Update jedi repos to develop as of Jan 28 2023 by shlyaeva · Pull Request #20 · JCSDA/ufs-bundle

shlyaeva · 2023-01-30T14:52:34Z

Updates tags of all JEDI repos to develop as of January 28 2023.
Pointers to branches in fv3-jedi/fv3-jedi-data can be changed back to feature/ufs_dom once the other 2 PRs are merged.

Goes with:

fv3-jedi: https://github.com/JCSDA-internal/fv3-jedi/pull/762
fv3-jedi-data: Merge develop in feature/ufs_dom JCSDA-internal/fv3-jedi-data#57

climbfuji · 2023-01-30T15:12:36Z

Excellent, thanks very much @shlyaeva. I am going to give this a test on my Mac.

cmgas · 2023-01-30T21:46:51Z

I am getting the following error on pcluster:

[ 10%] Linking CXX executable ../../../../bin/l95_forecast.x
ld: CMakeFiles/l95_forecast.x.dir/Forecast.cc.o: undefined reference to symbol 'nc_create'
ld: /mnt/experiments-efs/dom.heinzeller/spack-stack-dev-20230118/envs/skylab-dev/install/intel/2021.4.0/netcdf-c-4.8.1-nobfxbd/lib/libnetcdf.so.19: error adding symbols: DSO missing from command line
make[2]: *** [oops/l95/src/executables/CMakeFiles/l95_forecast.x.dir/build.make:120: bin/l95_forecast.x] Error 1
make[1]: *** [CMakeFiles/Makefile2:6135: oops/l95/src/executables/CMakeFiles/l95_forecast.x.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

climbfuji · 2023-01-30T21:49:06Z

I am getting something similar on my mac (this is actually the first piece of real work that I am doing today!!!):

Undefined symbols for architecture x86_64:
  "_nc_close", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
  "_nc_create", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
  "_nc_def_dim", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
  "_nc_def_var", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
  "_nc_enddef", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
  "_nc_put_var_double", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
  "_nc_put_var_int", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
  "_nc_strerror", referenced from:
      oops::detail::writer(atlas::FunctionSpace const&, atlas::FieldSet const&, oops::Variables const&, std::__1::vector<unsigned long, std::__1::allocator<unsigned long> > const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, unsigned long, unsigned long) in Forecast.cc.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [bin/l95_forecast.x] Error 1
make[1]: *** [oops/l95/src/executables/CMakeFiles/l95_forecast.x.dir/all] Error 2
make: *** [all] Error 2

Let me try to fix that, hopefully it solves your problems, too.

…8_bugfix_netcdf_c_oops Update branch for oops for fixing missing netcdf-c dependencies

shlyaeva · 2023-01-30T23:07:03Z

CMakeLists.txt

-ecbuild_bundle( PROJECT saber GIT "https://github.com/jcsda-internal/saber.git" BRANCH bugfix/add_missing_netcdf_dependency_to_build_system )  # updated from develop on nov 15
-ecbuild_bundle( PROJECT ioda  GIT "https://github.com/jcsda-internal/ioda.git"  TAG 876e7874fc917376500822157cda82c15ede02f8 )  # develop on nov 15
-ecbuild_bundle( PROJECT ufo   GIT "https://github.com/jcsda-internal/ufo.git"   TAG f95dd253a850debd1f1b391ec63a47f99c341efa )  # develop on nov 15
+ecbuild_bundle( PROJECT oops  GIT "https://github.com/jcsda-internal/oops.git"  BRANCH feature/ufs_fix_netcdf_c_dependencies ) # based on TAG e7335ffba1fa883ff19759634b7edf1ccd25fe80, which is develop on jan 28


@climbfuji thank you for fixing this! it would be good to merge this fix in oops develop (thanks for opening https://github.com/JCSDA-internal/oops/pull/2047)

shlyaeva · 2023-01-30T23:14:27Z

I am getting something similar on my mac

Interestingly, I was able to build and test this branch over the weekend, but then not again now (until Dom's fix, I haven't retested) from anew. I wonder if that's because the first time I was building on top of the previous build with feature/ufs_dom.

…soca_20230131 Update CMakeLists.txt

climbfuji

I am happy with those changes, now that we have soca updated and the build/linker errors fixed for the remaining S2S application.

shlyaeva · 2023-02-01T01:45:48Z

@climbfuji sounds good! I'll mark this and fv3-jedi and fv3-jedi-data as ready for merge into your branches

shlyaeva · 2023-02-01T01:47:15Z

@climbfuji once fv3-jedi and fv3-jedi-data PRs are merged, I'll update this back to pointing to feature/ufs_dom for fv3-jedi and fv3-jedi-data before it's merged.

CMakeLists.txt

climbfuji

I was about to make this change ;-)

…ng ATM warmstart configurations (#9) * updates to get things building/linking * using two different versions of fv3-jedi depending on UFS_APP * small change to ioda for expat linking * fix for building in container * update for godas * Updating with consolidated versions for atm/godas/s2s builds * Updated atlas version and README * updated readme * updated atlas version * updated README for cheyenne * updated README for cheyenne * Changed to hashes * Switched version of FMS. Might be able to remove it as an external now * Add vader and ufs-weather-model to .gitignore * Update CMakeLists.txt * Update CMakeLists.txt * Update CMakeLists.txt * More updates to CMakeLists.txt * Work in progress: README.md * Update soca branch in CMakeLists.txt * Use MPI compiler wrappers for external project ufs-weather-model * Attempt to fix dependency for gsw in CMakeLists.txt * Update README.md * Add missing imported library statements to CMakeLists.txt, update README.md * Catch unknown UFS_APP in top-level CMakeLists.txt * Point to branch feature/ufs_dom of fv3-jedi-data * WIP on README.md * Update CMakeLists.txt, now s2s compiles * Update JEDI repo versions in bundle CMakeLists * Update README.md * Update CMakeLists.txt * Update CMakeLists.txt * Update CMakeLists.txt * Update ufs-weather-model branch name * macOS OpenMP flags for ufs-weather-model * Fix macOS OpenMP linker issue * Temporarily add PRs.txt TMP_README_UFS_STANDALONE.sh * Update PRs.txt * Bug fix in CMakeLists.txt, update README.md * Add more info on ctests to README.md * Cleanup to finalize ufs atm build and warmstart tests * Bump eckit etc versions in CMakeLists.txt * Update jedi repos to develop as of Jan 28 2023 (#20) * Update jedi repos to develop as of Jan 28 2023 * Update branch for oops for fixing missing netcdf-c dependencies * Update CMakeLists.txt * Update oops tag in CMakeLists.txt * Change branches back to feature/ufs_dom --------- Co-authored-by: Dom Heinzeller <dom.heinzeller@icloud.com> --------- Co-authored-by: Mark Potts <Mark.Potts@noaa.gov> Co-authored-by: Francois Hebert <hebert@ucar.edu> Co-authored-by: Anna Shlyaeva <annash@ucar.edu>

Update jedi repos to develop as of Jan 28 2023

0244de4

shlyaeva requested a review from climbfuji January 30, 2023 14:52

climbfuji and others added 2 commits January 30, 2023 15:09

Update branch for oops for fixing missing netcdf-c dependencies

4ad0222

Merge pull request #1 from climbfuji/feature/atm-soca-s2s_dom_as_jan2…

2616c8e

…8_bugfix_netcdf_c_oops Update branch for oops for fixing missing netcdf-c dependencies

shlyaeva commented Jan 30, 2023

View reviewed changes

climbfuji and others added 2 commits January 31, 2023 09:42

Update CMakeLists.txt

0eee6f2

Merge pull request #2 from climbfuji/feature/atm-soca-s2s_dom_update_…

011af8d

…soca_20230131 Update CMakeLists.txt

climbfuji approved these changes Feb 1, 2023

View reviewed changes

shlyaeva marked this pull request as ready for review February 1, 2023 01:45

Update oops tag in CMakeLists.txt

a2c91b0

shlyaeva commented Feb 1, 2023

View reviewed changes

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Change branches back to feature/ufs_dom

31b292b

climbfuji approved these changes Feb 1, 2023

View reviewed changes

climbfuji merged commit f7023c9 into JCSDA:feature/atm-soca-s2s_dom Feb 1, 2023

shlyaeva deleted the feature/atm-soca-s2s_dom_as_jan28 branch February 1, 2023 15:45

climbfuji mentioned this pull request Feb 1, 2023

Update JEDI components (branches) in ufs-bundle #18

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Update jedi repos to develop as of Jan 28 2023#20

Update jedi repos to develop as of Jan 28 2023#20
climbfuji merged 7 commits intoJCSDA:feature/atm-soca-s2s_domfrom
shlyaeva:feature/atm-soca-s2s_dom_as_jan28

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