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software.hpc: Tracking PR#1

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camillescottatwork wants to merge 211 commits intomainucdavis/spack-ucdavis:mainfrom software.hpcucdavis/spack-ucdavis:software.hpcCopy head branch name to clipboard

+146,335-20,264

Commits

Commits on Jun 23, 2023

• [farm] reorg packages.yaml

  

  spack-user@peloton

  committed
  24f2a14

• [peloton] initital configurations.

  

  spack-user@peloton

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  4ae0037

• [peloton] core environment.

  

  spack-user@peloton

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  1e015e7

• [peloton] compilers from core environment.

  

  spack-user@peloton

  committed
  baf7283

Commits on Jun 28, 2023

• WIP main

  

  spack-user@peloton

  committed
  8c3b48f

Commits on Jun 30, 2023

• Split hpccf repo into version-pinned repos'

  

  spack-user@peloton

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  24e13f7

• Add v0.20 which removes many backported packages

  

  spack-user@peloton

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  339444d

Commits on Jul 11, 2023

• Peloton v0.20 production config.

  camillescottatwork

  committed
  bda0c15

• Peloton modulefiles post upgrade

  camillescottatwork

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  93d3e7f

• [peloton] v0.20 packages post peloton upgrade

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  4a3f58a

• Template for external gcc

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  fcb09f6

• [peloton] main env, post upgrade.

  camillescottatwork

  committed
  013dc60

Commits on Jul 21, 2023

• [peloton] update modulefiles

  

  spack-user@peloton

  committed
  30503e0

• Update gcc 7.5.0 compiler paths

  

  spack-user@peloton

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  90145ab

• Get working bwa-mem2 package.

  

  spack-user@peloton

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• add dashing package

  

  spack-user@peloton

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  023cc11

• bwa-mem2 patches.

  

  spack-user@peloton

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  1e35875

• idl package

  

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• coverm package

  

  spack-user@peloton

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• [peloton] many package updates in main environment.

  

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  4941aeb

• [peloton] reconcretized main lockfile

  

  spack-user@peloton

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  b094f09

• [peloton] remove unused core envuironment

  

  spack-user@peloton

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  530ebf7

• remove duplicates.txt

  camillescottatwork

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  8d3ea32

Commits on Aug 14, 2023

• [peloton] add numactl to main environment.

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  3c8df35

• Simple environment for EPYC CPU benchmarking.

  camillescottatwork

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  7bda7b7

• [peloton] add aocc to spack compiler configuration

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  b1965a8

• Edits to stream package.

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  7e14c0e

Commits on Aug 28, 2023

• [peloton] new modulefile

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  810828b

Commits on Aug 29, 2023

• [peloton] update for slurm patch

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  00a8382

Commits on Sep 15, 2023

• Bump the Slurm stack to use PMIx 4.2.6 + newer ucx and hwloc.

  OmenWild

  committed
  f571f93

• Bump the Slurm stack to use PMIx 4.2.6 + newer ucx and hwloc.

  OmenWild

  committed
  4bd22d8

• Comment out julia, does not build with Spack yet.

  OmenWild

  committed
  6b62eb4

• Normalize backports and hpccf environments

  

  spack-user@peloton

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  f640f06

• [peloton] bump minimap2 version.

  

  spack-user@peloton

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  d37e04a

• [peloton] reconcretize main

  

  spack-user@peloton

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  7c70897

• [peloton] regenerate modulefiles

  

  spack-user@peloton

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  26d0412

• [peloton] concretize benchmarking environment.

  

  spack-user@peloton

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  2817bb3

Commits on Sep 19, 2023

• Merge farm/franklin main

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  9929632

• Move ont-guppy and py-deeptools into forked

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  5c19d85

• [franklin][peloton] add new 'forked' repo

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  da261f6

• Fix package links

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  08aae6e

Commits on Sep 20, 2023

• [franklin] start v0.20 config

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  committed
  ac2238c

Commits on Oct 3, 2023

• [Peloton] [INC1724503] Update coverm to use the newest minimap2 ^[email protected]

  OmenWild

  committed
  b0b0141

• Snapshot.

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  committed
  e5190df

• [Peloton] [INC1724503] Update coverm to use the newest minimap2 ^[email protected]

  OmenWild

  committed
  4295a0e

Commits on Oct 6, 2023

• Snapshot.

  OmenWild

  committed
  bfbcf42

• [Peloton] Upgrade the external Slurm to 23.02.5

  OmenWild

  committed
  e937e6a

Commits on Oct 12, 2023

• [franklin] Initial base configs: common, core, software

  camillescottatwork

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  42d27f2

• [franklin] Mostly finalized core environment.

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  9698e32

• [franklin] concretized core environment

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  5967cf9

• Fork openssl to export proper environment variables to allow more builds with Ubuntu external

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  committed
  c47d7d1

• Fork slurm to bump to for emergency CVE release 2023-10-12 (v23.02.6)

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  committed
  ffc1c5d

• [franklin] Add merge script for common and software packages.yaml; Add software compilers.yaml

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  e57b65b

• [franklin] first pass software spack.yaml

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  committed
  bc836c0

• [franklin] add cuda 8

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  committed
  5f6df2b

Commits on Oct 14, 2023

• [franklin] external llvm; update slurm and envmod prefixes

  camillescottatwork

  committed
  568aa3b

• [franklin] convert templates from lua to tcl; sanitize extra relion fields between cpu and gpu

  camillescottatwork

  committed
  62447c8

• Fork unzip to fix build for oneapi

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  committed
  f687999

Commits on Oct 16, 2023

• [franklin] update relion templates and modulefile vars

  camillescottatwork

  committed
  2e3ea5b

• Remove some unnecessary packages.

  camillescottatwork

  committed
  63f55c3

• Add missing dbus dependency back in to Slurm package.py

  camillescottatwork

  committed
  2508a91

• [franklin] core: roll back to environment modules 5.2.0 due to tcl libs path regression; add more CUDAs

  camillescottatwork

  committed
  7c518ad

• [franklin] properly fill out mirrors.yaml

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  committed
  db73e4b

• [franklin] autoload:direct

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  f5aee24

• [franklin] force xmlto to use %gcc due to a OneAPI build bug.

  camillescottatwork

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  d0ed859

• [franklin] regenerated software packages.yaml

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  a45e0a4

• [franklin] reconcretize core.

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  1019612

• [franklin] reconcretize software

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  da432c5

• [franklin] generate tcl modulefiles.

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  2157c9f

Commits on Oct 17, 2023

• Snapshot.

  OmenWild

  committed
  7be4357

• [Peloton] Upgrade Slurm to the newest (23.02.6).

  OmenWild

  committed
  850b8b6

Commits on Oct 26, 2023

• Add a full featured squashfs for apptainer.

  OmenWild

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  6ae4f25

• Add an explicit version to apptainer.

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• TODO: move to the -forked repo.

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  OmenWild

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  08bef90

• Snapshot.

  OmenWild

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Commits on Nov 2, 2023

• [franklin] update modulefiles

  camillescottatwork

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  4dfd05c

• Update alphafold and dependencies

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  9ae9a16

• Update relion templates

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  114fea9

• Add wrappers for deepemhancer, topaz

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  8579276

• [franklin] main env: alphafold and variables, relion 5, relion variables update for new templates

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  ed8a76e

• Add relion 5-beta

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  e4bf99d

• [franklin] main env: reconcretize

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  d97e228

Commits on Nov 9, 2023

• Add gctf variant to relion

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  5fba200

• [franklin] reconcretize software

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  1bad84a

• Merge branch 'franklin-reorg' into versioned-reorganization

  camillescott

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  69b9c8d

Commits on Nov 27, 2023

• [Peloton] [INC1783336] Add Matlab R2023a as a Spack external.

  OmenWild

  committed
  3b201bb

• Snapshot.

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  3dc7316

Commits on Dec 14, 2023

• [Peloton] Upgrade slurm to the newest bugfix release (23-02-7).

  OmenWild

  committed
  7a3c747

• Snapshot.

  OmenWild

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  d6ad02a

Commits on Mar 1, 2024

• openmm

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• Merge branch 'versioned-reorganization' of github.com:ucdavis/spack-ucdavis into versioned-reorganization

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  c693645

Commits on Mar 7, 2024

• Move all packages that exist in both hpccf and builtin to forked

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  28c9f1f

• Bring in upstream changes to libxml2, preserving our +ftp variant

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  376fbf5

• Upstream changes to bpp-phyl-omics

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  615356f

• [package] openssl: merge upstream changes, preserve out dependent build environment

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  committed
  9c59419

• [package] bpp-phyl, bpp-popgen: upstream changes

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  committed
  ac2527f

• [package] bpp-core,seq-omics,seq,suite: upstream merge

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  76141f5

• [package] r-raster: remove backported package

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  6040aca

• [package] py-gdc-client: upstream merge

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  bb2ae10

• [package] r-units: remove essentially backported package

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  committed
  2d05859

• [package] blat: merge upstream

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  committed
  b53843a

• [package] htslib: merge major upstream changes; preserve our out-of-source build

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  committed
  d8363fe

• [package] circos: upstream changes

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  bc9722c

• [package] salmon: remove out outdated fork for upstream version

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  164c774

• [package] r-ensembldb: remove out outdated backport

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  54c5ad7

• [package] lmod: deprecate our fork for now (we don't use it anymore)

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  30e0973

• [package] for now, deprecate our maker

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  4e467ba

• [package] py-cyvcf2: upstream changes

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• [package] mark: deprecate in favor of upstream

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  5fc63b8

• [package] gffcompare: merge upstream changes

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  57610a3

• [package] motioncor2: upstream now patches binaries for cuda the same way we do, deprecate

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  committed
  9c8430a

• [package] libxpm: remove outdated backport

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  committed
  02f9c15

• [package] sailfish: bring in upstream changes (use tbb provider)

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  b8251af

• [package] unblur: deprecate fork, 1.0.2 now in upstream

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• [package] r-v8: deprecate fork for much newer upstream

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• [package] unzip: deprecate what appears to be a backport

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• [package] r-genomicfeatures: deprecate outdated backport

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  committed
  4caebb1

• [package] r-genomeinfodb: upstream is newer, deprecate our fork

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  committed
  39883c1

• [package] dbus: upstream now supports the --with-system-socket flag, which replaces the purpose of our local_state_dir implementation

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  committed
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• [package] libseccomp: upstream merge

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• [package] r-ggtree: upstream is newer, deprecate

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• [package] gatk: upstream has much newer versions, deprecate

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  committed
  8a5198e

• [package] plink-ng: merge upstream zlib=>zlib-api changes

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• [package] apptainer: bring in license from upstream

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  committed
  a87489c

• [package] gffread: update to new-style maintainers directive

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  committed
  acb2d9c

• [package] julia: deprecate our (non-working) julia in favor of much-updated upstream

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  committed
  9ce6e1b

• [package] py-dm-haiku: bring upstream license directive

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  committed
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• [package] r-bsgenome: remove outdated backport

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  committed
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• [package] r-terra: remove outdated backport

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  committed
  27cdacb

• [package] py-deeptools: deprecate our version in favor of upstream which is newer

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• [package] r-insight: remove outdated backport

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• [package] openmm: remove unneeded link to backports/openmm

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• [package] node-js: add v18.18.2 (farm liftover, 4abf72c)

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  9a10678

• [package] cmake: fork and bring in v3.28.1 (farm liftover)

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  b250e0c

• [package] homer: fork and liftover changes from farm

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  committed
  5c95ccd

• [package] npm: farm liftover; add v9.8.1 and installer arg fixes

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  committed
  54ec787

• [package] plink: lift over farm's fork with newer version, patch

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• [package] qualimap: bring over farm version with patch for java > 8

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  committed
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• [package] censor-norb: new package, bring over from farm branch

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  2f8b26d

• [package] distangsd: bring in farm -libdeflate update; update for newspack

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• [package] ngsrelate: bring in new package from farm, clean up

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• [package] py-basevar: bring in new package from farm, clean up

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• [package] py-logbook: bring in new package from farm, clean up

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  committed
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• [package] rstudio: bring over farm 2023.12.1-402 updates

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  committed
  f3b9495

• [modulefile] base.tcl: lift over deprecation functionality from farm

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• [modulefile] rstudio-server,turbovnc: bring over farm template changes

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Commits on Mar 8, 2024

• [package] delete backports repo; remove unneeded and dead backports links

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  committed
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• [package] glimpse2: remove link to v0.19 packages and move package

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  committed
  0ccb9ff

• [package] h5z-zfp: remove forked package in favor of fixed upstream

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  43d3028

• [package] remove v0.19 repo

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  d4d558d

• [package] flatten hpccf repo

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  committed
  9e8ebee

• [package] remove forked slurm; upstream properly does dbus and has newer versions

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  committed
  eb1bda2

• [package] openmm: need link to builtin for patched dependency bug

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  7b3210d

• [package] environment-modules: fork environment modules and support out-of-prefix etcdir

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  5228707

• [config] software.hpc: first pass core conf

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• [config] software.hpc: first pass core env

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Commits on Mar 23, 2024

• [lock] software.hpc: concretized core environment

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  cb2ba1b

• [config] software.hpc: finalized core environment config.

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  cf125c8

• [config] software.hpc: enable arch_folder for modules

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• [config] software.hpc: add spack-installed compilers to core config

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  23f02b6

• [meta] add .cvmfs to git ignore:

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  committed
  1ecbd5b

• [config] software.hpc: update main environment externals for core

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  d9e3251

• [config] software.hpc: regenerate main packages config

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  committed
  ec8c688

Commits on Apr 10, 2024

• [package] openblas: fork openblas and set a specific target for generic v2 and v3 to avoid incorrect Zen guess on v3 QEMU

  camillescottatwork

  committed
  816cf5d

• [package] linux-pam: fork and add libintl dependency

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  committed
  f5950bf

Commits on Apr 30, 2024

• [config] software.hpc: core environment externals, additional core packages, remove LD_LIBRARY_PATH from modules

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  committed
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Commits on May 13, 2024

• [config] software.hpc: convert compilers defined in packages.yaml

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  24bbafa

• [config] software.hpc: remove prequisites: direct from common modules config

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  committed
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• [env: main] software.hpc: main defs

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  committed
  a83df4a

• [config, env: core] software.hpc: fully peel off definitions from core

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  committed
  9bd63e0

Commits on Oct 4, 2024

• Add the older versions of virtualgl and turbovnc so they get added to

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  39d640d

Commits on Oct 17, 2024

• Update core externals

  camillescottatwork

  committed
  4f535c6

• Don't export modules from core environment

  camillescottatwork

  committed
  e49c32c

• [package] fork libjpeg-turbo

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  committed
  38bd0f2

• [package] fork phyluce

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  de73f0c

• [package] fork virtualgl

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  12bb665

• [package] add new turbovnc version:

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  329d8d1

• [lock] concretize core

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  fd92db3

• [env:main] Fix iq-tree version, remove phyluce, add code-server

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• [lock] concretize main

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  fe93257

• [env:main] camw: added [email protected]

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• [lock] reconcretize main

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  e07dcbf

Commits on Oct 21, 2024

• [package] node-js: backport

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  committed
  a09dfe0

• [package] npm: 10.9.0

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  c705122

• [package] re2c: backport re2c

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  committed
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• [package] rstudio: 2024.09.0-375

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• [env:main] [email protected]

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  c094276

• [lock] reconcretize main

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  fd7bdcf

Commits on Oct 22, 2024

• [env:main,env:core] change view projections to hardlinks to avoid cmfscatalog linking problem

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  committed
  c669bcd

Commits on Nov 15, 2024

• Remove some specs that won't concretize, expose prefix inspections

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  bfcc529

• [lock] : reconcretize main

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  b2fa22c

• [env:core] camw: added mpich, openmpi 5, and pmix 5

  

  Software User

  committed
  bc6b0b8

• [config] camw: package options for mpich, tweaking variants for openmpi

  

  Software User

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  1d42761

• [config] camw: use /dev/shm ramdisk as spack-stage dir; disable modulefile config in core entirely

  

  Software User

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• [lock] reconcretize core

  

  Software User

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  e3b736f

Commits on Dec 19, 2024

• Remove deprecated packages from forked

  

  Software User

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  1492650

• Add qualimap 2.3

  

  Software User

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  78659d4

• Fix for invalid target arch spec in armpl-gcc

  

  Software User

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  1315e39

• Fix openssl version dep for blat

  

  Software User

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  d29dd94

• Merge builtin changes to libxml2

  

  Software User

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  d9c9275

• merge builtin changes for openblas

  

  Software User

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• builtin changes for graphicsmagick

  

  Software User

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  118d9e5

• openblas patch from builtin

  

  Software User

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  03b361b

• Fork slurm for new version; for jdk for new version; implement mlxup package

  

  Software User

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  c831692

• Merge builtin changes for environment-modules

  

  Software User

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  90277e8

• Merge changes from builtin for genemark-et

  

  Software User

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  d360e5f

• [config:core] move source_cache to /dev/shm

  

  Software User

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  c179ecc

• Update core compilers, libs; bump to gcc 13.2

  

  Software User

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  6d8aa01

• [main] additional packages, fixed packages for main

  

  Software User

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  918fb4a

• reconcretize core

  

  Software User

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• reconcretize main

  

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