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Changing default NetCDF format to CDF5 and updating SCORPIO to v1.6.5 #6525

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merged 2 commits into from
Aug 6, 2024
Merged

Changing default NetCDF format to CDF5 and updating SCORPIO to v1.6.5 #6525

merged 2 commits into from
Aug 6, 2024

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jayeshkrishna
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@jayeshkrishna jayeshkrishna commented Jul 24, 2024 •
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The CDF5/64bit_data format gets rid of limitations (for all practical
purposes) on NetCDF variable size imposed by the older
CDF2/64bit_offset file format.

Also updating SCORPIO to v1.6.5

[BFB]
[NML]

@jayeshkrishna
Changing default NetCDF format to CDF5
ea2a936 
Changing the default NetCDF file format from CDF2 (64bit_offset)
to CDF5 (64bit_data).

The CDF5 format gets rid of limitations (for all practical
purposes) on NetCDF variable size imposed by the older CDF2
file format. Also note that all E3SM run scripts already
explicitly set the NetCDF file format to CDF5/64bit_data for all
production runs.
@jayeshkrishna jayeshkrishna added BFB PR leaves answers BFB SCORPIO The E3SM I/O library (derived from PIO) labels Jul 24, 2024
@jayeshkrishna jayeshkrishna requested a review from dqwu July 24, 2024 23:17
@jayeshkrishna jayeshkrishna self-assigned this Jul 24, 2024
jayeshkrishna added a commit that referenced this pull request Jul 29, 2024
@jayeshkrishna
Merge branch 'jayeshkrishna/driver/change_default_to_cdf5' into next …
cc73e45 
…(PR #6525)

The CDF5/64bit_data format gets rid of limitations (for all practical
purposes) on NetCDF variable size imposed by the older
CDF2/64bit_offset file format.

[BFB]

* jayeshkrishna/driver/change_default_to_cdf5:
  Changing default NetCDF format to CDF5
@jayeshkrishna jayeshkrishna mentioned this pull request Aug 2, 2024
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  • This PR assumes that all machines and tools (like cprnc) have support for PnetCDF or NetCDF (> 4.4.0). The cprnc tool on Anvil was re-built by @amametjanov with the latest modules to add support for CDF5.
  • This PR also causes runtime issues (when writing large variables) with SCORPIO version < 1.6.5 on machines that do not support PnetCDF (e.g. mappy)

@jayeshkrishna
Upgrading to SCORPIO v1.6.5
3758fdf 
SCORPIO v1.6.5 includes the following changes/fixes,

* Fix to support CDF5 file format when PnetCDF is not available

This upgrade fixes runtime issues when writing large variables
using the CDF5 file format on machines (like mappy) that do not
have support for PnetCDF
@jayeshkrishna jayeshkrishna requested review from rljacob and dqwu August 2, 2024 03:03
rljacob
rljacob approved these changes Aug 2, 2024
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Update the title and description to mention that SCORPIO is also updated.

jayeshkrishna added a commit that referenced this pull request Aug 2, 2024
@jayeshkrishna
Merge branch 'jayeshkrishna/driver/change_default_to_cdf5' into next …
2d17cb9 
…(PR #6525)

Re-merging branch to fix nightly test fails on mappy.

The CDF5/64bit_data format gets rid of limitations (for all practical
purposes) on NetCDF variable size imposed by the older
CDF2/64bit_offset file format.

Also updating SCORPIO to v1.6.5

[BFB]
[NML]

* jayeshkrishna/driver/change_default_to_cdf5:
  Upgrading to SCORPIO v1.6.5
@jayeshkrishna jayeshkrishna changed the title Changing default NetCDF format to CDF5 Changing default NetCDF format to CDF5 and updating SCORPIO to v1.6.5 Aug 2, 2024
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PR Preview Action v1.4.7
🚀 Deployed preview to https://E3SM-Project.github.io/E3SM/pr-preview/pr-6525/
on branch gh-pages at 2024-08-02 03:42 UTC

mahf708
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This change necessitates NetCDF-Fortran of a specific minimum, as per internal discussion. To avoid problems for users debugging missing symbols, could this PR be updated with a build-time check in the SCORPIO submodule for said specific minimum? Shouldn't be too hard to check this in the cmake logic.

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mahf708 commented Aug 6, 2024 •
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The following line should be edited in scorpio submod (potentially with a patch release or something?)
https://github.com/E3SM-Project/scorpio/blob/db9ea40da9fed50c8cdf6a7fa7f1a4d8e5aa1b00/CMakeLists.txt#L317

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The following line should be edited in scorpio submod (potentially with a patch release or something?) https://github.com/E3SM-Project/scorpio/blob/db9ea40da9fed50c8cdf6a7fa7f1a4d8e5aa1b00/CMakeLists.txt#L317

The next release of SCORPIO will include the version check for the NetCDF fortran library (it already includes the check for the NetCDF library) - to verify that it supports CDF5
FYI, this support has been around for a while and all E3SM machines should have a version of NetCDF library that supports CDF5

@jayeshkrishna jayeshkrishna requested a review from mahf708 August 6, 2024 14:23
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Sounds good to delay the check for the next release! Thanks!

@jayeshkrishna jayeshkrishna merged commit ebbf745 into master Aug 6, 2024
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@jayeshkrishna jayeshkrishna deleted the jayeshkrishna/driver/change_default_to_cdf5 branch August 6, 2024 14:57
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This PR introduces NML changes for the tests since it changes the default I/O type in the nameless,

Comparison failed between 'xxx_modelio.nml' with 'xxx_modelio.nml'
  BASE: pio_netcdf_format = '64bit_offset'
  COMP: pio_netcdf_format = '64bit_data'

@dqwu dqwu mentioned this pull request Aug 6, 2024
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@jayeshkrishna jayeshkrishna mentioned this pull request Aug 16, 2024
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