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add patch for h5py 2.10.0 with 2020a toolchains to avoid MPI_Init at import #10626

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merged 2 commits into from
May 12, 2020

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@boegel boegel commented May 12, 2020

This fix was also proposed upstream, see h5py/h5py#1544 .

It may get merged in slightly different form since the h5py developers don't seem to favor the top-level try + import mpi4py, but it's good enough to fix the h5py 2.10.0 release we're using.

I've verified that the Parallel HDF5 capabilities of h5py are preserved with this patch (using the example from https://docs.h5py.org/en/stable/mpi.html.

This should unblock #10191...

@boegel boegel added the 2020a before 2020a is released label May 12, 2020
@boegel boegel added this to the next release (4.2.1?) milestone May 12, 2020
@boegel boegel changed the title add patch for h5py 2.10.0 with 2020a toolchain to avoid MPI_Init at import add patch for h5py 2.10.0 with 2020a toolchains to avoid MPI_Init at import May 12, 2020
@boegel boegel force-pushed the h5py_fix_mpi_import branch from 98f16c0 to 8cc8c05 Compare May 12, 2020 18:02
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boegel commented May 12, 2020

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node2526.golett.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) CPU E5-2680 v3 @ 2.50GHz (haswell), Python 2.7.5
See https://gist.github.com/919d51663f86542b1bbe36c459ad5500 for a full test report.

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LGTM

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ocaisa commented May 12, 2020

Test report by @ocaisa
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
generoso - Linux centos linux 7.6.1810, x86_64, Intel(R) Xeon(R) CPU E5-2660 v4 @ 2.00GHz, Python 3.6.8
See https://gist.github.com/9e2e6c5bb2abd3c3034ee673626f7774 for a full test report.

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boegel commented May 12, 2020

Test report by @boegel
SUCCESS
Build succeeded for 10 out of 10 (4 easyconfigs in this PR)
node3410.kirlia.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 2.7.5
See https://gist.github.com/dc4cf4cf93626574c65a5a9628d808dd for a full test report.

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ocaisa commented May 12, 2020

Going in, thanks for making the effort to solve this @boegel

@ocaisa ocaisa merged commit f5005a1 into easybuilders:develop May 12, 2020
@boegel boegel deleted the h5py_fix_mpi_import branch May 12, 2020 19:12
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Test report by @akesandgren
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
b-an03.hpc2n.umu.se - Linux ubuntu 16.04, x86_64, Intel(R) Xeon(R) CPU E5-2690 v4 @ 2.60GHz, Python 2.7.12
See https://gist.github.com/85908c4d57fb16b8981a0c2c6f3c7a7b for a full test report.

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Test report by @verdurin
SUCCESS
Build succeeded for 8 out of 8 (2 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.8.2003, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/96808787645e2253a9d8a0121753a91e for a full test report.

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boegel commented May 13, 2020

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in this PR)
node3152.skitty.os - Linux centos linux 7.7.1908, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/d5e8f864661c9ee158a4ec88f713f85c for a full test report.

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5 participants