Build workflow utilities with CMake. #264
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I cloned the feature/cmake branch on Hera and ran build_workflow_utils.sh without doing anything else. I got this error: I noticed it didn't know the target (other build scripts source machine-setup.sh) so I first added "target=hera" to test and then tried adding a line to source machine-setup.sh. It got "hera" as the target either way but it still error: I'm not experienced with cmake...am I missing something? Thanks! |
… compiled files. bugfix in build_workflow_utils.sh hack. nceplibs-ncio now creates the module ncio and not fv3gfs_ncio.
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@KateFriedman-NOAA |
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@aerorahul Thanks for the fix! I updated my clone of feature/cmake on Hera and all workflow util codes built, woohoo!
Question...why not on wcoss_dell_p3? Are we waiting for a library update there? |
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I did not build on wcoss_dell_p3. I was lazy. But, it should build. |
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@aerorahul Gotcha, I'll try the build on WCOSS-Dell and report any issues. I ran a cycle test overnight on Hera with feature/cmake. The gdasechgres job segfaulted: /scratch1/NCEPDEV/stmp4/Kate.Friedman/comrot/cmake/logs/2020090118/gdasechgres.log.1 I reran with module_base.hera using hpc-stack to test that but it segfaulted similarly: /scratch1/NCEPDEV/stmp4/Kate.Friedman/comrot/cmake/logs/2020090118/gdasechgres.log I see mention of module_ncio, do we need to load an additional module at runtime? Thanks! Also, there is some additional updating/cleanup/decommissioning work to be done on feature/cmake (e.g. remove unneeded build scripts). I had to do some updating to get the branch ready to run so I'll finish that and commit those updates. |
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@KateFriedman-NOAA The cleanup/decommissioning should be done in a separate branch and not in |
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@KateFriedman-NOAA |
…_nc.fd. When going from nemsio to netcdf, the linking of ip, sp and w3nco changed from _d to _4.
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@KateFriedman-NOAA |
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@aerorahul Thanks for the fix! I updated my clone on Hera, reran build_workflow_utils.sh and then rewound the failed gdasechgres job. The job completed successfully! /scratch1/NCEPDEV/stmp4/Kate.Friedman/comrot/cmake/logs/2020090118/gdasechgres.log I also ran the gdasechgres job in my feature/hpc-stack test (symlinked workflow execs to feature/cmake execs) and it also completed successfully: /scratch1/NCEPDEV/stmp4/Kate.Friedman/comrot/stacktest1/logs/2020090118/gdasechgres.log I am letting my cmake test on Hera continue forward another cycle. I want to run a cycle on both Orion and WCOSS-Dell, and repeat the test on Hera for a reproducibility check. I'll have a commit shortly to add workflow_utils to the build_all and linking scripts so it builds/links out of the box again. Further cleanup and decommissioning will happen in a follow-up PR. |
- add build_workflow_utils.sh to build_all.sh - add workflow utils exec symlinks to link_fv3gfs.sh since these execs no longer land in /exec folder - add workflow_utils build to partial_build.sh and fv3gfs_build.cfg for use by build_all - turn off builds in fv3gfs_build.cfg that are now covered by workflow_utils build - move machine-setup source in build_workflow_utils.sh before target is needed Further cleanup and decommissioning of consolidated builds will come in follow-up commit/PR. Refs: #264
- Add $target to build_workflow_utils.sh command in build_all.sh - Move machine-setup source back down into if-block in build_workflow_utils.sh Refs: #264
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@aerorahul The analcalc jobs are failing in my test of feature/cmake on Hera. Can you take a look? Thanks! /scratch1/NCEPDEV/stmp4/Kate.Friedman/comrot/cmake/logs/2020090200/gdasanalcalc.log |
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@WalterKolczynski-NOAA @KateFriedman-NOAA |
Will do |
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Did what I could to cross-check against existing makefiles/build scripts with my rudimentary knowledge of cmake and the library dependencies. I suspect most of my comments will be either covered by cmake picking up library dependencies or just inconsequential changes. It's also possible I missed a flag being set somewhere, though I tried to check both the build script and the makefile.
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@WalterKolczynski-NOAA |
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Sorry for the hold-up. I've resolved all the ones that are definitely taken care of. I will leave it to your discretion about what to do with the remainder and whether they are impactful or not. |
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@WalterKolczynski-NOAA Thanks again for the careful review. |
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@KateFriedman-NOAA Go ahead and merge if you are satisfied. |
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Thanks for cmake-ifying these codes @aerorahul ! Tested branch on Hera, Orion, and WCOSS-Dell. Ran fine. Duplicate run on Hera reproduced output.
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Reran build_workflow_utils.sh on WCOSS-Dell, Hera, and Orion after commit at 1d7776d. Build ran fine. |
This PR enables the utilities under
sorc/to be built usingcmake. modulefiles forhera,orionandwcoss_dell_p3are added that load hpc-stack.These workflow utilities were compiled on
heraandorion, but not onwcoss_dell_p3These workflow utilities were compiled on
macOS, EMC Linux box (RHEL7), Docker with GNU and IntelOneAPI containers.All utilities built as expected. They were not tested against the hand-written makefiles on the supported HPC's for reproducibility.
Minor changes in 3 Fortran source codes
syndat_qctropcy.fd/qctropcy.f,gfs_bufr.fd/meteorg.f, andfv3nc2nemsio.fd/fv3_main.f90were required to get these utilities to be compiled with GNU Fortran.