use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2 by boegel · Pull Request #18236 · easybuilders/easybuild-easyconfigs

boegel · 2023-06-29T16:25:39Z

ncbi-vdb 2.11.2 depending on HDF5 1.10.x makes it incompatible with other easyconfigs of the 2021b generation, R/4.1.2-foss-2021b for example, which causes problems (cfr. #17686)

There's an easy fix to make ncbi-vdb compatible with HDF5 1.12.x, which we already did for ncbi-vdb 3.0.0, see #17140

….2 from check for single dependency variant per easyconfig generation

boegel · 2023-06-29T16:27:47Z

@boegelbot please test @ generoso
EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb"
CORE_CNT=16

boegelbot · 2023-06-29T16:30:09Z

@boegel: Request for testing this PR well received on login1

PR test command 'EB_PR=18236 EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_18236 --ntasks="16" ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 11171

Test results coming soon (I hope)...

Details

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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).

boegelbot · 2023-06-29T16:38:04Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
cnx1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2690 v3 @ 2.60GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/13acef69f31b5469760acc87bf248702 for a full test report.

boegel · 2023-06-29T16:44:03Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3169.skitty.os - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/boegel/46620bcfe829b9ea470635e694e79f4a for a full test report.

Micket · 2023-06-29T16:44:14Z

Test report by @Micket
SUCCESS
Build succeeded for 4 out of 4 (1 easyconfigs in total)
vera-c1 - Linux Rocky Linux 8.7, x86_64, Intel Xeon Processor (Skylake), Python 3.6.8
See https://gist.github.com/Micket/db882537a4d033e7934f4879d0b8ac63 for a full test report.

…-vdb 2.11.2

boegel · 2023-06-29T16:53:42Z

@boegelbot please test @ jsc-zen2
EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb"
CORE_CNT=16

boegelbot · 2023-06-29T16:57:08Z

@boegel: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18236 EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18236 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2921

Test results coming soon (I hope)...

Details

- notification for comment with ID 1613528242 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).

branfosj · 2023-06-29T16:57:57Z

Test report by @branfosj
FAILED
Build succeeded for 18 out of 20 (4 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/6f3215095c9345dbcdb91de36e195142 for a full test report.

boegelbot · 2023-06-29T17:04:27Z

Test report by @boegelbot
FAILED
Build succeeded for 7 out of 9 (4 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/685128cc2af2ea9f2ba420840ee092dc for a full test report.

branfosj · 2023-06-29T17:25:33Z

Test report by @branfosj
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
bear-pg0105u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Platinum 8360Y CPU @ 2.40GHz (icelake), Python 3.6.8
See https://gist.github.com/branfosj/43599b085973a0e0b89a1d354c2dfc50 for a full test report.

branfosj · 2023-06-29T17:31:19Z

@boegelbot please test @ jsc-zen2
EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb"
CORE_CNT=16

boegelbot · 2023-06-29T17:32:08Z

@branfosj: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18236 EB_ARGS="ncbi-vdb-2.11.2-gompi-2021b.eb HISAT2-2.2.1-gompi-2021b.eb SKESA-2.4.0-gompi-2021b_saute.1.3.0_1.eb shovill-1.1.0-gompi-2021b.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18236 --ntasks="16" ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2923

Test results coming soon (I hope)...

Details

- notification for comment with ID 1613572746 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).

branfosj · 2023-06-29T17:32:32Z

#18237 for fixing the Velvet source download

boegelbot · 2023-06-29T17:37:36Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/0bb14da9dcfb118e01c9c7a88e526ae7 for a full test report.

branfosj · 2023-06-29T17:39:23Z

Going in, thanks @boegel!

boegel added 2 commits June 29, 2023 18:20

use patch to make ncbi-vdb 2.11.2 compatible with HDF5 1.12.2

b11c428

remove exception for HDF5 1.10.x dependency variant via ncbi-vdb 2.11…

b5427ea

….2 from check for single dependency variant per easyconfig generation

boegel added bug fix change labels Jun 29, 2023

boegel added this to the next release (4.7.3?) milestone Jun 29, 2023

boegel mentioned this pull request Jun 29, 2023

{bio}[foss/2021b] Trinity v2.15.1, BLAT v3.7, RSEM v1.3.3 w/ Python 3.9.6 #17686

Merged

add checksum for ncbi-vdb-3.0.0_hdf5_api.patch in easyconfig for ncbi…

6f3fe40

…-vdb 2.11.2

branfosj approved these changes Jun 29, 2023

View reviewed changes

branfosj merged commit fbc3b32 into easybuilders:develop Jun 29, 2023

boegel deleted the ncbi-vdb-2.x_HDF5-1.12.x_2021b branch June 29, 2023 19:18

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boegel commented Jun 29, 2023

Uh oh!

boegel commented Jun 29, 2023

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boegelbot commented Jun 29, 2023

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boegel commented Jun 29, 2023

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boegel commented Jun 29, 2023

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branfosj commented Jun 29, 2023

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boegelbot commented Jun 29, 2023

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boegelbot commented Jun 29, 2023

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branfosj commented Jun 29, 2023

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