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Fix lack of optimisation for SHAPEIT4 v4.1.3#12206

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boegel merged 4 commits intoeasybuilders:developfrom
verdurin:20210219093002_new_pr_SHAPEIT4413
Feb 19, 2021
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Fix lack of optimisation for SHAPEIT4 v4.1.3#12206
boegel merged 4 commits intoeasybuilders:developfrom
verdurin:20210219093002_new_pr_SHAPEIT4413

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@verdurin verdurin commented Feb 19, 2021

(created using eb --new-pr)

@verdurin verdurin changed the title Fix lack of optimisation {bio}[foss/2019b] SHAPEIT4 v4.1.3 - Fix lack of optimisation Feb 19, 2021
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verdurin commented Feb 19, 2021

Fixes issue #12204

@verdurin verdurin added this to the next release (4.3.3?) milestone Feb 19, 2021
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verdurin commented Feb 19, 2021

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux centos linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/e0e6ab91bfbffdae662f355e297b80ac for a full test report.

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@verdurin I think we can avoid a patch file here by just using buildopts, see also #12207

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verdurin commented Feb 19, 2021

@boegel I think we still need to patch out hard-coded HTSlib versions etc.

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Comment thread easybuild/easyconfigs/s/SHAPEIT4/SHAPEIT4-4.1.3-foss-2019b.eb Outdated
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boegel commented Feb 19, 2021

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3501.doduo.os - Linux RHEL 8.2, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/cde9356413305ee657c78714e297d584 for a full test report.

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boegel commented Feb 19, 2021

@boegelbot please test @ generoso

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boegelbot commented Feb 19, 2021

@boegel: Request for testing this PR well received on generoso

PR test command 'EB_PR=12206 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_12206 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 13884

Test results coming soon (I hope)...

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boegelbot commented Feb 19, 2021

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-c1-s-1 - Linux centos linux 8.2.2004, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/b10b582b0ddc0b2197ec41f27df4b5c2 for a full test report.

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boegel commented Feb 19, 2021

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3101.skitty.os - Linux centos linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz, Python 3.6.8
See https://gist.github.com/4d2491d1ea46f8979c7b6c762508d4cc for a full test report.

@boegel boegel changed the title {bio}[foss/2019b] SHAPEIT4 v4.1.3 - Fix lack of optimisation Fix lack of optimisation for SHAPEIT4 v4.1.3 Feb 19, 2021
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lgtm

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boegel commented Feb 19, 2021

Going in, thanks @verdurin!

@boegel boegel merged commit a2e3cdc into easybuilders:develop Feb 19, 2021
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