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openmpi: 3.1.3 -> 4.0.0 #54877

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merged 10 commits into from Feb 22, 2019
Merged

openmpi: 3.1.3 -> 4.0.0 #54877

merged 10 commits into from Feb 22, 2019

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markuskowa
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@markuskowa markuskowa commented Jan 29, 2019 •
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Motivation for this change

This update removes some deprecated MPI-1 symbols. This breaks some applications still using these outdated symbols. Fortunately it is a simple function name change in most cases.

Upgrade guide: https://www.open-mpi.org/software/ompi/major-changes.php
Removed symbols: https://www.open-mpi.org/faq/?category=mpi-removed

CC potentially affected maintainers @costrouc @abbradar @bzizou

Things done
  • Add upstream patch to mpi4py
  • patch deprecated functions in scalapack
  • Add upstream patch to globalarrays
  • Add upstream patches to hfd5-mpi
  • added an entry to the release notes
  • Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS)
  • Built on platform(s)
    • NixOS
    • macOS
    • other Linux distributions
  • Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
  • Tested compilation of all pkgs that depend on this change using nix-shell -p nox --run "nox-review wip"
  • Tested execution of all binary files (usually in ./result/bin/)
  • Determined the impact on package closure size (by running nix path-info -S before and after)
    -> ~+3MB
  • Assured whether relevant documentation is up to date
  • Fits CONTRIBUTING.md.

@markuskowa markuskowa mentioned this pull request Jan 29, 2019
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@markuskowa markuskowa added this to the 19.03 milestone Jan 29, 2019
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@GrahamcOfBorg build python36Packages.mpi4py python36Packages.tensorflow
@GrahamcOfBorg build lammps-mpi dl-poly-classic-mpi siesta-mpi quantum-espresso-mpi

dotlambda
dotlambda requested changes Jan 29, 2019
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You should add the pythonPackages. prefix to the last commit message.

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markuskowa commented Jan 29, 2019 •
edited

@GrahamcOfBorg build python36Packages.mpi4py
@GrahamcOfBorg build python36Packages.tensorflow
@GrahamcOfBorg build lammps-mpi
@GrahamcOfBorg build dl-poly-classic-mpi
@GrahamcOfBorg build siesta-mpi
@GrahamcOfBorg build quantum-espresso-mpi
@GrahamcOfBorg build gromacsDoubleMpi

@markuskowa markuskowa mentioned this pull request Feb 4, 2019
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markuskowa commented Feb 6, 2019 •
edited

Maybe I beat the timeout this time
@GrahamcOfBorg build scalapack

@markuskowa markuskowa mentioned this pull request Feb 16, 2019
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This pull request has been mentioned on Nix community. There might be relevant details there:

https://discourse.nixos.org/t/nixos-19-03-feature-freeze/1950/30

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@GrahamcOfBorg build scalapack

FRidh
FRidh approved these changes Feb 21, 2019
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Looks good to me. In case we find packages that we can't trivially fix we can still include 3.1.3, but that's for then.

@markuskowa
openmpi: 3.1.3 -> 4.0.0
3ed9664 
openmpi-4.0.0 removes deprecated MPI-1 symbols.
For upgrade guide see:
https://www.open-mpi.org/faq/?category=mpi-removed
markuskowa and others added 9 commits February 21, 2019 15:08
@markuskowa
release-notes: add note about openmpi-4.0.0 upgrade.
c26a79a 
Add link to openmpi upgrade guide, regarding deprecated MPI-1 symbols.
@markuskowa
openmpi: Use external hwloc and libevent
840716a 
Recommended in the upgrade guide:
https://www.open-mpi.org/software/ompi/major-changes.php
@markuskowa
globalarrays: add openmpi-4 compatibility patches
c0bc7a3
@markuskowa
globalarrays: use autoreconfHook
47a7745
@markuskowa
scalapack: add openmpi4 compatibility patch
4aa90ac
@markuskowa
pythonPackages.mpi4py: add patch for openmpi-4.0.0 compatibility
10e5cfd
@markuskowa
scalapack: update meta data
dbf5135 
* Set platform from linux -> x86_64-linux
  Scalapack does not seem to run properly on ARM (failing tests)

* Add markuskowa as maintainer
@markuskowa
openmpi: add patch for mpi tests on machines with less than 4 cores
c6f039e 
Fix a bug that ignores OMPI_MCA_rmaps_base_oversubscribe (upstream patch).
This bug breaks the test from libs, such as scalapack,
on machines with less than 4 cores.
@markuskowa
hdf5: add openmpi-4 compatibility patches
99ca454
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@FRidh That was my first thought to include the old version as well but I am optimistic that it should not be necessary.

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markuskowa commented Feb 21, 2019 •
edited

@GrahamcOfBorg build hdf5-mpi

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The PR would be ready for merging.

@markuskowa markuskowa merged commit 5c8c258 into NixOS:master Feb 22, 2019
@markuskowa markuskowa deleted the upd-openmpi4 branch February 22, 2019 08:31
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@markuskowa thank you thank you for this work. I will greatly benefit from this PR.

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Reviewers

@ryantm ryantm ryantm requested changes

@dotlambda dotlambda dotlambda requested changes

@FRidh FRidh FRidh approved these changes

@matthewbauer matthewbauer Awaiting requested review from matthewbauer

@Mic92 Mic92 Awaiting requested review from Mic92

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6.topic: nixos 6.topic: python 8.has: changelog 8.has: clean-up 8.has: documentation 10.rebuild-darwin: 101-500 10.rebuild-linux: 101-500 11.by: package-maintainer
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