Add recipe for libpnetcdf #21797

xylar · 2023-01-19T10:37:42Z

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conda-forge-webservices · 2023-01-19T10:38:05Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipes/libpnetcdf) and found it was in an excellent condition.

I do have some suggestions for making it better though...

For recipes/libpnetcdf:

License is not an SPDX identifier (or a custom LicenseRef) nor an SPDX license expression.

Documentation on acceptable licenses can be found here.

xylar · 2023-01-19T10:42:13Z

recipes/libpnetcdf/meta.yaml

+  recipe-maintainers:
+    - xylar


@zklaus, would you be willing to be a maintainer of the PNetCDF library? It seems like it would make sense since you're a maintainer (and a very helpful one!) for parallelio.

Sure, can do 👍

Great, thank you! Feel free to review and recommend changes.

xylar · 2023-01-19T12:40:10Z

@conda-forge/help-c-cpp, this is ready for your review.

xylar · 2023-01-19T12:42:02Z

recipes/libpnetcdf/meta.yaml

+  ignore_run_exports_from:
+    - netcdf-fortran


We have had trouble with run_exports from netcdf-fortran in the parallellio feedstock, so I'm assuming that might be an issue here, too.
https://github.com/conda-forge/parallelio-feedstock/blob/main/recipe/meta.yaml#L33-L34

xylar · 2023-02-15T02:05:21Z

@conda-forge/help-c-cpp, I'm sure you have a giant backlog but just wanting to check in about when you might be able to review this.

recipes/libpnetcdf/meta.yaml

carterbox · 2023-02-22T02:40:56Z

recipes/libpnetcdf/meta.yaml

+  commands:
+    - pnetcdf-config --all
+    - test ! -f ${PREFIX}/lib/libpnetcdf.a
+    - test -f ${PREFIX}/lib/libpnetcdf${SHLIB_EXT}
+    - pnetcdf-config --has-c++      | grep -q yes
+    - pnetcdf-config --has-fortran  | grep -q yes
+    - pnetcdf-config --netcdf4      | grep -q enabled


This recipe has a run_export which means there should be some existence tests for header files and package config files?

Again, good call. I've added these. Let's see how the testing goes.

xylar · 2023-02-22T05:10:13Z

@carterbox, thank you for your review and your patience with my inexperience at this. This is ready for you to re-reveiw when you get a chance.

xylar · 2023-02-22T05:11:48Z

@conda-forge/help-c-cpp, ready for review!

carterbox · 2023-03-07T01:54:28Z

recipes/libpnetcdf/meta.yaml

+  host:
+    - {{ mpi }}
+    # these need to be listed twice so conda build picks up the pins
+    - libnetcdf


There is an overlinking warning on OSX for libnetcdf. Please check that you're not static linking.

https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=662403&view=logs&j=e35d4f76-8ff2-5536-d795-df91e63eb9f7&t=fa7b4b17-b6ff-5c9c-8cfc-15f888c92310&l=7450

Is this the issue holding up this PR? The build link is no longer there, can you re trigger? And if possible give more detail as to the issue - the configure line above clearly specifies shared and not static libraries.

@jedwards4b, I reran the CI yesterday. I believe this is the equivalent line in the latest run:
https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=722946&view=logs&j=e35d4f76-8ff2-5536-d795-df91e63eb9f7&t=fa7b4b17-b6ff-5c9c-8cfc-15f888c92310&l=4270

WARNING (libpnetcdf): run-exports library package conda-forge::libnetcdf-4.8.1-mpi_openmpi_hb9a5949_6 in requirements/run but it is not used (i.e. it is overdepending or perhaps statically linked? If that is what you want then add it to `build/ignore_run_exports`)

Here is the same but for mpich instead of openmpi:
https://dev.azure.com/conda-forge/feedstock-builds/_build/results?buildId=722946&view=logs&j=e35d4f76-8ff2-5536-d795-df91e63eb9f7&t=fa7b4b17-b6ff-5c9c-8cfc-15f888c92310&l=7598

@carterbox, I believe the issue is that static libraries were shipped with libnetcdf until v4.9.0: conda-forge/libnetcdf-feedstock#140.

It seems like the easiest option might be to migrate straight to a later libnetcdf. Is the best way to do that just to add a conda_build_config.yaml with the desired pin? Or is there a way to bring in the migrator into the recipe somehow?

@jedwards4b, is there any way that my recipe could be misconfigured (for OSX in particular) and not be linking libpnetcdf with libnetcdf at all?

Linking pnetcdf to netcdf is a new feature and one that I haven't used. Do you need it? What if we just remove the netcdf dependancy?

I see, I assumed it was required. We can remove it.

What about netcdf-fortran? I guess it can't need that either if it doesn't need netcdf-c?

@jedwards4b, I think I'm starting to understand. I have --with-netcdf4=${PREFIX} in the build and I will need to remove that if we're not using libnetcdf. Otherwise, I see (predictably):

------------------------------------------------------------ Missing NetCDF-4 header files 'netcdf.h' or 'netcdf_meta.h' required to build PnetCDF with NetCDF-4 support. Use option --with-netcdf4=/path/to/implementation to specify the location of NetCDF-4 installation. In addition, please make sure the MPI C compiler is compatible with the one used to build NetCDF-4. Check 'config.log' for more information. Stopping ... ------------------------------------------------------------

Would that be your suggestion to begin with? Build without the --with-netcdf4 flag?

Assuming that's the case, I'll try removing it.

Will replace this with a migrators once we have a feedstock.

xylar · 2023-06-14T15:52:49Z

recipes/libpnetcdf/meta.yaml

+  recipe-maintainers:
+    - xylar
+    - zklaus
+    - jedwards4b


@jedwards4b, are you also interested in being a maintainer? If so, your help would be quite valuable.

Sure, please add me as a maintainer. Thanks

xylar · 2023-06-14T16:47:07Z

@conda-forge/help-c-cpp, ready for review!

xylar · 2023-06-14T16:59:19Z

@conda-forge/help-c-cpp and @carterbox, I have removed libnetcdf and netcdf-fortran as dependencies at least for now. We can explore in the feedstock whether we can add libnetcdf back as a dependency without the overdependency warning.

mahf708

In the interest of getting this merged :)

xylar · 2023-07-06T08:34:35Z

Thanks a bunch @carterbox. I know this was a slog.

xylar commented Jan 19, 2023

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xylar commented Jan 19, 2023

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xylar force-pushed the libpnetcdf branch from bd2b788 to 06db9f7 Compare February 22, 2023 04:35

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xylar mentioned this pull request Jun 14, 2023

Build with pnetcdf? conda-forge/parallelio-feedstock#14

Closed

xylar closed this Jun 14, 2023

xylar reopened this Jun 14, 2023

xylar added 7 commits June 14, 2023 14:53

Add recipe for libpnetcdf

70a052b

Debug make check

ba306ef

Comment out tests

9e9c562

Add zklaus

47b2dfb

Remove unneeded hdf5 dependency

5bbbdf9

Add --with-mpi

3468f5b

Add tests for package config and include files

405bf18

xylar force-pushed the libpnetcdf branch from 06db9f7 to 86ef54f Compare June 14, 2023 12:53

Pin to libnetcdf 4.9.1 and netcdf-fortran 4.6

a00f9d6

Will replace this with a migrators once we have a feedstock.

xylar force-pushed the libpnetcdf branch from 86ef54f to a00f9d6 Compare June 14, 2023 13:18

xylar added 3 commits June 14, 2023 16:39

Remove libnetcdf and netcdf-fortran

70a5082

Remove --with-netcdf4 flag

957d257

Disable check for netcdf4 for now

eecabba

xylar commented Jun 14, 2023

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xylar requested a review from carterbox June 14, 2023 16:46

github-actions bot added review-requested and removed Awaiting author contribution labels Jun 14, 2023

mahf708 approved these changes Jul 1, 2023

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carterbox closed this Jul 6, 2023

carterbox reopened this Jul 6, 2023

carterbox merged commit 497e346 into conda-forge:main Jul 6, 2023

xylar deleted the libpnetcdf branch July 6, 2023 08:34

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Add recipe for libpnetcdf #21797

Add recipe for libpnetcdf #21797

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Add recipe for libpnetcdf #21797

Add recipe for libpnetcdf #21797

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