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{bio}[GCCcore/9.3.0] SeqLib v1.2.0, fermi-lite v20190320, SSW v1.1#12856

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branfosj merged 6 commits intoeasybuilders:developfrom
jfgrimm:20210512182929_new_pr_SeqLib120
May 21, 2021
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{bio}[GCCcore/9.3.0] SeqLib v1.2.0, fermi-lite v20190320, SSW v1.1#12856
branfosj merged 6 commits intoeasybuilders:developfrom
jfgrimm:20210512182929_new_pr_SeqLib120

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@jfgrimm jfgrimm commented May 12, 2021 •
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(created using eb --new-pr)

BWA will need to be rebuilt with the updated easyblock

jfgrimm and others added 3 commits May 12, 2021 18:29
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adding easyconfigs: SeqLib-1.2.0-GCC-9.3.0.eb, fermi-lite-20190320-GC…
4a3867b 
…Ccore-9.3.0.eb, SSW-1.1-GCCcore-9.3.0.eb and patches: SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch, fermi-lite-20190320_avoid-bwa-namespace-conflict.patch, fermi-lite-20190320_build-shared-lib.patch, SSW-1.1_build-cpp-lib.patch
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Add missing SeqLib patch
b834de0
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Add whitespace before SHLIB_EXT
0d82dfc
@jfgrimm jfgrimm mentioned this pull request May 13, 2021
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Comment thread easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-9.3.0.eb Outdated
Comment thread easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-9.3.0.eb Outdated
Comment thread easybuild/easyconfigs/s/SSW/SSW-1.1_build-cpp-lib.patch
Comment thread easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-9.3.0.eb
Comment thread easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-9.3.0.eb
Comment thread easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-9.3.0.eb
@Micket Micket added the new label May 13, 2021
@Micket Micket added this to the 4.x milestone May 13, 2021
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@jfgrimm jfgrimm requested a review from Micket May 17, 2021 09:27
@jfgrimm jfgrimm mentioned this pull request May 18, 2021
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jfgrimm commented May 18, 2021

Test report by @jfgrimm
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node031.pri.viking.alces.network - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6138 CPU @ 2.00GHz, Python 2.7.5
See https://gist.github.com/9799571c5196e166f96f6fbcafc3c53f for a full test report.

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lgtm

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Micket commented May 19, 2021

@boegelbot please test @ generoso

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boegelbot commented May 19, 2021

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

PR test command 'EB_PR=12856 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_12856 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 17259

Test results coming soon (I hope)...

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- notification for comment with ID 844057626 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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boegelbot commented May 19, 2021

Test report by @boegelbot
FAILED
Build succeeded for 2 out of 3 (3 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/50bd978a2f0a4eac2fea4198f1fd16dd for a full test report.

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jfgrimm commented May 19, 2021

It's failing on #include "bwa/bwa.h" because BWA hasn't been rebuilt against the updated easyblock

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Micket commented May 19, 2021

@boegelbot please test @ generoso
EB_ARGS="--rebuild BWA-0.7.17-GCC-9.3.0.eb fermi-lite-20190320-GCCcore-9.3.0.eb SSW-1.1-GCCcore-9.3.0.eb SeqLib-1.2.0-GCC-9.3.0.eb "

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boegelbot commented May 19, 2021

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

PR test command 'EB_PR=12856 EB_ARGS="--rebuild BWA-0.7.17-GCC-9.3.0.eb fermi-lite-20190320-GCCcore-9.3.0.eb SSW-1.1-GCCcore-9.3.0.eb SeqLib-1.2.0-GCC-9.3.0.eb " /apps/slurm/default/bin/sbatch --job-name test_PR_12856 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 17261

Test results coming soon (I hope)...

Details

- notification for comment with ID 844078683 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

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boegelbot commented May 19, 2021

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 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/9c0dc58e4abf87cd4bd1494b33264434 for a full test report.

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branfosj commented May 21, 2021

Test report by @branfosj
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
bear-pg0211u08b.bear.cluster - Linux RHEL 8.3, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/6353f7d43735e8d97614f98c9f57435d for a full test report.

@branfosj branfosj modified the milestones: 4.x, 4.4.0 May 21, 2021
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branfosj commented May 21, 2021

Test report by @branfosj
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux Ubuntu 20.04, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.8.5
See https://gist.github.com/8016711d88f68bdf25145f3baea064e6 for a full test report.

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branfosj commented May 21, 2021

Going in, thanks @jfgrimm!

@branfosj branfosj merged commit 5d1ebc4 into easybuilders:develop May 21, 2021
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