{data}[foss/2022a] PyTables v3.8.0 by deniskristak · Pull Request #17143 · easybuilders/easybuild-easyconfigs

deniskristak · 2023-01-18T11:03:06Z

adding easyconfigs:
PyTables-3.8.0-foss-2022a.eb
and patches:
PyTables-3.8.0-fix-libs.patch

dependency for:
#17142

…s-3.8.0-fix-libs.patch

verdurin · 2023-01-18T11:55:25Z

@boegelbot please test @ generoso

verdurin · 2023-01-18T11:55:35Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-01-18T11:57:09Z

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

PR test command 'EB_PR=17143 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_17143 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2069

Test results coming soon (I hope)...

Details

- notification for comment with ID 1386934575 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).

verdurin · 2023-01-18T12:00:13Z

Test report by @verdurin
SUCCESS
Build succeeded for 3 out of 3 (1 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/7c3351b806042c7f4fd5eebfd8c1758a for a full test report.

verdurin

Looks fine.

boegelbot · 2023-01-18T12:02:00Z

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/c8bcfdbdb0bf44ac0d36530907a5260a for a full test report.

…d source tarball from PyPI, use proper dependency for py-cpuinfo, change scikit-build to build dependency

boegel · 2023-01-18T12:17:02Z

@boegelbot please test @ generoso

boegelbot · 2023-01-18T12:20:11Z

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

PR test command 'EB_PR=17143 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17143 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10023

Test results coming soon (I hope)...

Details

- notification for comment with ID 1386961878 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 · 2023-01-18T12:26:26Z

Test report by @boegel
SUCCESS
Build succeeded for 2 out of 2 (2 easyconfigs in total)
node3102.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/b77d3a6c06561018b408aa770bded9a4 for a full test report.

boegelbot · 2023-01-18T12:29:46Z

Test report by @boegelbot
SUCCESS
Build succeeded for 2 out of 2 (2 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/eb5916bab3365edf3e895a919cfe1f0d for a full test report.

verdurin · 2023-01-18T12:35:14Z

Test report by @verdurin
FAILED
Build succeeded for 3 out of 4 (2 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/0d5caac2932a4fb2709929f077158827 for a full test report.

verdurin · 2023-01-18T12:37:39Z

@boegel @deniskristak :

Using pip 22.0.4 from /eb/maint/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/pip (python 3.10)
Processing /dev/shm/PyTables/3.8.0/foss-2022a/tables/tables-3.8.0
  Preparing metadata (pyproject.toml): started
  Running command Preparing metadata (pyproject.toml)
  /tmp/eb-csvtvkbh/lzo_version_datenir9f4za.c: In function main:
  /tmp/eb-csvtvkbh/lzo_version_datenir9f4za.c:2:5: warning: implicit declaration of function lzo_version_date [-Wimplicit-fun
ction-declaration]
      2 |     lzo_version_date();
        |     ^~~~~~~~~~~~~~~~
  /tmp/eb-csvtvkbh/BZ2_bzlibVersionr5gf45ob.c: In function main:
  /tmp/eb-csvtvkbh/BZ2_bzlibVersionr5gf45ob.c:2:5: warning: implicit declaration of function BZ2_bzlibVersion [-Wimplicit-fun
ction-declaration]
      2 |     BZ2_bzlibVersion();
        |     ^~~~~~~~~~~~~~~~
  /tmp/eb-csvtvkbh/blosc_list_compressorsy1h7p4r2.c: In function main:
  /tmp/eb-csvtvkbh/blosc_list_compressorsy1h7p4r2.c:2:5: warning: implicit declaration of function blosc_list_compressors [-W
implicit-function-declaration]
      2 |     blosc_list_compressors();
        |     ^~~~~~~~~~~~~~~~~~~~~~
  /eb/maint/software/binutils/2.38-GCCcore-11.3.0/bin/ld: cannot find -lblosc: No such file or directory
  collect2: error: ld returned 1 exit status
  * Using Python 3.10.4 (main, May  9 2022, 14:08:45) [GCC 11.3.0]
  * Found cython 0.29.28
  * USE_PKGCONFIG: True
  * pkg-config header dirs for HDF5: /eb/maint/software/HDF5/1.12.2-gompi-2022a/include
  * pkg-config library dirs for HDF5: /eb/maint/software/HDF5/1.12.2-gompi-2022a/lib
  * Found HDF5 headers at ``/eb/maint/software/HDF5/1.12.2-gompi-2022a/include``, library at ``/eb/maint/software/HDF5/1.12.2-gompi-2022a/lib``.
  * Found LZO 2 headers at ``/eb/maint/software/LZO/2.10-GCCcore-11.3.0/include``, the library is located in the standard system search dirs.
  * Skipping detection of LZO 1 since LZO 2 has already been found.
  * Found bzip2 headers at ``/eb/maint/software/bzip2/1.0.8-GCCcore-11.3.0/include``, the library is located in the standard system search dirs.
  * Could not find blosc headers and library; using internal sources.
  * pkg-config header dirs for blosc2: /eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/include
  * pkg-config library dirs for blosc2: /eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/lib64
  * Found blosc2 headers at ``/eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/include``, library at ``/eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/lib64``.
  .. WARNING:: Unsupported Blosc2 version installed! Blosc2 2.5.0+ required. Found version 2.4.3.  Update it via `pip install blosc2 -U.`
  Compiling tables/utilsextension.pyx because it changed.
  [1/1] Cythonizing tables/utilsextension.pyx
  Compiling tables/hdf5extension.pyx because it changed.
  [1/1] Cythonizing tables/hdf5extension.pyx
  Compiling tables/tableextension.pyx because it changed.
  [1/1] Cythonizing tables/tableextension.pyx
  Compiling tables/linkextension.pyx because it changed.
  [1/1] Cythonizing tables/linkextension.pyx
  Compiling tables/_comp_lzo.pyx because it changed.
  [1/1] Cythonizing tables/_comp_lzo.pyx
  Compiling tables/_comp_bzip2.pyx because it changed.
  [1/1] Cythonizing tables/_comp_bzip2.pyx
  Compiling tables/lrucacheextension.pyx because it changed.
  [1/1] Cythonizing tables/lrucacheextension.pyx
  Compiling tables/indexesextension.pyx because it changed.
  [1/1] Cythonizing tables/indexesextension.pyx
  SSE2 detected and enabled
  AVX2 detected and enabled
  .. ERROR:: Unable to find the blosc2 library.
  error: subprocess-exited-with-error

   Preparing metadata (pyproject.toml) did not run successfully.
   exit code: 1

verdurin · 2023-01-18T12:38:34Z

The Blosc2 build did succeed.

boegel · 2023-01-18T12:40:30Z

I'll take a look at how I managed to mess this up...

boegel · 2023-01-18T12:52:07Z

@verdurin Please try again with 2c465f4 ?

verdurin · 2023-01-18T13:46:10Z

Test report by @verdurin
FAILED
Build succeeded for 1 out of 2 (2 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/395c677f3c88f30eb4555fad8301aa5e for a full test report.

verdurin · 2023-01-18T13:47:29Z

@boegel seems to be the same error (note the message about Blosc2 version:

Processing /dev/shm/PyTables/3.8.0/foss-2022a/tables/tables-3.8.0
  Preparing metadata (pyproject.toml): started
  Running command Preparing metadata (pyproject.toml)
  /tmp/eb-cxz6g_o7/lzo_version_datefkmh8nht.c: In function main:
  /tmp/eb-cxz6g_o7/lzo_version_datefkmh8nht.c:2:5: warning: implicit declaration of function lzo_version_date [-Wimplicit-fun
ction-declaration]
      2 |     lzo_version_date();
        |     ^~~~~~~~~~~~~~~~
  /tmp/eb-cxz6g_o7/BZ2_bzlibVersionj5c8gddd.c: In function main:
  /tmp/eb-cxz6g_o7/BZ2_bzlibVersionj5c8gddd.c:2:5: warning: implicit declaration of function BZ2_bzlibVersion [-Wimplicit-fun
ction-declaration]
      2 |     BZ2_bzlibVersion();
        |     ^~~~~~~~~~~~~~~~
  * Using Python 3.10.4 (main, May  9 2022, 14:08:45) [GCC 11.3.0]
  * Found cython 0.29.28
  * USE_PKGCONFIG: True
  * pkg-config header dirs for HDF5: /eb/maint/software/HDF5/1.12.2-gompi-2022a/include
  * pkg-config library dirs for HDF5: /eb/maint/software/HDF5/1.12.2-gompi-2022a/lib
  * Found HDF5 headers at ``/eb/maint/software/HDF5/1.12.2-gompi-2022a/include``, library at ``/eb/maint/software/HDF5/1.12.2-gompi-2022a/lib``.
  * Found LZO 2 headers at ``/eb/maint/software/LZO/2.10-GCCcore-11.3.0/include``, the library is located in the standard system search dirs.
  * Skipping detection of LZO 1 since LZO 2 has already been found.
  * Found bzip2 headers at ``/eb/maint/software/bzip2/1.0.8-GCCcore-11.3.0/include``, the library is located in the standard system search dirs.
  * pkg-config header dirs for blosc: /eb/maint/software/Blosc/1.21.3-GCCcore-11.3.0/include
  * pkg-config library dirs for blosc: /eb/maint/software/Blosc/1.21.3-GCCcore-11.3.0/lib64
  * Found blosc headers at ``/eb/maint/software/Blosc/1.21.3-GCCcore-11.3.0/include``, library at ``/eb/maint/software/Blosc/1.21.3-GCCcore-11.3.0/lib64``.
  * pkg-config header dirs for blosc2: /eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/include
  * pkg-config library dirs for blosc2: /eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/lib64
  * Found blosc2 headers at ``/eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/include``, library at ``/eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/lib64``.
  .. WARNING:: Unsupported Blosc2 version installed! Blosc2 2.5.0+ required. Found version 2.4.3.  Update it via `pip install blosc2 -U.`
  Compiling tables/utilsextension.pyx because it changed.
  [1/1] Cythonizing tables/utilsextension.pyx
  Compiling tables/hdf5extension.pyx because it changed.
  [1/1] Cythonizing tables/hdf5extension.pyx
  Compiling tables/tableextension.pyx because it changed.
  [1/1] Cythonizing tables/tableextension.pyx
  Compiling tables/linkextension.pyx because it changed.
  [1/1] Cythonizing tables/linkextension.pyx
  Compiling tables/_comp_lzo.pyx because it changed.
  [1/1] Cythonizing tables/_comp_lzo.pyx
  Compiling tables/_comp_bzip2.pyx because it changed.
  [1/1] Cythonizing tables/_comp_bzip2.pyx
  Compiling tables/lrucacheextension.pyx because it changed.
  [1/1] Cythonizing tables/lrucacheextension.pyx
  Compiling tables/indexesextension.pyx because it changed.
  [1/1] Cythonizing tables/indexesextension.pyx
  .. ERROR:: Unable to find the blosc2 library.
  error: subprocess-exited-with-error

   Preparing metadata (pyproject.toml) did not run successfully.
   exit code: 1

boegel · 2023-01-18T14:04:43Z

.. WARNING:: Unsupported Blosc2 version installed! Blosc2 2.5.0+ required. Found version 2.4.3.  Update it via `pip install blosc2 -U.`
  Compiling tables/utilsextension.pyx because it changed.

@verdurin I'm very confused by this, because I'm not seeing this at all (and neither does the bot, apparently)...

edit: my installation has:

  * Found blosc2 headers at ``/software/PyTables/3.8.0-foss-2022a/include``, library at ``/software/Blosc2/2.4.3-GCCcore-11.3.0/lib64``.

while yours has:

 * Found blosc2 headers at ``/eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/include``, library at ``/eb/maint/software/Blosc2/2.4.3-GCCcore-11.3.0/lib64``.

So in my case it's somehow picking up the wrong Blosc2 headers...

boegel · 2023-01-18T15:02:46Z

The Blosc2 C library is vendored along with the blosc2 Python package, see https://github.com/Blosc/python-blosc2/tree/main/blosc2

Looks like we'll need to do some patching to convince it to use the provided Blosc2 dependency...

… to make sure that blosc2 and PyTables effectively use that Blosc2 dependency

boegel · 2023-01-19T19:47:28Z

@boegelbot please test @ generoso

boegelbot · 2023-01-19T19:50:09Z

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

PR test command 'EB_PR=17143 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_17143 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10033

Test results coming soon (I hope)...

Details

- notification for comment with ID 1397513095 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 · 2023-01-19T19:50:58Z

Test report by @boegel
SUCCESS
Build succeeded for 3 out of 3 (3 easyconfigs in total)
node3129.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/518cac526cd69c4bf2bf5b3b55139539 for a full test report.

boegelbot · 2023-01-19T19:54:49Z

Test report by @boegelbot
SUCCESS
Build succeeded for 3 out of 3 (3 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/678b2c3f2c2f0cde4d2ca0ac4f45984d for a full test report.

verdurin · 2023-01-20T09:15:27Z

Test report by @verdurin
SUCCESS
Build succeeded for 3 out of 3 (3 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/13f295cfa892999013a8a985f4daed03 for a full test report.

easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb

easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb

Co-authored-by: Adam Huffman <verdurin@users.noreply.github.com>

verdurin

Looks fine.

verdurin · 2023-01-20T10:55:37Z

Going in, thanks @deniskristak!

adding easyconfigs: PyTables-3.8.0-foss-2022a.eb and patches: PyTable…

741152e

…s-3.8.0-fix-libs.patch

deniskristak mentioned this pull request Jan 18, 2023

{data}[foss/2022a] scib v1.1.1, scikit-misc v0.1.4, pydot v1.4.2, Deprecated v1.2.13 w/ Python 3.10.4 #17142

Merged

verdurin previously approved these changes Jan 18, 2023

View reviewed changes

boegel changed the title ~~PyTables & patch~~ {data}[foss/2022a] PyTables v3.8.0 Jan 18, 2023

boegel added the update label Jan 18, 2023

boegel added this to the 4.x milestone Jan 18, 2023

use Blosc2 instead of Blosc as dependency for PyTables 3.8.0, downloa…

01d0652

…d source tarball from PyPI, use proper dependency for py-cpuinfo, change scikit-build to build dependency

boegel dismissed verdurin’s stale review via 01d0652 January 18, 2023 12:16

boegel added 2 commits January 18, 2023 13:41

add missing binutils build dependency for py-cpuinfo 9.0.0

1a48e8f

add back Blosc dependency for PyTables 3.8.0

2c465f4

update to Blosc2 2.6.1 as dependency for PyTables 3.8.0 + add patches…

296c498

… to make sure that blosc2 and PyTables effectively use that Blosc2 dependency

verdurin requested changes Jan 20, 2023

View reviewed changes

easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb Outdated Show resolved Hide resolved

easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb Outdated Show resolved Hide resolved

easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-11.3.0.eb Show resolved Hide resolved

deniskristak and others added 3 commits January 20, 2023 09:55

Update easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb

4d0a597

Co-authored-by: Adam Huffman <verdurin@users.noreply.github.com>

Update easybuild/easyconfigs/p/PyTables/PyTables-3.8.0-foss-2022a.eb

5a49df4

Co-authored-by: Adam Huffman <verdurin@users.noreply.github.com>

Fix long line after correcting description text

be07e0a

verdurin approved these changes Jan 20, 2023

View reviewed changes

verdurin modified the milestones: 4.x, next release (4.7.1?) Jan 20, 2023

verdurin merged commit c6db9e2 into easybuilders:develop Jan 20, 2023

easybuilders deleted a comment from boegelbot Jan 20, 2023

boegel mentioned this pull request Feb 15, 2023

{data}[foss/2022a] PyTables v3.8.0 w/ Python 3.10.4 #17018

Closed

boegel mentioned this pull request Apr 11, 2023

{lib}[foss/2021b] PyTables v3.8.0 w/ Python 3.9.6 #17550

Closed

2 tasks

sassy-crick pushed a commit to sassy-crick/easybuild-easyconfigs that referenced this pull request Jan 29, 2024

Updated to be in line with PR easybuilders#17143

2346663

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