

    Co-authored-by: github-actions <github-actions@github.com>

commit 3f7c439
Author: Mosè Giordano <giordano@users.noreply.github.com>
Date:   Tue Aug 13 00:08:57 2024 +0200

    [LLVMCompilerRT] Update to v17.0.6 (#9246)

    * [LLVMCompilerRT] Update to v17.0.6

    * [LLVMCompilerRT] Define `__STDC_FORMAT_MACROS` to make `PRId64` available
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jmeziere commented Sep 11, 2024

@vchuravy It looks like everything is good now. Sorry for all of the messy commits, it was a steep learning curve. Could you check it out to see if it looks good?

vchuravy
vchuravy approved these changes Sep 12, 2024
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Looks reasonable to me, but it would be great if @maleadt could also give it a look.

maleadt
maleadt reviewed Sep 12, 2024
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jmeziere commented Sep 13, 2024

@vchuravy I think everything should be good to merge now.

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jmeziere commented Sep 17, 2024

@vchuravy Do you think it's good to merge?

@vchuravy vchuravy merged commit 6bf67ea into JuliaPackaging:master Sep 17, 2024
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