NF_DEF_VAR_DEFLATE not compiled with netcdf version 4.2.1

[sit23]

When compiling Isca on a machine in China, we used netcdf 4.2.1 but it could not find the NF_DEF_VAR_DEFLATE command used here:
https://github.com/ExeClim/Isca/blob/master/src/shared/mpp/include/mpp_io_write.inc#L516

By commenting this line out the program compiles fine. Perhaps this is a command that is only present in more recent netcdf installs, and so shouldn't be compiled when using some versions of netcdf 4?

[wanglei5212749]

Hi, I have checked the netcdf version 4.1.3 and I find that the NF_DEF_VAR_DEFLATE is a netcdff-77 function. The usage of it is to deflate the variable to a small storage. However, there are two prerequisites to use this function. First, the variable to be deflated must has a netCDF-4 feature. Second, this function can't be used when using parallel I/O for writing data.

[sit23]

OK - thanks @wanglei5212749. That's good to know. Given that this function compiles OK with later NETCDF versions, do you think those requirements changed between NETCDF versions?

[wanglei5212749]

In my view, most of the climate models use a parallel I/O for writing data. And sometimes we use "--disable-netcdf-4" parameter when compile netcdf to avoid some library conflicts. This means we just build a netCDF-3 library without support for the netCDF-4 formats or functions(see here: https://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html).
In any of this two conditions, we can not use NF_DEF_VAR_DEFLATE function because the interface of NF_DEF_VAR_DEFLATE is not existing in the netcdf library we compiled. and it will cause a compile-error when we compile the model.

[wanglei5212749]

To avoid this error, We have two ways. (1)we can recompile the netcdf library we used to make it support for the netCDF-4 formats or functions(But still not use the parallel I/O for writing data). (2)we just comment this line to avoid the compile-error and this will not cause any difference to the model simulation performance except that it may have a little large disk storage. Also we can just comment the usage of #ifndef use_netCDF3 directly to avoid the compile-error.

[wanglei5212749]

OK - thanks @wanglei5212749. That's good to know. Given that this function compiles OK with later NETCDF versions, do you think those requirements changed between NETCDF versions?

In this condition, I think this problem has little relationship with the version we used, But may be caused by that we don't have the netCDF-4 formats or functions supported. Maybe can be tested by another netcdf library with the netCDF-4 formats or functions supported to see if this compile-error still existed.

[gregcolyer]

I'm not sure I'm following exactly, but option (1) should be what happens normally, i.e. new netCDF features are supported but not used by default (e.g. for created output files). So maybe this is broken by --disable-netcdf-4 and a different workaround for the library conflicts is needed. (Have you tried --disable-dap instead, mentioned in the documentation page linked to above?) According to git blame, the whole of mpp_io_write.inc is from the original GFDL import, so it hasn't changed in 3 years.

[gregcolyer]

Or under option (2), can you set the flag use_netCDF3 (matching the downgraded library) so that the #ifndef fails as intended?

[wanglei5212749]

Or under option (2), can you set the flag use_netCDF3 (matching the downgraded library) so that the #ifndef fails as intended?

Yes can set a definition for use_netCDF3 instead.

[RuthG]

We'll add a mention of this in the debug docs to help users who run into similar issues.