fix installation of Bioconductor 3.11 bundle on aarch64 #11417

terjekv · 2020-10-01T14:44:09Z

(created using eb --new-pr)

Eventually fixes #11393

terjekv · 2020-10-02T04:11:01Z

Test report by @terjekv
FAILED
Build succeeded for 6 out of 7 (1 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/cd491e68799cbbb3cc2a97c377c8431d for a full test report.

boegel · 2020-10-02T08:56:30Z

@boegelbot please test @ generoso

boegelbot · 2020-10-02T09:00:09Z

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

PR test command 'EB_PR=11417 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11417 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8001

Test results coming soon (I hope)...

- notification for comment with ID 702610622 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).

terjekv · 2020-10-02T11:16:57Z

Test report by @terjekv
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/3b8c20372e1a17fde286f81e2645f7da for a full test report.

boegelbot · 2020-10-02T11:44:55Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
generoso-x-3 - 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/3916226388b5195e04be1996b5e1c984 for a full test report.

terjekv · 2020-10-03T03:03:12Z

Test report by @terjekv
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/d78180e3380421bc2fad685204288bb7 for a full test report.

terjekv · 2020-10-03T08:53:45Z

Test report by @terjekv
FAILED
Build succeeded for 2 out of 3 (1 easyconfigs in this PR)
arm1 - Linux ubuntu 18.04, AArch64, UNKNOWN (aarch64), Python 3.6.9
See https://gist.github.com/9f46ac2a6e606970807ee4b5fbc8e8bb for a full test report.

…d2712a57d5dff6f0bd478d7d18.

terjekv · 2020-10-03T16:14:16Z

Test report by @terjekv
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/5c9abc6009600e556df09bb6f0d8d779 for a full test report.

terjekv · 2020-10-04T10:42:17Z

Test report by @terjekv
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
arm1 - Linux ubuntu 18.04, AArch64, UNKNOWN (aarch64), Python 3.6.9
See https://gist.github.com/d1ad930dcce6014d01990ff2069b0e17 for a full test report.

terjekv · 2020-10-04T16:43:17Z

Test report by @terjekv
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
ninhursaga.uio.no - Linux RHEL 8.2, x86_64, Intel(R) Xeon(R) Silver 4216 CPU @ 2.10GHz (cascadelake), Python 3.6.8
See https://gist.github.com/cb778007bb67dea0ba613138d2abb517 for a full test report.

branfosj · 2020-10-04T17:55:31Z

Test report by @branfosj
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in this PR)
bear-pg0305u03a.bear.cluster - Linux RHEL 7.6, POWER, 8335-GTX (power9le), Python 3.6.8
See https://gist.github.com/c0a1a6f49a9c06542d73ad5e5aed3a84 for a full test report.

terjekv · 2020-10-04T18:02:58Z

Both of the aarch64 units I have access to are currently down. I'll try to have someone look at it tomorrow, but last I saw the testing had long since past LEA and other troublemakers:

[...]
== installing extension IlluminaHumanMethylation450kmanifest 0.4.0 (242/262)...
== installing extension IlluminaHumanMethylationEPICmanifest 0.3.0 (243/262)...
== installing extension IlluminaHumanMethylation450kanno.ilmn12.hg19 0.6.0 (244/262)...
client_loop: send disconnect: Broken pipe

terjekv · 2020-10-06T13:13:39Z

No longer a WIP. This looks good. Testing on arm again today.

boegel · 2020-10-07T06:48:35Z

@terjekv Is a test report coming up?

terjekv · 2020-10-07T07:16:37Z

Yeah, I thought I started it last night. Sorry. Let me kick one off.
Edit: And remember to do it against develop... Sigh. Let me start over.

verdurin · 2020-10-07T10:49:02Z

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.8.2003, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/e3bdb1e4dd751df521669055460eb686 for a full test report.

terjekv · 2020-10-07T10:56:12Z

Test report by @verdurin
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in this PR)
easybuild.novalocal - Linux centos linux 7.8.2003, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 2.7.5
See https://gist.github.com/e3bdb1e4dd751df521669055460eb686 for a full test report.

@verdurin This has to be built against latest Develop. It's the same issue I ran into, as underlying EasyConfigs have changed.

terjekv · 2020-10-08T19:04:13Z

Test report by @terjekv
FAILED
Build succeeded for 0 out of 20 (1 easyconfigs in this PR)
arm2 - Linux ubuntu 18.04, AArch64, UNKNOWN, Python 3.6.9
See https://gist.github.com/968cdc2438cc87d34d5eac22d1867b17 for a full test report.

terjekv · 2020-10-08T23:57:16Z

Test report by @terjekv
FAILED
Build succeeded for 0 out of 20 (1 easyconfigs in this PR)
arm2 - Linux ubuntu 18.04, AArch64, UNKNOWN, Python 3.6.9
See https://gist.github.com/968cdc2438cc87d34d5eac22d1867b17 for a full test report.

Sigh, unzip is a system dependency for Python:

== FAILED: Installation ended unsuccessfully (build directory: /home/terjekv/.local/easybuild/build/Python/3.8.2/GCCcore-9.3.0): build failed (first 300 chars): cmd "unzip -qq /h
ome/terjekv/.local/easybuild/sources/p/Python/extensions/setuptools-45.2.0.zip" exited with exit code 127 and output:
/bin/bash: unzip: command not found

terjekv · 2020-10-09T05:41:03Z

Test report by @terjekv
FAILED
Build succeeded for 17 out of 20 (1 easyconfigs in this PR)
arm2 - Linux ubuntu 18.04, AArch64, UNKNOWN, Python 3.6.9
See https://gist.github.com/a2b1e3300c90884886f8e4064e4110a2 for a full test report.

terjekv · 2020-10-09T17:11:06Z

Test report by @terjekv
SUCCESS
Build succeeded for 3 out of 3 (1 easyconfigs in this PR)
arm2 - Linux ubuntu 18.04, AArch64, UNKNOWN, Python 3.6.9
See https://gist.github.com/b80ca5c715108accc49be382f3062b4e for a full test report.

boegel · 2020-10-09T18:24:28Z

Test report by @terjekv
FAILED
Build succeeded for 0 out of 20 (1 easyconfigs in this PR)
arm2 - Linux ubuntu 18.04, AArch64, UNKNOWN, Python 3.6.9
See https://gist.github.com/968cdc2438cc87d34d5eac22d1867b17 for a full test report.

Sigh, unzip is a system dependency for Python:
== FAILED: Installation ended unsuccessfully (build directory: /home/terjekv/.local/easybuild/build/Python/3.8.2/GCCcore-9.3.0): build failed (first 300 chars): cmd "unzip -qq /h
ome/terjekv/.local/easybuild/sources/p/Python/extensions/setuptools-45.2.0.zip" exited with exit code 127 and output:
/bin/bash: unzip: command not found

We have easyconfigs for UnZip, so we should add it as a build dep for Python, see #10427.

terjekv · 2020-10-11T12:38:32Z

Test report by @terjekv
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
arm2 - Linux ubuntu 18.04, AArch64, UNKNOWN, Python 3.6.9
See https://gist.github.com/6919d7d54c31e11e0a10c26b641b30c3 for a full test report.

easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch

easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch

…asyconfigs into 20201001164359_new_pr_R-bundle-Bioconductor311

boegel · 2020-10-12T18:05:35Z

@boegelbot please test @ generoso

boegelbot · 2020-10-12T18:15:09Z

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

PR test command 'EB_PR=11417 EB_ARGS= /apps/slurm/default/bin/sbatch --job-name test_PR_11417 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8057

Test results coming soon (I hope)...

- notification for comment with ID 707268736 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).

boegel

lgtm

boegel · 2020-10-12T20:52:57Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in this PR)
node3407.kirlia.os - Linux centos linux 7.8.2003, x86_64, Intel(R) Xeon(R) Gold 6240 CPU @ 2.60GHz (cascadelake), Python 2.7.5
See https://gist.github.com/2452f534a8feed0ce045ab283aec22c6 for a full test report.

boegelbot · 2020-10-12T20:54:54Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
generoso-x-2 - 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/f7e55f421d8c158f0f63c7df8a9e49d2 for a full test report.

boegel · 2020-10-13T07:14:10Z

Going in, thanks @terjekv!

aarch64-fixing.

36875fc

terjekv changed the title ~~aarch64-fixing.~~ WIP: aarch64-fixes for R-bundle-Bioconductor-3.11-foss-2020a-R.4.0.0 Oct 1, 2020

terjekv added aarch64 Related to Arm 64-bit (aarch64) EESSI Related to EESSI project labels Oct 1, 2020

terjekv added 7 commits October 1, 2020 16:48

Remove pointless buildopt

a28fee1

Make flowClust use external GSL.

4338a18

Reinstate tests..

8ffcb86

Reinstate extensions from latest develop.

d84268b

Reinstate LEA.

5dd0771

Whitespace fixes.

44a7daa

More whitespace fixes.

b223605

Adding JADE as a dependency as per testing.

38a3b56

Adding aws as a dependency for GLAD.

60f4b73

easybuilders deleted a comment from boegelbot Oct 3, 2020

boegel added this to the next release (4.3.1) milestone Oct 3, 2020

Removing extensions already added by easybuilders@55fab02#diff-f2a7cc…

f9131ec

…d2712a57d5dff6f0bd478d7d18.

LEA 'support' for aarch64 and POWER. Needs testing.

00f4e49

terjekv added 3 commits October 4, 2020 14:22

LEA 'support' for aarch64 and POWER, now with the actual patch.

6036743

Futher LEA fixes from @zao.

2c2a5d4

Update checksums for LEA patch.

ef27868

terjekv mentioned this pull request Oct 4, 2020

R-bundle-Bioconductor-3.11-foss-2020a-R-4.0.0.eb failures on aarch64. #11393

Closed

11 tasks

easybuilders deleted a comment from boegelbot Oct 5, 2020

terjekv changed the title ~~WIP: aarch64-fixes for R-bundle-Bioconductor-3.11-foss-2020a-R.4.0.0~~ aarch64-fixes for R-bundle-Bioconductor-3.11-foss-2020a-R.4.0.0 Oct 6, 2020

terjekv mentioned this pull request Oct 11, 2020

add missing UnZip dependency for Python 3.8.2 #11458

Merged

boegel requested changes Oct 12, 2020

View reviewed changes

easybuild/easyconfigs/r/R-bundle-Bioconductor/mzR-2.22.0_use-external-boost.patch Show resolved Hide resolved

easybuild/easyconfigs/r/R-bundle-Bioconductor/LEA-3.0.0_support_aarch64_and_ppc64le.patch Show resolved Hide resolved

boegel changed the title ~~aarch64-fixes for R-bundle-Bioconductor-3.11-foss-2020a-R.4.0.0~~ fix installation of Bioconductor 3.11 bundle on aarch64 Oct 12, 2020

boegel added the bug fix label Oct 12, 2020

terjekv and others added 3 commits October 12, 2020 17:29

Add patch comments.

23c4a76

Restore missing extensions.

3131b2c

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

efb429f

…asyconfigs into 20201001164359_new_pr_R-bundle-Bioconductor311

boegel approved these changes Oct 12, 2020

View reviewed changes

boegel merged commit 7b7eb1a into easybuilders:develop Oct 13, 2020

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fix installation of Bioconductor 3.11 bundle on aarch64 #11417

fix installation of Bioconductor 3.11 bundle on aarch64 #11417

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fix installation of Bioconductor 3.11 bundle on aarch64 #11417

fix installation of Bioconductor 3.11 bundle on aarch64 #11417

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