{data}[gompi/2022b,iimpi/2022b] HDF5 v1.14.0, netCDF v4.9.0 #17107

jfgrimm · 2023-01-13T17:19:21Z

we'll have to see if packages support 1.14, according to the documentation:

Applications that were created with earlier HDF5 releases may not compile with 1.14 by default.

The API Compatibility Macros in HDF5 allow users to work around this issue. Users can specify a compatibility macro mapping for the version of HDF5 that an application was built with. For example, a 1.10 application can be built with 1.14 using either an application or library mapping as follows:

To compile an application built with a version of HDF5 that includes deprecated symbols (the default), specify: -DH5_USE_110_API (autotools) or -DH5_USE_110_API:BOOL=ON (CMake)

To build an HDF5 library with the 1.10 APIs specify --with-default-api-version=v110 (Autotools) or -DDEFAULT_API_VERSION:STRING=v110 (CMake).

However, users will not be able to take advantage of some of the new features in 1.14 if using these compatibility mappings.

requires:

{tools}[GCCcore/12.2.0] Szip v2.1.1 #17113

(created using eb --new-pr)

…2b.eb, Szip-2.1.1-GCCcore-12.2.0.eb, netCDF-4.9.0-gompi-2022b.eb, netCDF-4.9.0-iimpi-2022b.eb

branfosj · 2023-01-13T17:43:16Z

See the netCDF issues in #16834

jfgrimm · 2023-01-16T10:47:53Z

split Szip into its own PR

…asyconfigs into 20230113171916_new_pr_HDF51140

verdurin · 2023-01-27T12:47:00Z

@jfgrimm is this at all affected by the discussion today about HDF5?

jfgrimm · 2023-01-27T12:49:19Z

@jfgrimm is this at all affected by the discussion today about HDF5?

No, only #17093 (since that contains a -serial version)

boegel · 2023-02-15T17:06:26Z

@boegelbot please test @ generoso

boegelbot · 2023-02-15T17:10:13Z

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

PR test command 'EB_PR=17107 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17107 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10243

Test results coming soon (I hope)...

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boegelbot · 2023-02-15T18:19:01Z

Test report by @boegelbot
FAILED
Build succeeded for 3 out of 4 (4 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/77820a64e62b266647ed35845a360535 for a full test report.

boegel · 2023-02-15T18:31:56Z

Same problems with the tests as in #16834 ... :-/

The following tests FAILED:
	161 - nc_test4_run_par_test (Timeout)

jfgrimm · 2023-02-16T11:32:36Z

do you know exactly where in that it hangs? nc_test4_run_par_test runs several tests:

tst_mpi_parallel
tst_parallel
tst_parallel3
tst_parallel4
tst_parallel5
tst_parallel6
tst_parallel_zlib
tst_parallel_compress
tst_nc4perf
tst_mode
tst_simplerw_coll_r
tst_quantize_par

edit: netCDF hangs on the nc_get_vara_float calls in nc_test4/tst_parallel5.c on generoso, not really sure why. Other tests also use that function without hanging

jfgrimm · 2023-02-16T17:56:59Z

Test report by @jfgrimm
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node067.pri.viking.alces.network - Linux CentOS Linux 7.9.2009, x86_64, Intel(R) Xeon(R) Gold 6138 CPU @ 2.00GHz (skylake_avx512), Python 3.6.8
See https://gist.github.com/23c2ff758fe3cfd98acd2ef4911ded62 for a full test report.

jfgrimm · 2023-02-17T11:38:19Z

@boegelbot please test @ generoso

boegelbot · 2023-02-17T11:40:10Z

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

PR test command 'EB_PR=17107 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17107 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10261

Test results coming soon (I hope)...

- notification for comment with ID 1434519185 processed

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-02-17T12:48:05Z

Test report by @boegelbot
FAILED
Build succeeded for 3 out of 4 (4 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/4a30d3324efd4c34186e16c743da360d for a full test report.

jfgrimm · 2023-02-17T14:35:37Z

@boegelbot please test @ generoso
EB_ARGS=netCDF-4.9.0-gompi-2022b.eb

boegelbot · 2023-02-17T14:40:09Z

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

PR test command 'EB_PR=17107 EB_ARGS="netCDF-4.9.0-gompi-2022b.eb" EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17107 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10265

Test results coming soon (I hope)...

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boegelbot · 2023-02-17T14:48:25Z

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/8411e2ac9868ea71f89f6943c9c1b795 for a full test report.

jfgrimm · 2023-02-17T15:05:06Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-02-17T15:07:09Z

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

PR test command 'EB_PR=17107 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17107 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2211

Test results coming soon (I hope)...

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boegelbot · 2023-02-17T15:51:56Z

Test report by @boegelbot
FAILED
Build succeeded for 3 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/93af5230f339d3df28803f118dedf1b9 for a full test report.

zao · 2023-02-20T13:14:34Z

Test report by @zao
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
eb-u2204 - Linux Ubuntu 22.04, x86_64, AMD Ryzen 9 3900X 12-Core Processor, Python 3.10.6
See https://gist.github.com/b9d241657288c4f081757fa4d65ba6d1 for a full test report.

boegel · 2023-02-28T08:28:33Z

@jfgrimm What's the plan with this (from failed test report on jsc-zen2):

The following tests FAILED:
	161 - nc_test4_run_par_test (Timeout)

jfgrimm · 2023-02-28T10:12:57Z

@boegelbot please test @ jsc-zen2
EB_ARGS=netCDF-4.9.0-iimpi-2022b.eb

boegelbot · 2023-02-28T10:17:08Z

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

PR test command 'EB_PR=17107 EB_ARGS="netCDF-4.9.0-iimpi-2022b.eb" /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17107 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2276

Test results coming soon (I hope)...

- notification for comment with ID 1447911596 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 · 2023-02-28T11:14:39Z

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/ad080802816c68b26ffed623d604ae6a for a full test report.

jfgrimm · 2023-02-28T12:07:54Z

@boegel should be good to go now, tests problematic for generoso/jsc-zen2 are now skipped in both gompi and iimpi variants

boegel · 2023-02-28T13:02:46Z

@boegelbot please test @ generoso

boegelbot · 2023-02-28T13:05:16Z

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

PR test command 'EB_PR=17107 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17107 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10381

Test results coming soon (I hope)...

- notification for comment with ID 1448142269 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 · 2023-02-28T13:46:50Z

Test report by @boegelbot
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
cns3 - 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/c217a81063c5a459e000d0d88187c02e for a full test report.

verdurin · 2023-02-28T14:30:54Z

Test report by @verdurin
SUCCESS
Build succeeded for 10 out of 10 (4 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/960f005a78b8e44b1c81ed7c7db2ba8a for a full test report.

boegel

lgtm

boegel · 2023-02-28T15:03:10Z

Test report by @boegel
SUCCESS
Build succeeded for 4 out of 4 (4 easyconfigs in total)
node3104.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/df413c8ba036e97b0e4ee69eefe16912 for a full test report.

boegel · 2023-02-28T15:37:38Z

Going in, thanks @jfgrimm!

adding easyconfigs: HDF5-1.14.0-gompi-2022b.eb, HDF5-1.14.0-iimpi-202…

ce56fbd

…2b.eb, Szip-2.1.1-GCCcore-12.2.0.eb, netCDF-4.9.0-gompi-2022b.eb, netCDF-4.9.0-iimpi-2022b.eb

jfgrimm added the update label Jan 13, 2023

jfgrimm added this to the 4.x milestone Jan 13, 2023

split Szip into separate PR

4a0620c

jfgrimm changed the title ~~{data}[gompi/2022b,iimpi/2022b] HDF5 v1.14.0, Szip v2.1.1, netCDF v4.9.0~~ {data}[gompi/2022b,iimpi/2022b] HDF5 v1.14.0, netCDF v4.9.0 Jan 18, 2023

jfgrimm mentioned this pull request Jan 18, 2023

{data}[GCCcore/12.2.0] HDF5 v1.14.0 (serial), Szip v2.1.1 #17093

Open

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

3bd1f38

…asyconfigs into 20230113171916_new_pr_HDF51140

jfgrimm mentioned this pull request Jan 25, 2023

{lang}[foss/2022b] R v4.2.2 #17200

Merged

2 tasks

disable parallel5 szip tests since they hang on generoso

db77789

jfgrimm added 2 commits February 17, 2023 13:35

remove unneccessary patch from netCDF w/ iimpi

a3241c8

use sed to disable parallel Szip, zlib tests for gompi version instead

0403e2d

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jfgrimm added 2 commits February 17, 2023 14:23

fix missing closing sed quotes

c69f27f

use absolute path to file to sed

1eaec41

easybuilders deleted a comment from boegelbot Feb 17, 2023

reinstate preconfigopts sed for netCDF w/ iimpi

72540b2

jfgrimm mentioned this pull request Feb 28, 2023

{data}[foss/2022b, GCCcore/12.2.0] GDAL v3.6.2 w/ Python 3.10.8, libgeotiff v1.7.1 #17198

Merged

8 tasks

boegel approved these changes Feb 28, 2023

View reviewed changes

boegel merged commit 300e004 into easybuilders:develop Feb 28, 2023

boegel mentioned this pull request Feb 28, 2023

{data}[gompi/2022.10] netCDF-Fortran v4.6.0, netCDF v4.9.0, HDF5 v1.12.2, Szip v2.1.1 #16834

Closed

boegel modified the milestones: 4.x, next release (4.7.1) Mar 15, 2023

Neves-P mentioned this pull request Nov 29, 2023

{2023.06}[foss/2023a] OpenFOAM v10 EESSI/software-layer#404

Merged

5 tasks

Neves-P mentioned this pull request Dec 15, 2023

Skip netCDF v4.9.2 tests on ARM EESSI/software-layer#425

Open

{data}[gompi/2022b,iimpi/2022b] HDF5 v1.14.0, netCDF v4.9.0 #17107

{data}[gompi/2022b,iimpi/2022b] HDF5 v1.14.0, netCDF v4.9.0 #17107

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jfgrimm commented Jan 13, 2023 • edited by boegel

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