Fix #438, add three PDI deactivation option through CMake

[JAuriac]

Missing the case where paraconf is missing.

List of things to check before making a PR

Before merging your code, please check the following:

• you have added a line describing your changes to the Changelog;
• you have added unit tests for any new or improved feature;
• In case you updated dependencies, you have checked pdi/docs/CheckList.md
• you have checked your code format:
  • you have checked that you respect all conventions specified in CONTRIBUTING.md;
  • you have checked that the indentation and formatting conforms to the .clang-format;
  • you have documented with doxygen any new or changed function / class;
• you have correctly updated the copyright headers:
  • your institution is in the copyright header of every file you (substantially) modified;
  • you have checked that the end-year of the copyright there is the current one;
• you have updated the AUTHORS file:
  • you have added yourself to the AUTHORS file;
  • if this is a new contribution, you have added it to the AUTHORS file;
• you have added everything to the user documentation:
  • any new CMake configuration option;
  • any change in the yaml config;
  • any change to the public or plugin API;
  • any other new or changed user-facing feature;
  • any change to the dependencies;
• you have correctly linked your MR to one or more issues:
  • your MR solves an identified issue;
  • your commit contain the Fix #issue keyword to autoclose the issue when merged.

[jbigot]

Warning you're updating the tutorial. This is unrelated

[benoitmartin88]

I think this PR is almost ready for merge. Just a few changes are needed.

[JAuriac]

Warning you're updating the tutorial. This is unrelated

The tutorial previously used broke the CI.

[JAuriac]

Warning you're updating the tutorial. This is unrelated

The tutorial previously used broke the CI.

Changing back to tutorial @ 7334107.

[benoitmartin88]

I don't see the example being run here. It should, with pdi and no-pdi.

[JAuriac]

The example is now run with "PDI_example_trace_C" as part of the PDI tests, then on its own for no-PDI.

[benoitmartin88]

In addition to my review: it seems like you are testing that the scripts work directly in CI, could you not test locally by using the same docker images as in CI ? This would avoid small intermediate commits.

[JAuriac]

In addition to my review: it seems like you are testing that the scripts work directly in CI, could you not test locally by using the same docker images as in CI ? This would avoid small intermediate commits.

Related PR : #595

[Yushan-Wang]

Is this file still necessary, as discussed yesterday? I would keep this local, not on git.

[benoitmartin88]

I'm not sure all the tests and example are run depending on the run configuration.
For instance, the example should run with PDI and no-pdi, with and without paraconf on the system, and this is not currently the case.

[benoitmartin88]

Why deactivate benchmarking ?

[JAuriac]

This is temporary, waiting for a definitive commit.

[JAuriac]

Now reactivated with the following commit.

[benoitmartin88]

Why deactivate fortran, hdf5 and netcdf plugins ?

[JAuriac]

Example's CMakeLists does not use or account for those options, the cmake command here returns a warning of ignored option.

[benoitmartin88]

Why deactivate dhf5 and netcdf plugins ?

[JAuriac]

Tests' CMakeLists does not use or account for those options, the cmake command here returns a warning of ignored option.

[benoitmartin88]

I'm not sure if this is correct. It looks like the example is only run if paraconf is found on the system.
As a reminder, here is what should be run:

n/a	PDI	no-pdi
paraconf system	test PDI, example	test no-pdi, exemple
no paraconf system (use embedded)	test PDI, exemple	test no-pdi

[JAuriac]

The example is already included in the "test PDI" part (so the left column "PDI" is always run).
The if condition of this file only runs the top-right case, to run the example with no-pdi only with the system's paraconf.