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Suite sparse #33

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waebbl
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@waebbl waebbl commented Nov 18, 2018 •
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Updated to version 5.4.0.

Uses one single package to install the complete suite, instead of several shared packages.
Needs >=magma-2 if cuda USE flag is set, which is currently not in official tree, so current magma-2.4.0 package is included.

TODO:

  • revdeps for the shared packages
  • update deps of revdep packages to alternatively use this package
  • fix CUDA compile failure in spqr (works in 5.4.0)
  • package testing: main Makefile has only coverage testing for some of the libs, no other tests. Most of the libs have a demo program which seems to be used for basic testing purposes. These are built and called during compile stage and work. The test-suite make cov currently fails inside the cholmod module with a core dump.
  • ebuild testing: use of metis vs. parmetis, use of all possible combinations of virtual/blas and virtual/lapack

@waebbl waebbl self-assigned this Nov 18, 2018
@waebbl waebbl added help wanted don't merge not ready for merging labels Nov 18, 2018
@waebbl waebbl force-pushed the SuiteSparse branch 2 times, most recently from 9f22cba to 7818093 Compare November 20, 2018 21:56
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waebbl commented Nov 21, 2018

Reverse dependencies of suitesparse-4.2.1 packages:
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/suitesparseconfig
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/amd
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/btf
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/camd
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/ccolamd
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/cholmod
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/colamd
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/cxsparse
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/klu
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/ldl
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/spqr
https://qa-reports.gentoo.org/output/genrdeps/rindex/sci-libs/umfpack

Removing suitesparse included packages from the lists this gives:

  • dev-lang/julia (currently masked for removal)
  • dev-libs/igraph
  • dev-python/cvxopt
  • media-libs/gegl[umfpack]
  • sci-chemistry/apbs[fetk]
  • sci-mathematics/glpk
  • sci-mathematics/lpsolve
  • sci-mathematics/octave[sparse]
  • sci-libs/ceres-solver[sparse]
  • sci-libs/coinor-clp[glpk,sparse]
  • sci-libs/mc
  • sci-libs/punc
  • sci-libs/scipy[sparse]
  • sci-libs/sundials[sparse]

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tamiko commented Nov 22, 2018

Thanks a lot for working on this!
I will try the new package and comment back on how it went asap :-)

@waebbl waebbl force-pushed the SuiteSparse branch 3 times, most recently from 181d4b7 to 57f4f44 Compare November 25, 2018 19:21
@waebbl waebbl removed the don't merge not ready for merging label Nov 25, 2018
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tamiko commented Nov 26, 2018

What I have done:

  • removed metis-5 hard mask,
  • pushed parmetis-4 to the main gentoo tree.

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tamiko commented Nov 26, 2018

Can we do the magma version bump independently? If yes, would you mind opening a pull request?

tamiko
tamiko suggested changes Nov 26, 2018
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waebbl commented Nov 26, 2018

What I have done:

  • removed metis-5 hard mask,
  • pushed parmetis-4 to the main gentoo tree.

We need to test then, if there are still any packages which break with metis-5 and/or parmetis-4. Have you also removed the hard-mask of parmetis-4 on science overlay?
I haven't yet tested with metis-5, but as it's included in the tarball and they use it by default, I thought it should work. But I will do the testing before releasing this.

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waebbl commented Nov 26, 2018

Can we do the magma version bump independently? If yes, would you mind opening a pull request?

Yes of course. On the official or science tree I will do those commits in separate PRs. I'm opening one, after work.

@tamiko
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tamiko commented Nov 26, 2018

@waebbl Here is a quick try on fixing up the dependencies: gentoo/gentoo#10490

@waebbl waebbl mentioned this pull request Nov 28, 2018
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@waebbl waebbl force-pushed the SuiteSparse branch 2 times, most recently from e5be053 to f062574 Compare December 1, 2018 10:53
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tamiko commented Apr 15, 2019

@waebbl ping, Shall we revive the suitesparse effort at some point? :-)

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waebbl commented Apr 21, 2019

@waebbl ping, Shall we revive the suitesparse effort at some point? :-)

Definitely! It has been on hold for some time already, but I'd like to continue this

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waebbl commented Jul 19, 2019 •
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@tamiko Removed magma for the commit. Will prepare a separate PR for this now, which I will push to ::gentoo.
There has been an update to suitesparse to version 5.4.0. There's also an update for magma to version 2.5.1_alpha1 or alternatively to 2.5.0. I'm going to check both of them.
I will prioritize the package, so hopefully we will get it into the tree soon.
I haven't yet tested or build the new release.

@waebbl
sci-libs/suitesparse: bump to version 5.4.0
11f9f22 
With update to 5.4.0 the package no longer comes in several shared
packages, but in a single package containing the complete suite of
sparse matrix packages.
Restricts tests for now, as they fail in cholmod module.

Package-Manager: Portage-2.3.69, Repoman-2.3.12
Manifest-Sign-Key: 0x2E246A4E715AA683
Signed-off-by: Bernd Waibel <[email protected]>
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