[gompi/2022.05] in-place update to netCDF v4.9.0 by boegel · Pull Request #15677 · easybuilders/easybuild-easyconfigs

boegel · 2022-06-13T18:15:09Z

I intended to actually open #15676 with netCDF v4.9.0, but apparently I managed to screw that up 😅

(opened as draft PR, because compilation fails even though it worked fine with v4.8.1...)

boegel · 2022-06-13T18:19:45Z

@boegelbot please test @ generoso

boegelbot · 2022-06-13T18:20:09Z

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

PR test command 'EB_PR=15677 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15677 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8707

Test results coming soon (I hope)...

Details

- notification for comment with ID 1154235429 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).

boegelbot · 2022-06-13T18:22:04Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/d6033fc36e12f40370953eee16f8293f for a full test report.

jfgrimm · 2022-06-16T14:58:36Z

/project/boegelbot/Rocky8/haswell/software/binutils/2.38-GCCcore-11.3.0/bin/ld: ../liblib/libnetcdf.a(ncjson.c.o): in function `NCJreclaim':
ncjson.c:(.text+0xa50): multiple definition of `NCJreclaim'; CMakeFiles/nczhdf5filters.dir/NCZhdf5filters.c.o:NCZhdf5filters.c:(.text+0xac0): first defined here
/project/boegelbot/Rocky8/haswell/software/binutils/2.38-GCCcore-11.3.0/bin/ld: ../liblib/libnetcdf.a(ncjson.c.o): in function `NCJnew':
ncjson.c:(.text+0xb10): multiple definition of `NCJnew'; CMakeFiles/nczhdf5filters.dir/NCZhdf5filters.c.o:NCZhdf5filters.c:(.text+0xb80): first defined here
/project/boegelbot/Rocky8/haswell/software/binutils/2.38-GCCcore-11.3.0/bin/ld: ../liblib/libnetcdf.a(ncjson.c.o): in function `NCJnewstringn':
ncjson.c:(.text+0xb60): multiple definition of `NCJnewstringn'; CMakeFiles/nczhdf5filters.dir/NCZhdf5filters.c.o:NCZhdf5filters.c:(.text+0xbd0): first defined here
/project/boegelbot/Rocky8/haswell/software/binutils/2.38-GCCcore-11.3.0/bin/ld: ../liblib/libnetcdf.a(ncjson.c.o): in function `NCJnewstring':
ncjson.c:(.text+0xc20): multiple definition of `NCJnewstring'; CMakeFiles/nczhdf5filters.dir/NCZhdf5filters.c.o:NCZhdf5filters.c:(.text+0xc90): first defined here
/project/boegelbot/Rocky8/haswell/software/binutils/2.38-GCCcore-11.3.0/bin/ld: ../liblib/libnetcdf.a(ncjson.c.o): in function `NCJparse':
ncjson.c:(.text+0x1160): multiple definition of `NCJparse'; CMakeFiles/nczhdf5filters.dir/NCZhdf5filters.c.o:NCZhdf5filters.c:(.text+0x1080): first defined here
/project/boegelbot/Rocky8/haswell/software/binutils/2.38-GCCcore-11.3.0/bin/ld: ../liblib/libnetcdf.a(ncjson.c.o): in function `NCJdictget':
ncjson.c:(.text+0x1190): multiple definition of `NCJdictget'; CMakeFiles/nczhdf5filters.dir/NCZhdf5filters.c.o:NCZhdf5filters.c:(.text+0x11a0): first defined here
/project/boegelbot/Rocky8/haswell/software/binutils/2.38-GCCcore-11.3.0/bin/ld: ../liblib/libnetcdf.a(ncjson.c.o): in function `NCJcvt':
ncjson.c:(.text+0x1220): multiple definition of `NCJcvt'; CMakeFiles/nczhdf5filters.dir/NCZhdf5filters.c.o:NCZhdf5filters.c:(.text+0x1230): first defined here

branfosj · 2022-06-21T20:31:44Z

It is not the cause of the build failure we are seeing, but we must add https://patch-diff.githubusercontent.com/raw/Unidata/netcdf-c/pull/2412.patch in to get the correct library name.

branfosj · 2022-06-21T20:57:21Z

The:

# HDF5 version detection is missed in netCDF 4.8.1 when HDF5_C_LIBRARY, HDF5_INCLUDE_DIR, and HDF5_HL_LIBRARY are set
local_hdf5_version_fix = '-DHDF5_VERSION=$EBVERSIONHDF5'

is no longer needed.

Also, this issue is in building the static libs (-DBUILD_SHARED_LIBS=OFF). The failure does not happen when building the shared libs (-DBUILD_SHARED_LIBS=ON).

…ERSION configure option which is no longer needed

boegel · 2022-06-22T12:47:53Z

I've opened an issue upstream for this: Unidata/netcdf-c#2419

zao · 2022-06-22T17:34:08Z

I commented with a bit of analysis in the upstream issue, a workaround for us may be to patch netcdf_json.h to have the function declarations and definitions static to prevent them from having linkage. Haven't tested this outside of a standalone repro case.

…e via 'make test'

boegel · 2022-06-23T08:30:54Z

@boegelbot please test @ generoso

boegelbot · 2022-06-23T08:35:09Z

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

PR test command 'EB_PR=15677 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15677 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 8762

Test results coming soon (I hope)...

Details

- notification for comment with ID 1164114153 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 · 2022-06-23T08:46:49Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3138.skitty.os - Linux RHEL 8.4, x86_64, Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/e76f04add8a812e808e59da149a0d69f for a full test report.

boegelbot · 2022-06-23T08:47:19Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/956d3a95dba88d789168a4e89aaa4de8 for a full test report.

branfosj · 2022-06-23T09:14:05Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0105u36b.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/d35ddebedb4d347ed05e0e7bd614a719 for a full test report.

branfosj · 2022-06-23T09:19:23Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux RHEL 8.6, x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.6.8
See https://gist.github.com/5069393d6e047eca078099ad4e25c203 for a full test report.

branfosj · 2022-06-23T09:20:35Z

@boegelbot please test @ jsc-zen2

boegelbot · 2022-06-23T09:22:08Z

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

PR test command 'EB_PR=15677 EB_ARGS= /opt/software/slurm/bin/sbatch --job-name test_PR_15677 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 1326

Test results coming soon (I hope)...

Details

- notification for comment with ID 1164165503 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 · 2022-06-23T09:23:22Z

Test report by @branfosj
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bear-pg0211u03a.bear.cluster - Linux Ubuntu 20.04.2 LTS (Focal Fossa), x86_64, Intel(R) Xeon(R) Gold 6248 CPU @ 2.50GHz (cascadelake), Python 3.8.5
See https://gist.github.com/4ad92b4dfecf8fc97272159ae476e08c for a full test report.

boegelbot · 2022-06-23T09:32:34Z

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 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/62200f598fc4a7a8f1f9a8d7c7d92d15 for a full test report.

branfosj

lgtm

branfosj · 2022-06-23T09:36:37Z

Going in, thanks @boegel!

boegel · 2022-06-23T09:39:50Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
node3601.doduo.os - Linux RHEL 8.4, x86_64, AMD EPYC 7552 48-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/89f8e5a4dc87489ded04da5a791de61b for a full test report.

boegel · 2022-06-23T09:59:28Z

Test report by @boegel
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
fair-mastodon-c6g-2xlarge-0001 - Linux Rocky Linux 8.5, AArch64, ARM UNKNOWN (graviton2), Python 3.6.8
See https://gist.github.com/338898ca1d25185e90bd36c9cd895a45 for a full test report.

[gompi/2022.05] in-place update to netCDF v4.9.0

d0e8259

boegel added update change labels Jun 13, 2022

boegel added this to the next release (4.5.6?) milestone Jun 13, 2022

boegel added 2 commits June 22, 2022 13:42

add patch to fix library name for netCDF v4.9.0 + get rid of -DHDF5_V…

08cc268

…ERSION configure option which is no longer needed

add missing zstd dependency for netCDF v4.9.0

a33ec53

branfosj mentioned this pull request Jun 22, 2022

{data}[foss/2022.05] GDAL v3.5.0 w/ Python 3.10.4 #15746

Merged

1 task

add patch file to fix linking error for netCDF v4.9.0 + run test suit…

001aa3e

…e via 'make test'

boegel marked this pull request as ready for review June 23, 2022 08:30

branfosj approved these changes Jun 23, 2022

View reviewed changes

branfosj merged commit fc56c2b into easybuilders:develop Jun 23, 2022

boegel deleted the 20220613164029_new_pr_netCDF481 branch June 23, 2022 10:04

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boegel commented Jun 13, 2022

Uh oh!

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