Fix doxygen warnings, turn on WARN_AS_ERROR #392
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fossell
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@edwardhartnett - Thank you for providing this list. The DTC would like to help with the effort to initiate proper documentation in the existing code base as well as establish documentation standards for code developers. Would you be able/willing to meet to help get us started in the right direction or perhaps you have resources, examples already you can point us to? |
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I'm absolutely happy to help by meeting at any time. Most of the warnings are pretty self-explanatory. Let's take an example:
So when I look at AVIATION.f, around line 231, here's what I see: So the problem here is that the legacy documentation has not been converted to doxygen. THe legacy documentation block should be removed, and a doxygen documentation block added, just before the SUBROUTINE line, which contains the documentation for this subroutine. Once this documentation is converted to doxygen, this warning will go away. |
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@WenMeng-NOAA - Our team is starting to tackle this issue of translating current UPP routines to use Doxygen documentation syntax. As we make progress, would you prefer PRs for sets of files as they're ready, or wait until we make changes in all routines and submit the bulk of these documentation updates in one PR? |
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@fossell Multiple PRs would be easy for reviewing and merging. Thanks! |
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I strongly recommend that each programmer working on doxygen conversion start with one code file, and put that up for PR, tagging me for review. As we work through the issues, each programmer will learn how to do documentation in a way that's similar to the way the rest of the UPP documentation is done. Doxygen offers many alternatives - we don't want each programmer finding their own way of doing things - we want to follow common doxygen idioms, and have all our doxygen look similar. We have worked out a lot of the problems on the NCEPLIBS team, and the UPP team should not have to re-engineer all that. Once each programmer gets one or two single-file doxygen PRs through, they can start doing 5 or 6 files per PR. No more than that please, if you want effective review. At that point I will bring in some other members of the NCEPLIBS team to help review the doxygen. Also, please make all doxygen PRs separate from code changes. Doxygen PRs should have changes only to lines of comments - never to any lines of code. Keep your code changes for a separate PR after the documentation is done. This makes it easy to make large numbers of changes (as is required) without any chance of breaking code. |
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@edwardhartnett - thanks for your suggestions, this all sounds good to me. Appreciate your willingness to review these PRs and help us learn leverage from your experience. Our initial plan is to just convert the existing content to doxygen syntax, like you did with AVIATION.f, and not pursue any further enhancements at this time. Does that sound like a reasonable approach or do you recommend other things to consider? |
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That is a good approach and there is plenty of work there. In doing that, every programmer will learn the common doxygen tags, and such fancy tricks as tables, lists, and references. Once that is complete, all the programmers involved will have a good understanding of doxygen. Those who are interested can read the documentation and tutorials to learn more advanced doxygen techniques and more ways to make the documentation beautiful as well as informative. |
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kayeekayee
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Mar 7, 2022
Fixes the doxygen warnings in CALGUST.f Please review this subroutine. Thank you.
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* Doxygen for CALDRG.f * This is part of Issue #392 Fixes the doxygen warnings in CALGUST.f Please review this subroutine. Thank you.
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@WenMeng-NOAA - @kayeekayee is going to be ramping up work on these doxygen updates which means a handful of PRs coming through. We'd like to have @edwardhartnett review them, or at least an initial batch, to provide comments and suggestions before merging. Ka Yee had issues assigning Ed as a reviewer, but I'll work with her to resolve that problem. As future PRs for this come in we'll wait for Ed's review initially until we have a good feel for it. If you'd like us to take a different approach in coordinating these PRs with you, just let us know. @edwardhartnett - Let us know if you're still willing to review a few of these for us. #451 has already been merged, but feel free to look or just comment on forthcoming PRs. |
kayeekayee
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Mar 8, 2022
Fixes the doxygen warnings in CALSTRM.f
Please review this subroutine. Thank you.
kayeekayee
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Mar 18, 2022
Fixes the doxygen warnings in CALHEL.f CALHEL2.f CALHEL3.f Please review this subroutine. Thank you.
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kayeekayee
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Mar 30, 2022
Fixes the doxygen warnings in CALLCL.f CALMCVG.f CALMICT.f
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Fixes the doxygen warnings in CALPBL.f CALPBLREGIME.f CALPOT.f CALPW.f.
kayeekayee
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Fixes the doxygen warnings in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f.
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@edwardhartnett @fossell Please review this PR if all the warnings are being fixed or not. Let me know if I missed any. Thank you. |
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Turn on WARN_AS_ERROR in your Doxyfile.in and doxygen will tell you. ;-) |
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@kayeekayee - It looks like the version of doxygen on Cheyenne is 1.8.6 and it's not recognizing the WARN_AS_ERROR tag, so it doesn't immediately fail when encountering an error. I tried on my laptop with v1.9.3 and it does fail as soon as there is an error. Even without this tag, on Cheyenne when I make the docs it produces a list of warnings about what is not completely documented yet. (I'm not sure about what version is on Hera and what the behavior is there) In many cases it looks like it's certain parameters of routines you already started to translate to doxygen are not documented. I'm guessing that this is just a result of documentation that was never developers never put in there in the first place or updates to the code that were never documented, so during this initial phase of translating only what's existing, these are still missing complete documentation. For example, CALGUST.f produces a warning about LPBL, ZPBL, and GUST not being documented, because LPBL and ZPBL are not listed with an @param in the doxygen block, and GUST is listed as out, when in fact in the code it's inout. Other routines may not have been updated at all, e.g. VRBLS2D_mod.f. In fact most module routines are not doxygenated. @edwardhartnett - Is there a flag/tag in the doxyfile.in that will list the files only (not all members of all files) that are not documented at all given a certain source directory? Without spitting out all of the warnings? The WARN_* options I looked at didn't seem to quite get at that. Or is it best to just make run down the list of files in our source directory? Do all routines need to have a @something for doxygen to even consider it? @kayeekayee - I think we have two things to attack here, 1) make sure all source code is being recognized and included by doxygen for the documentation, and 2) updating routines with incomplete documentation. |
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Doxygen will consider all files which are included in the Doxyfile INPUT field, and which have at the top of the file:
There is not a lot of warning control. You get what you get. I think there is a separate warning setting for warnings for undocumented functions and warnings for missing parameters. Indeed, different versions of doxygen respond slightly differently to warnings. On the NCEPLIBS project, we take 1.8.7 (IIRC) as canonical because that's what GitHub CI uses in its ubuntu-latest distribution. It's expected that hand-maintained documentation will drift and contain mistakes, so it's not at all surprising that there are missing or incorrect parameters. You must simply work through the list and fix all the warnings. Then the WARN_AS_ERROR flag can be turned on, and you will never have to do it again. ;-) Fortunately, fixing doxygen warnings is easy work. |
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@edwardhartnett - Thanks! This is very helpful. We will keep tackling this with the goal of being able to turn that WARN_AS_ERROR flag on and never look back. :) |
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@camshe - This is an ongoing effort so probably one to be aware of. |
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* Changes to support 2D Decomposition shape changes. Full I dimension remains in all arrays bu t SURFCE is altered to use isx:iex bounds which are equivalent to IM which is equivalent to 1:IM * test of commit only added one comment to PROCESS.f * comment test 2 * Added more routines to 2D decomposition * Changed isx and iex to ISTA and IEND in listed routines. ISTA had prior use in MDL2P.f and that needed changing. IEND had prior use in PARA_CONFIG, changed to IENDJ in PARA_CONFIG2 where needed PARA_CONFIG did not need changing * test commit of new base into clone * repair of a bunch of changed routines somehow corrupted by a merge 5/3/2021 * fixed 5/25 problem * added ctlblk change to support ista and iend partial I dimensons * added para_range2 to PARA_RANGE.f to support 2D decomposition * Modified MPI_FIRST.f to support a 2D decomposition but the actual numbers used remain the 1D special case and the changes just add two more indices for start and end I domains and logic to convert scatter counts and displacements to the product of the I and J subdomain sizes rather than I full domain x J subdomain. * Added support for halo settings of 2D boundaries i.e ista_2l to match the 1D analogs long present in the source 6/1/2021 * Added definitions for ista_2u, and ista_2u in MPI_FIRST.f * Reshaped arrays in MDL2FLD.f to support 2D decomposition. Modified TWO (only) loops to try thie * Remove TIMEF.f. * 20210702 JesseMeng modify MPI_FIRST.f MDLFLD.f for 2D decomposition * 20210706 BoCui modify INITPOST_GFS_NETCDF_PARA.f * 20210707 JesseMeng modified grib2_module.f for 2d decomposition * test version INITPOST_GFS_NETCDF_PARA.f * test version INITPOST_GFS_NETCDF_PARA.f and MPI_FIRST.f * 20210713 BoCui test INITPOST_GFS_NETCDF_PARA.f, MPI_FIRST.f and ALLOCATE_ALL.f * 20210713 BoCui test INITPOST_GFS_NETCDF_PARA.f, MPI_FIRST.f and ALLOCATE_ALL.f * 20210719 BoCui Modified CLDRAD.f for 2d decomposition * 20210816 Jesse Meng commit George's EXCH update for 1 layer 2D halos transforming * 20210816 Jesse Meng remove ifcore in EXCH * 20210903 Bo Cui update ALLOCATE_ALL.f after new merge from 'upstream/develop' * 20210903 Bo Cui Added new routines to 2D decomposition * 20210903 Jesse Meng fixed the ieql allocation bug in ALLOCATE_ALL.f * 20210904 Bo Cui fixed CLDRAD.f * 20210913 Jesse Meng commit progress of 2D decomposition * 20210917 Bo Cui add new routines to 2D decomposition * 20210917 Jesse Meng remove 4 legacy files * 20210917 Jesse Meng remove legacy code SLP_NMM EXCH2 * 20210917 Jesse Meng remove legacy code INITPOST_GFS_SIGIO.f INITPOST_GFS_NEMS.f * 20210917 Jesse Meng add INITPOST_GFS_NEMS.f back to avoid compiling error. * 20210930 Jesse Meng add George's itag/numx entry and progress on 2D decompose * 20211015 Jesse Meng progress on 2D DECOMPOSITION * 20211017 Bo Cui add new subroutines to UPP 2D decomposition * 20211026 Jesse Meng commit progress in 2D DECOMPOSITION * 20211026 Jesse Meng fix INITPOST_GFS_NETCDF_PARA.f for 2D DECOMPOSITION * 20211026 Jesse Meng update SURFCE.f for 2D DECOMPOSITION * 20211103 Jesse Meng commit progress of 2D DECOMPOSITION * 20211106 Bo Cui commit progress of 2D decomposition * 20211109 Jesse Meng updates for 2D DECOMPOSITION * 20211110 Jesse Meng updates in 2D DECOMPOSITION * 20211112 Jesse Meng updates for 2D DECOMPOSITION * 20211115 Jesse Meng updates for 2D DECOMPOSITION * 20211119 Jesse Meng updates for 2D DECOMPOSITION * 20211201 Jesse Meng move CALVOR to UPP_PHYSICS module; implement fullpole in MPI_FIRST * 20211202 Jesse Meng minor update of MPI_FIRST using mpi_allgatherv * 20211203 Jesse Meng implement fullpole in MDL2THANDPV and CALDIV * 20211207 Jesse Meng update MISCLN.f SURFCE.f * 20211208 Jesse Meng add parm/hafs_nosat files * 20211213 Bo Cui updates for 2D decomposition * 20211213 Jesse Meng update the merged 'upstream/develop' and 'post_2d_decomp' branch to 2d_decomp style * 20211215 Jesse Meng use i=0:im+1 for GFS in MPI_FIRST and EXCH * 20211216 Jesse Meng minor update UPP_PHYSICS for i=0:im+1 expansion * 20220104 Jesse Meng add George's minor fix in EXHC.f * 20220118 Jesse Meng commit George's cleaned up code. * 20220203 Jesse Meng - update MAPSSLP.f to be consistent with develop branch. * 20220222 Jesse Meng add checkcoords flag in EXCH.f to move around George's debug code. * 20220302 Jesse Meng Restrict computation from undefined grids * 20220304 Bo Cui Add a reset of numx=1 if remainder of num_procs/numx is not 0 * 20220310 Jesse Meng Add a reset of numx=1 if(numx>num_procs/2) * 20220322 Jesse Meng mpi_allgatherv change communicator to MPI_COMM_COMP * 20220328 Jesse Meng bug fix for passing 2d subarrays between subroutines * 20220328 Jesse Meng minor fix for CLDRAD call BOUND variable array size * 20220330 Jesse Meng fix cloud cover variabes full field collection in 2d decomp * 20220401 Jesse Meng minor fix for CALMCVG.f and update CALUPDHEL.f with develop * 20220414 BoCui sync and merge UPP/develop into post_2d_decomp (#7) * Added lambert conformal projection for FV3SAR and handled composite reflectivity correctly (#14) (#2) * exec is selectable for executable directory (#448) * Doxygen for CALGUST (#451) * Doxygen for CALDRG.f * This is part of Issue #392 Fixes the doxygen warnings in CALGUST.f Please review this subroutine. Thank you. * The fix in CALUPDHEL.f (#458) * Modify CALUPDHEL.f for restricting undefined grids in computation. * Update VERSION to 10.0.12. * Bug fix for SLLEVEL bound issue when not RUC LSM (#463) Co-authored-by: Tracy <tracy.hertneky@noaa.gov> * Doxygen caldrg caldwcp calgust refinement (#464) * Further refinement to the tables and logs. * Further refinement to the tables and logs. (#455) * This is part of Issue #392 (#460) Fixes the doxygen warnings in CALHEL.f CALHEL2.f CALHEL3.f Please review this subroutine. Thank you. * Unify global and regional FV3 read interfaces (#453) * Unify the interfaces for reading FV3 outputs in netcdf. * Remove interface INITPOST_GFS_NETCDF_PARA. * Remove INITPOST_GFS_NETCDF.f. * Remove the capability of serial netcdf reading FV3 outputs. * Correct reading rswinc. * Remove duplication in CLDRAD.f. * Remove duplicated avgalbedo reading * Add changes for reading pwat from model. * Clean up commented out code * Clean up duplicated lines * Add ability to compile script to use non-intel compilers; add Cheyenne modulefiles for gnu and intel (#468) * Add cheyenne modulefile * Intel 19 --> 2021 * Add ability to specify compiler; move all existing modulefiles to ${name}_intel since they are all for intel compilers; add "cheyenne_gnu" modulefile * Revert move of intel modulefiles; now the implicit default for a modulefile is intel, only gnu and other compilers will have the compiler name appended to the modulefile * Allow for lua modulefiles with ".lua" appended * This is part of Issue #392 (#465) Fixes the doxygen warnings in CALLCL.f CALMCVG.f CALMICT.f * This is part of Issue #392 (#466) Fixes the doxygen warnings in CALPBL.f CALPBLREGIME.f CALPOT.f CALPW.f. * Doxygen in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. (#467) * This is part of Issue #392. Fixes the doxygen warnings in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. * Fixed typo. * Update to PR #458. * Doxygen in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f (#469) * This is part of Issue #392. Fixes the doxygen warnings in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f. * Fixed minor bug in CALVOR.f. * Update to PR#453. * More updates. * 20220411 Bo Cui 2D decompositio CALVOR.f and INITPOST_NETCDF.f * 20220411 Bo Cui update doxgen and global and regional FV3 read interface * 20220414 Bo Cui: remove read_netcdf_2d_scatter and read_netcdf_3d_scatter from INITPOST_NETCDF.f * 20220415 Bo Cui delete CALVOR.f, add exch of gdlon in INITPOST_NETCDF.f * 20220421 Bo Cui Doxygen in UPP_PHYSICS.f,add restriction run 2D decomp only for GFS/FV3R in WRFPOST.f Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: Wen Meng <wen.meng@noaa.gov> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: kayeekayee <kayee.wong@noaa.gov> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> * 20220502 Bo Cui code cleanup * 20220512 Jesse Meng minor fix for INITPOST_GFS_NEMS_MPIIO.f calling EXCH * 20220525 Jesse Meng minor fix to 2d_decomp syntax * Update VERSION to 11.0.0 * 20220607 Jesse Meng add variable declaration block in PARA_RANGE.f * 20220608 Jesse Meng remove blank spaces in sorc/ncep_post.fd/AllGETHERV_GSD.f * Add 2D decomp overview documentation (#6) * Add 2D decomp overview documentation * Update 2D overview Co-authored-by: George Vandenberghe <George.Vandenberghe@noaa.gov> Co-authored-by: wx15gv <George.Vandenberghe@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a1.ncep.noaa.gov> Co-authored-by: Bo Cui <Bo.Cui@noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a2.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a2.ncep.noaa.gov> Co-authored-by: Jesse.Meng <Jesse.Meng@noaa.gov> Co-authored-by: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: kayeekayee <kayee.wong@noaa.gov> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> Co-authored-by: Jesse Meng <jmeng@Orion-login-4.HPC.MsState.Edu> Co-authored-by: Kate Fossell <fossell@ucar.edu>
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* NOAA GSL UPP updates (NOAA-EMC#413) * Turn on GSD cloud ceiling calculation for RRFS dev. * Updates to UPP for RRFS applications (#3) * Updates to UPP for RRFS applications: 1) Adding a RRFS-specific .xml control file and a corresponding .txt flat file. Note that script changes (pending) are needed to leverage the new flat file. However, this code will work in current real-time configurations. 2) Adding GSL experimental ceiling diagnostics, GSL visibility diagnostic, and GSL sea-level pressure reduction (MAPS). Also adding TKE and aerosol number concentrations. 3) Code clean-up for ceiling-related diagnostics; added comments, etc. 4) Removing several non-needed variables, originally inherited from FV3-SAR community configuration. * Updating UPP control files to specify GRIB2 generating center as "noaa_fsl_boulder" and the generating process as "hrrr". The "hrrr" specification is temporary, and will eventually be switched to "rrfs" once required changes to the "NCEPLIBS-g2tmpl" library are available. (#4) * Fix some out-of-bounds reads that caused the RRFS UPP to crash. (#5) * Adding README file (#7) * Adding README file to describe process of making a "flat" file. * Updates to README to improve explanation of input/output files. * Code to read in Flash Flood Guidance (FFG) and Average Recurrence Interval (ARI) precipitation datasets for comparison with model QPF within UPP. * Fixed a syntax error in SURFCE.f * Getting rid of GRIB1 output option to be consistent with rest of code. * Changing field numbers to avoid conflict with existing RRFS-dev1 fields. * Putting exceedance grids in flat files for testing in RRFS UPP. * Corrected the 1h and run total precip names for calculating exceedances in SURFCE.f * Bug fix in SURFCE.f if statements. * Removing changes to RQSTFLD.F since GRIB1 is no longer used in UPP. * Merging NOAA-GSL development on top of NOAA-EMC UPP for testing. * Correcting minor typos in SURFCE.f to allow testing. * Update code based on testing with RRFS cases. * Update part of the code based on current EMC develop branch for comparing the test results with the merged version.(#9) * Fixed several bugs in the code. * Modifications to SURFCE.f to check for existence of FFG files. * Bug fixes for FFG file existence check, and changes to handle rotated lat-lon grid interpolation for FFG * Bug fixes for FFG existence checks in SURFCE.f * Another bug fix for SURFCE.f * Updating XML and flat txt files to include a 65th vertical level to be consistent with updated FV3LAM model with higher model top. (#13) * Code cleanup for QPF - FFG comparison. Comparison put into subroutine. * Cleanup of SURFCE.f; moving the FFG comparisons into a subroutine. * Final cleanup of exceedance code for QPF vs FFG. * Removing some commented out variable declarations. * Additional cleanup recommended by Ming: we really only need two exceedance variables; one for 1h FFG and one for run total FFG exceedances. * Further cleanup of FFG code, simplifying to two fields (1h acc and run total acc) * Adding ARI comparison fields for 2y, 5y, 10y, and 100y ARIs. * Changes to output 9 soil levels from FV3LAM if we are running 9 level RUC LSM. * Adding flat txt file for UPP. * Commenting out the use of the ARI exceedances for now. We can switch them on later. * Bug fix in INITPOST_NETCDF.f : need to use both ncid2d and ncid3d in this subroutine! * Adding NOAA-GSL code changes on top of latest NOAA-EMC UPP. * Couple of bug fixes in NOAA-EMC code. Bugs were leading to PRMSL and -10C REFD being all zeroes. * Cleaning up code to get rid of unnecessary differences from EMC. * Putting all new GSL variables into EMC's unified post_avblflds.xml. Note that EMC's unified post_avblflds.xml does not validate using the avblflds Schema. * Updating postconfig-NT.txt file for GSL RRFS based on merged post_avblflds.xml file. * Adding RRFS control files to makefile. * Changing back scale for WEASD_ON_SURFACE to previous default, thanks to suggestion from Wen Meng. * Reverting name of cldfra based on feedback from Eric Aligo. * Reverting changes in fv3lam_post_avblflds.xml since GSL new variables are now included in post_avblflds.xml * Changing experimental ceiling level type from "ceiling" to "cloud_ceilng" * Updating 3drtma_postcntrl.xml with revised name for GSD_EXP_CEILING. This also affects postxconfig-NT-3drtma.txt. postxconfig-NT-fv3lam_rrfs.txt also changed due to changes in post_avblflds.xml * Introducing if statement for call of NGMSLP, to avoid calling unless it is needed. Co-authored-by: Ming.Hu <Ming.Hu@noaa.gov> Co-authored-by: Christina Holt <56881914+christinaholtNOAA@users.noreply.github.com> Co-authored-by: Christina Holt <Christina.Holt@noaa.gov> Co-authored-by: Jaymes Kenyon <jaymes.kenyon@noaa.gov> Co-authored-by: Samuel Trahan (NOAA contractor) <39415369+SamuelTrahanNOAA@users.noreply.github.com> * Doxygen for CALDWP.f * Further refinement. * Doxygen CALDRG.f (NOAA-EMC#424) * Doxygen for CALDRG.f * Delete CALDWP.f * Revert "Delete CALDWP.f" This reverts commit 575cd93. * Sync changes from UPP for GFSV16 (NOAA-EMC#422) * Add gtg code as submodule. * Remove manage_externals. * Sync with the changes from GFSV16. * Add change logs for POSTGRB2TBL default setting. * Disable recursive checkout on gtg code (NOAA-EMC#427) * add option to build with GTG code or stubs (NOAA-EMC#430) * add option to build with GTG code or stubs * make IP optional depending on GTG option. * GTG code depends on a file that only resides in the gtg repo * fix a big boo-boo * move sorc/post_gtg.fd to sorc/ncep_post.fd/post_gtg.fd and update build path to GTG * correct the name of the submodule. fix mixed indents * move map_routines.F90 into the GTG src list * Add options in build script (NOAA-EMC#435) * Add command line arguments in compile_upp.sh for options, e.g. building with gtg code, building with wrfio stub code, turning on cmake verbose. * Remove legacy GNU make capability. * Clean up legacy read interfaces (NOAA-EMC#437) * Remove read interfaces INITPOST_GFS_NEMS, INITPOST_GFS_NEMS_MPIIO and INITPOST_GFS_NMM. * Change linking order for w3nco and nemsio * Remove INITPOST_GFS_NETCDF * Remove INITPOST_GFS_NEMS.f, INITPOST_GFS_NETCDF.f, INITPOST_NEMS.f, INITPOST_NEMS_MPIIO.f from UPP code. * Fix build failture. * Clean up legacy makefile * Clean up another two makefiles * Add back INITPOST_GFS_NETCDF * Port UPP develop branch on wcoss2 (NOAA-EMC#439) * Add changes for WCOSS2 Acorn. * Add changes for Dogwood. * Add changes for WCOSS2. * Change modulefile on wcoss2 in LUA format based on Kate's comments. * Add machine recognition for cactus and WCOSS1 P3.5 based on Eric's comments * Exception handling if anl input not found (NOAA-EMC#443) (NOAA-EMC#444) * modified: scripts/exgdas_atmos_nceppost.sh * modified: scripts/exgfs_atmos_nceppost.sh * Update regional FV3 read interface with parallel netcdf read (NOAA-EMC#441) * Changes for parallel netcdf read for regional FV3 interface * Clean up debugging code * Replace small with the one defined in params_mod based on Huiya's comments. * Update documentation to reflect updates to develop (fortran namelist/RQSTFLD removal) (NOAA-EMC#445) * exec is selectable for executable directory (NOAA-EMC#448) * Doxygen for CALGUST (NOAA-EMC#451) * Doxygen for CALDRG.f * This is part of Issue NOAA-EMC#392 Fixes the doxygen warnings in CALGUST.f Please review this subroutine. Thank you. * The fix in CALUPDHEL.f (NOAA-EMC#458) * Modify CALUPDHEL.f for restricting undefined grids in computation. * Update VERSION to 10.0.12. * Bug fix for SLLEVEL bound issue when not RUC LSM (NOAA-EMC#463) Co-authored-by: Tracy <tracy.hertneky@noaa.gov> * Doxygen caldrg caldwcp calgust refinement (NOAA-EMC#464) * Further refinement to the tables and logs. * Further refinement to the tables and logs. (NOAA-EMC#455) * This is part of Issue NOAA-EMC#392 (NOAA-EMC#460) Fixes the doxygen warnings in CALHEL.f CALHEL2.f CALHEL3.f Please review this subroutine. Thank you. * Unify global and regional FV3 read interfaces (NOAA-EMC#453) * Unify the interfaces for reading FV3 outputs in netcdf. * Remove interface INITPOST_GFS_NETCDF_PARA. * Remove INITPOST_GFS_NETCDF.f. * Remove the capability of serial netcdf reading FV3 outputs. * Correct reading rswinc. * Remove duplication in CLDRAD.f. * Remove duplicated avgalbedo reading * Add changes for reading pwat from model. * Clean up commented out code * Clean up duplicated lines * Add ability to compile script to use non-intel compilers; add Cheyenne modulefiles for gnu and intel (NOAA-EMC#468) * Add cheyenne modulefile * Intel 19 --> 2021 * Add ability to specify compiler; move all existing modulefiles to ${name}_intel since they are all for intel compilers; add "cheyenne_gnu" modulefile * Revert move of intel modulefiles; now the implicit default for a modulefile is intel, only gnu and other compilers will have the compiler name appended to the modulefile * Allow for lua modulefiles with ".lua" appended * This is part of Issue NOAA-EMC#392 (NOAA-EMC#465) Fixes the doxygen warnings in CALLCL.f CALMCVG.f CALMICT.f * This is part of Issue NOAA-EMC#392 (NOAA-EMC#466) Fixes the doxygen warnings in CALPBL.f CALPBLREGIME.f CALPOT.f CALPW.f. * Doxygen in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. (NOAA-EMC#467) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. * Fixed typo. * Update to PR NOAA-EMC#458. * Doxygen in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f (NOAA-EMC#469) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f. * Fixed minor bug in CALVOR.f. * Update to PR#453. * More updates. * Doxygen in EXCH.f, FDLVL.f, FILL_PSETFLD.f, FRZLVL.f, and FRZLVL2.f. (NOAA-EMC#470) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in EXCH.f, FDLVL.f, FILL_PSETFLD.f, FRZLVL.f, and FRZLVL2.f. * Minor fix and Added new features from Ed's comments. * Format enhancement from Edward's comments. * Updated documentation. * Doxygen in GFSPOSTSIG.F NGMFLD.f OTLFT.f OTLIFT.f PARA_RANGE.f PROCESS.f and retrieve_index.f. (NOAA-EMC#477) * This is part of Issue NOAA-EMC#392. Fix the doxygen warnings in GFSPOSTSIG.F NGMFLD.f OTLFT.f OTLIFT.f PARA_RANGE.f PROCESS.f and retrieve_index.f. * Minor fix. * Update table for NGMFLD.f. * Doxygen in GET_BITS.f, GPVS.f, LFMFLD.f, LFMFLD_GFS.f, MDL2P.f, MDL2STD_P.f, MDL2THANDPV.f, and MSFPS.f. (NOAA-EMC#474) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in GET_BITS.f, GPVS.f, LFMFLD.f, LFMFLD_GFS.f, MDL2P.f, MDL2STD_P.f, MDL2THANDPV.f, and MSFPS.f. * Minor fix. * Doxygen in kinds_mod.F, native_endianness.f, UPP_MATH.f and UPP_PHYSICS.f. (NOAA-EMC#479) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in kinds_mod.F, native_endianness.f, UPP_MATH.f and UPP_PHYSICS.f. * Further enhancement from Ed's comment. * Bug fix in UPP build script on Catcus (NOAA-EMC#481) * Doxygen in SCLFLD.f SELECT_CHANNELS.f SET_OUTFLDS.f SETUP_SERVERS.f SMOOTH.f TRPAUS.f TRPAUS_NAM.f WETFRZLV.f WRFPOST.f and ZENSUN.f (NOAA-EMC#480) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in SCLFLD.f SELECT_CHANNELS.f SET_OUTFLDS.f SETUP_SERVERS.f SMOOTH.f TRPAUS.f TRPAUS_NAM.f WETFRZLV.f WRFPOST.f ZENSUN.f * Further enhancement from Ed's comment. * Update readme (NOAA-EMC#486) * Starting UPP version numbers with 10.0.0 for develop branch * Add codeowners file to develop * Update README * Formatting updates * update inline post supported applications * Additional updates to supported models Co-authored-by: Kate Fossell <you@example.com> * Doxygen in GFSPOST.F (NOAA-EMC#476) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in GFSPOST.F and GFSPOSTSIG.F. * Testing:revert GFSPOST.F * Testing: Revert GFSPOSTSIG.F and test GFSPOST.F only. * Convert list to a table. * Add more document. * Add more document. * Add more document. * Fixed indentation. * Minor fixes. * Further refinement from Ed's comment. * Doxygen in INITPOST.F, INITPOST_GFS_NEMS_MPIIO, INITPOST_NEMS.f and INITPOST_NETCDF.f. (NOAA-EMC#473) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in INITPOST.F, INITPOST_GFS_NEMS_MPIIO, INITPOST_NEMS.f and INITPOST_NETCDF.f. * Minor fix. * Minor fix. * Further refinement from Ed's comments. * Minor bug fix. * This is part of Issue NOAA-EMC#392. (NOAA-EMC#487) Fixes the doxygen warnings in BOUND.f. * fix a bug in AOD calculation (NOAA-EMC#489) * fixed a bug in AOD calculation * add mie aod and surface dust pm10 * remove enddo in line 5211 in CLDRAD.f * parm updates for dust pm10 * increment version of develop (NOAA-EMC#502) Co-authored-by: Kate Fossell <you@example.com> * Add camshe to codeowners for public docs and run script (NOAA-EMC#506) Co-authored-by: Kate Fossell <you@example.com> * Update gfs itag files for in-line post. (NOAA-EMC#508) * Merge release/public-v3 (NOAA-EMC#509) * run_upp script got the following updates: -updated directory name -updated executable path -added error message for binarynemsiompiio option -added netcdfpara option * Further refinement from Tracy's comment. * Minor fix. * More minor change from Tracy. * Link update from Tracy. * Documentation updates for release * minor updates based on comments * minor revisions to documentation * Increment version for public release * update informat - only netcdfpara * Removed netcdf option and rename GFS input file names. * Minor change. Co-authored-by: kayee <kayee.wong@noaa.gov> Co-authored-by: Tracy <hertneky@ucar.edu> Co-authored-by: Kate Fossell <you@example.com> * Documentation changes (NOAA-EMC#511) * Remove mention of Guassian grid for FV3 * Fix latest change to table * Remove app-specific tables * 2D Decomposition (NOAA-EMC#339) * Changes to support 2D Decomposition shape changes. Full I dimension remains in all arrays bu t SURFCE is altered to use isx:iex bounds which are equivalent to IM which is equivalent to 1:IM * test of commit only added one comment to PROCESS.f * comment test 2 * Added more routines to 2D decomposition * Changed isx and iex to ISTA and IEND in listed routines. ISTA had prior use in MDL2P.f and that needed changing. IEND had prior use in PARA_CONFIG, changed to IENDJ in PARA_CONFIG2 where needed PARA_CONFIG did not need changing * test commit of new base into clone * repair of a bunch of changed routines somehow corrupted by a merge 5/3/2021 * fixed 5/25 problem * added ctlblk change to support ista and iend partial I dimensons * added para_range2 to PARA_RANGE.f to support 2D decomposition * Modified MPI_FIRST.f to support a 2D decomposition but the actual numbers used remain the 1D special case and the changes just add two more indices for start and end I domains and logic to convert scatter counts and displacements to the product of the I and J subdomain sizes rather than I full domain x J subdomain. * Added support for halo settings of 2D boundaries i.e ista_2l to match the 1D analogs long present in the source 6/1/2021 * Added definitions for ista_2u, and ista_2u in MPI_FIRST.f * Reshaped arrays in MDL2FLD.f to support 2D decomposition. Modified TWO (only) loops to try thie * Remove TIMEF.f. * 20210702 JesseMeng modify MPI_FIRST.f MDLFLD.f for 2D decomposition * 20210706 BoCui modify INITPOST_GFS_NETCDF_PARA.f * 20210707 JesseMeng modified grib2_module.f for 2d decomposition * test version INITPOST_GFS_NETCDF_PARA.f * test version INITPOST_GFS_NETCDF_PARA.f and MPI_FIRST.f * 20210713 BoCui test INITPOST_GFS_NETCDF_PARA.f, MPI_FIRST.f and ALLOCATE_ALL.f * 20210713 BoCui test INITPOST_GFS_NETCDF_PARA.f, MPI_FIRST.f and ALLOCATE_ALL.f * 20210719 BoCui Modified CLDRAD.f for 2d decomposition * 20210816 Jesse Meng commit George's EXCH update for 1 layer 2D halos transforming * 20210816 Jesse Meng remove ifcore in EXCH * 20210903 Bo Cui update ALLOCATE_ALL.f after new merge from 'upstream/develop' * 20210903 Bo Cui Added new routines to 2D decomposition * 20210903 Jesse Meng fixed the ieql allocation bug in ALLOCATE_ALL.f * 20210904 Bo Cui fixed CLDRAD.f * 20210913 Jesse Meng commit progress of 2D decomposition * 20210917 Bo Cui add new routines to 2D decomposition * 20210917 Jesse Meng remove 4 legacy files * 20210917 Jesse Meng remove legacy code SLP_NMM EXCH2 * 20210917 Jesse Meng remove legacy code INITPOST_GFS_SIGIO.f INITPOST_GFS_NEMS.f * 20210917 Jesse Meng add INITPOST_GFS_NEMS.f back to avoid compiling error. * 20210930 Jesse Meng add George's itag/numx entry and progress on 2D decompose * 20211015 Jesse Meng progress on 2D DECOMPOSITION * 20211017 Bo Cui add new subroutines to UPP 2D decomposition * 20211026 Jesse Meng commit progress in 2D DECOMPOSITION * 20211026 Jesse Meng fix INITPOST_GFS_NETCDF_PARA.f for 2D DECOMPOSITION * 20211026 Jesse Meng update SURFCE.f for 2D DECOMPOSITION * 20211103 Jesse Meng commit progress of 2D DECOMPOSITION * 20211106 Bo Cui commit progress of 2D decomposition * 20211109 Jesse Meng updates for 2D DECOMPOSITION * 20211110 Jesse Meng updates in 2D DECOMPOSITION * 20211112 Jesse Meng updates for 2D DECOMPOSITION * 20211115 Jesse Meng updates for 2D DECOMPOSITION * 20211119 Jesse Meng updates for 2D DECOMPOSITION * 20211201 Jesse Meng move CALVOR to UPP_PHYSICS module; implement fullpole in MPI_FIRST * 20211202 Jesse Meng minor update of MPI_FIRST using mpi_allgatherv * 20211203 Jesse Meng implement fullpole in MDL2THANDPV and CALDIV * 20211207 Jesse Meng update MISCLN.f SURFCE.f * 20211208 Jesse Meng add parm/hafs_nosat files * 20211213 Bo Cui updates for 2D decomposition * 20211213 Jesse Meng update the merged 'upstream/develop' and 'post_2d_decomp' branch to 2d_decomp style * 20211215 Jesse Meng use i=0:im+1 for GFS in MPI_FIRST and EXCH * 20211216 Jesse Meng minor update UPP_PHYSICS for i=0:im+1 expansion * 20220104 Jesse Meng add George's minor fix in EXHC.f * 20220118 Jesse Meng commit George's cleaned up code. * 20220203 Jesse Meng - update MAPSSLP.f to be consistent with develop branch. * 20220222 Jesse Meng add checkcoords flag in EXCH.f to move around George's debug code. * 20220302 Jesse Meng Restrict computation from undefined grids * 20220304 Bo Cui Add a reset of numx=1 if remainder of num_procs/numx is not 0 * 20220310 Jesse Meng Add a reset of numx=1 if(numx>num_procs/2) * 20220322 Jesse Meng mpi_allgatherv change communicator to MPI_COMM_COMP * 20220328 Jesse Meng bug fix for passing 2d subarrays between subroutines * 20220328 Jesse Meng minor fix for CLDRAD call BOUND variable array size * 20220330 Jesse Meng fix cloud cover variabes full field collection in 2d decomp * 20220401 Jesse Meng minor fix for CALMCVG.f and update CALUPDHEL.f with develop * 20220414 BoCui sync and merge UPP/develop into post_2d_decomp (#7) * Added lambert conformal projection for FV3SAR and handled composite reflectivity correctly (#14) (#2) * exec is selectable for executable directory (NOAA-EMC#448) * Doxygen for CALGUST (NOAA-EMC#451) * Doxygen for CALDRG.f * This is part of Issue NOAA-EMC#392 Fixes the doxygen warnings in CALGUST.f Please review this subroutine. Thank you. * The fix in CALUPDHEL.f (NOAA-EMC#458) * Modify CALUPDHEL.f for restricting undefined grids in computation. * Update VERSION to 10.0.12. * Bug fix for SLLEVEL bound issue when not RUC LSM (NOAA-EMC#463) Co-authored-by: Tracy <tracy.hertneky@noaa.gov> * Doxygen caldrg caldwcp calgust refinement (NOAA-EMC#464) * Further refinement to the tables and logs. * Further refinement to the tables and logs. (NOAA-EMC#455) * This is part of Issue NOAA-EMC#392 (NOAA-EMC#460) Fixes the doxygen warnings in CALHEL.f CALHEL2.f CALHEL3.f Please review this subroutine. Thank you. * Unify global and regional FV3 read interfaces (NOAA-EMC#453) * Unify the interfaces for reading FV3 outputs in netcdf. * Remove interface INITPOST_GFS_NETCDF_PARA. * Remove INITPOST_GFS_NETCDF.f. * Remove the capability of serial netcdf reading FV3 outputs. * Correct reading rswinc. * Remove duplication in CLDRAD.f. * Remove duplicated avgalbedo reading * Add changes for reading pwat from model. * Clean up commented out code * Clean up duplicated lines * Add ability to compile script to use non-intel compilers; add Cheyenne modulefiles for gnu and intel (NOAA-EMC#468) * Add cheyenne modulefile * Intel 19 --> 2021 * Add ability to specify compiler; move all existing modulefiles to ${name}_intel since they are all for intel compilers; add "cheyenne_gnu" modulefile * Revert move of intel modulefiles; now the implicit default for a modulefile is intel, only gnu and other compilers will have the compiler name appended to the modulefile * Allow for lua modulefiles with ".lua" appended * This is part of Issue NOAA-EMC#392 (NOAA-EMC#465) Fixes the doxygen warnings in CALLCL.f CALMCVG.f CALMICT.f * This is part of Issue NOAA-EMC#392 (NOAA-EMC#466) Fixes the doxygen warnings in CALPBL.f CALPBLREGIME.f CALPOT.f CALPW.f. * Doxygen in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. (NOAA-EMC#467) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. * Fixed typo. * Update to PR NOAA-EMC#458. * Doxygen in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f (NOAA-EMC#469) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f. * Fixed minor bug in CALVOR.f. * Update to PR#453. * More updates. * 20220411 Bo Cui 2D decompositio CALVOR.f and INITPOST_NETCDF.f * 20220411 Bo Cui update doxgen and global and regional FV3 read interface * 20220414 Bo Cui: remove read_netcdf_2d_scatter and read_netcdf_3d_scatter from INITPOST_NETCDF.f * 20220415 Bo Cui delete CALVOR.f, add exch of gdlon in INITPOST_NETCDF.f * 20220421 Bo Cui Doxygen in UPP_PHYSICS.f,add restriction run 2D decomp only for GFS/FV3R in WRFPOST.f Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: Wen Meng <wen.meng@noaa.gov> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: kayeekayee <kayee.wong@noaa.gov> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> * 20220502 Bo Cui code cleanup * 20220512 Jesse Meng minor fix for INITPOST_GFS_NEMS_MPIIO.f calling EXCH * 20220525 Jesse Meng minor fix to 2d_decomp syntax * Update VERSION to 11.0.0 * 20220607 Jesse Meng add variable declaration block in PARA_RANGE.f * 20220608 Jesse Meng remove blank spaces in sorc/ncep_post.fd/AllGETHERV_GSD.f * Add 2D decomp overview documentation (#6) * Add 2D decomp overview documentation * Update 2D overview Co-authored-by: George Vandenberghe <George.Vandenberghe@noaa.gov> Co-authored-by: wx15gv <George.Vandenberghe@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a1.ncep.noaa.gov> Co-authored-by: Bo Cui <Bo.Cui@noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a2.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a2.ncep.noaa.gov> Co-authored-by: Jesse.Meng <Jesse.Meng@noaa.gov> Co-authored-by: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: kayeekayee <kayee.wong@noaa.gov> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> Co-authored-by: Jesse Meng <jmeng@Orion-login-4.HPC.MsState.Edu> Co-authored-by: Kate Fossell <fossell@ucar.edu> * Fix for absv computation in RRFS (NOAA-EMC#516) * read in dx/dy instead of calculating them (NOAA-EMC#523) * read in dx/dy instead of caculating them * add the change log for dxdy code change * change 2011 to 2022 in the change log * Upgrade intel/impi version to 2022.1.2 on Hera and Orion (NOAA-EMC#527) * Update modulefiles on hera. * tweaking hera.lua * Update modulefile on orion * add spack-based ci. (NOAA-EMC#528) * add spack-based ci. replace dependency on w3nco with w3emc. Update w3emc to 2.9.2 on all machines (wcoss2 is already at 2.9.2) * remove deprecated hera and orion env. modulefiles * update nemsio version to 2.5.4. Flush cache * First attempt to add RRFS_dev development on top of latest EMC develop branch * Geting rid of unnecesary changes in MISCLN.f * Making reading in of wet1 consistent with new netcdf parallel read. * Updating fix files. * Bringing in the latest EMC develop branch. * Cosmetic changes to be consistent with EMC's develop branch Co-authored-by: Ming.Hu <Ming.Hu@noaa.gov> Co-authored-by: Christina Holt <56881914+christinaholtNOAA@users.noreply.github.com> Co-authored-by: Christina Holt <Christina.Holt@noaa.gov> Co-authored-by: Jaymes Kenyon <jaymes.kenyon@noaa.gov> Co-authored-by: Samuel Trahan (NOAA contractor) <39415369+SamuelTrahanNOAA@users.noreply.github.com> Co-authored-by: kayee <kayee.wong@noaa.gov> Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> Co-authored-by: Kate Fossell <fossell@ucar.edu> Co-authored-by: Kate Fossell <you@example.com> Co-authored-by: lipan-NOAA <li.pan@noaa.gov> Co-authored-by: Tracy <hertneky@ucar.edu> Co-authored-by: George Vandenberghe <George.Vandenberghe@noaa.gov> Co-authored-by: wx15gv <George.Vandenberghe@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a1.ncep.noaa.gov> Co-authored-by: Bo Cui <Bo.Cui@noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a2.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a2.ncep.noaa.gov> Co-authored-by: Jesse.Meng <Jesse.Meng@noaa.gov> Co-authored-by: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com> Co-authored-by: Jesse Meng <jmeng@Orion-login-4.HPC.MsState.Edu> Co-authored-by: LinZhu-NOAA <lin.l.zhu@noaa.gov>
EricJames-NOAA
added a commit
to NOAA-GSL/UPP
that referenced
this issue
Sep 14, 2022
* Connect to IFI * Correct CAPE&CIN calculations * Changes to get IFI working. * NOAA GSL UPP updates (NOAA-EMC#413) * Turn on GSD cloud ceiling calculation for RRFS dev. * Updates to UPP for RRFS applications (#3) * Updates to UPP for RRFS applications: 1) Adding a RRFS-specific .xml control file and a corresponding .txt flat file. Note that script changes (pending) are needed to leverage the new flat file. However, this code will work in current real-time configurations. 2) Adding GSL experimental ceiling diagnostics, GSL visibility diagnostic, and GSL sea-level pressure reduction (MAPS). Also adding TKE and aerosol number concentrations. 3) Code clean-up for ceiling-related diagnostics; added comments, etc. 4) Removing several non-needed variables, originally inherited from FV3-SAR community configuration. * Updating UPP control files to specify GRIB2 generating center as "noaa_fsl_boulder" and the generating process as "hrrr". The "hrrr" specification is temporary, and will eventually be switched to "rrfs" once required changes to the "NCEPLIBS-g2tmpl" library are available. (#4) * Fix some out-of-bounds reads that caused the RRFS UPP to crash. (#5) * Adding README file (#7) * Adding README file to describe process of making a "flat" file. * Updates to README to improve explanation of input/output files. * Code to read in Flash Flood Guidance (FFG) and Average Recurrence Interval (ARI) precipitation datasets for comparison with model QPF within UPP. * Fixed a syntax error in SURFCE.f * Getting rid of GRIB1 output option to be consistent with rest of code. * Changing field numbers to avoid conflict with existing RRFS-dev1 fields. * Putting exceedance grids in flat files for testing in RRFS UPP. * Corrected the 1h and run total precip names for calculating exceedances in SURFCE.f * Bug fix in SURFCE.f if statements. * Removing changes to RQSTFLD.F since GRIB1 is no longer used in UPP. * Merging NOAA-GSL development on top of NOAA-EMC UPP for testing. * Correcting minor typos in SURFCE.f to allow testing. * Update code based on testing with RRFS cases. * Update part of the code based on current EMC develop branch for comparing the test results with the merged version.(#9) * Fixed several bugs in the code. * Modifications to SURFCE.f to check for existence of FFG files. * Bug fixes for FFG file existence check, and changes to handle rotated lat-lon grid interpolation for FFG * Bug fixes for FFG existence checks in SURFCE.f * Another bug fix for SURFCE.f * Updating XML and flat txt files to include a 65th vertical level to be consistent with updated FV3LAM model with higher model top. (#13) * Code cleanup for QPF - FFG comparison. Comparison put into subroutine. * Cleanup of SURFCE.f; moving the FFG comparisons into a subroutine. * Final cleanup of exceedance code for QPF vs FFG. * Removing some commented out variable declarations. * Additional cleanup recommended by Ming: we really only need two exceedance variables; one for 1h FFG and one for run total FFG exceedances. * Further cleanup of FFG code, simplifying to two fields (1h acc and run total acc) * Adding ARI comparison fields for 2y, 5y, 10y, and 100y ARIs. * Changes to output 9 soil levels from FV3LAM if we are running 9 level RUC LSM. * Adding flat txt file for UPP. * Commenting out the use of the ARI exceedances for now. We can switch them on later. * Bug fix in INITPOST_NETCDF.f : need to use both ncid2d and ncid3d in this subroutine! * Adding NOAA-GSL code changes on top of latest NOAA-EMC UPP. * Couple of bug fixes in NOAA-EMC code. Bugs were leading to PRMSL and -10C REFD being all zeroes. * Cleaning up code to get rid of unnecessary differences from EMC. * Putting all new GSL variables into EMC's unified post_avblflds.xml. Note that EMC's unified post_avblflds.xml does not validate using the avblflds Schema. * Updating postconfig-NT.txt file for GSL RRFS based on merged post_avblflds.xml file. * Adding RRFS control files to makefile. * Changing back scale for WEASD_ON_SURFACE to previous default, thanks to suggestion from Wen Meng. * Reverting name of cldfra based on feedback from Eric Aligo. * Reverting changes in fv3lam_post_avblflds.xml since GSL new variables are now included in post_avblflds.xml * Changing experimental ceiling level type from "ceiling" to "cloud_ceilng" * Updating 3drtma_postcntrl.xml with revised name for GSD_EXP_CEILING. This also affects postxconfig-NT-3drtma.txt. postxconfig-NT-fv3lam_rrfs.txt also changed due to changes in post_avblflds.xml * Introducing if statement for call of NGMSLP, to avoid calling unless it is needed. Co-authored-by: Ming.Hu <Ming.Hu@noaa.gov> Co-authored-by: Christina Holt <56881914+christinaholtNOAA@users.noreply.github.com> Co-authored-by: Christina Holt <Christina.Holt@noaa.gov> Co-authored-by: Jaymes Kenyon <jaymes.kenyon@noaa.gov> Co-authored-by: Samuel Trahan (NOAA contractor) <39415369+SamuelTrahanNOAA@users.noreply.github.com> * Doxygen for CALDWP.f * Further refinement. * Doxygen CALDRG.f (NOAA-EMC#424) * Doxygen for CALDRG.f * Delete CALDWP.f * Revert "Delete CALDWP.f" This reverts commit 575cd93. * Sync changes from UPP for GFSV16 (NOAA-EMC#422) * Add gtg code as submodule. * Remove manage_externals. * Sync with the changes from GFSV16. * Add change logs for POSTGRB2TBL default setting. * Disable recursive checkout on gtg code (NOAA-EMC#427) * add option to build with GTG code or stubs (NOAA-EMC#430) * add option to build with GTG code or stubs * make IP optional depending on GTG option. * GTG code depends on a file that only resides in the gtg repo * fix a big boo-boo * move sorc/post_gtg.fd to sorc/ncep_post.fd/post_gtg.fd and update build path to GTG * correct the name of the submodule. fix mixed indents * move map_routines.F90 into the GTG src list * Add options in build script (NOAA-EMC#435) * Add command line arguments in compile_upp.sh for options, e.g. building with gtg code, building with wrfio stub code, turning on cmake verbose. * Remove legacy GNU make capability. * Clean up legacy read interfaces (NOAA-EMC#437) * Remove read interfaces INITPOST_GFS_NEMS, INITPOST_GFS_NEMS_MPIIO and INITPOST_GFS_NMM. * Change linking order for w3nco and nemsio * Remove INITPOST_GFS_NETCDF * Remove INITPOST_GFS_NEMS.f, INITPOST_GFS_NETCDF.f, INITPOST_NEMS.f, INITPOST_NEMS_MPIIO.f from UPP code. * Fix build failture. * Clean up legacy makefile * Clean up another two makefiles * Add back INITPOST_GFS_NETCDF * Port UPP develop branch on wcoss2 (NOAA-EMC#439) * Add changes for WCOSS2 Acorn. * Add changes for Dogwood. * Add changes for WCOSS2. * Change modulefile on wcoss2 in LUA format based on Kate's comments. * Add machine recognition for cactus and WCOSS1 P3.5 based on Eric's comments * Connect to latest version of libIFI, but in an ugly way. Also, this is sending the wrong CAPE, CIN, and APCP * Exception handling if anl input not found (NOAA-EMC#443) (NOAA-EMC#444) * modified: scripts/exgdas_atmos_nceppost.sh * modified: scripts/exgfs_atmos_nceppost.sh * Update regional FV3 read interface with parallel netcdf read (NOAA-EMC#441) * Changes for parallel netcdf read for regional FV3 interface * Clean up debugging code * Replace small with the one defined in params_mod based on Huiya's comments. * Update documentation to reflect updates to develop (fortran namelist/RQSTFLD removal) (NOAA-EMC#445) * Output libIFI-style diagnostic NetCDF files on full grid instead of per-rank. * exec is selectable for executable directory (NOAA-EMC#448) * Send the right CAPE, CIN, and APCP to libIFI * IFI connection: disable smoothing and precision drop. Add more diagnostic output. All results match standalone program. * IFI smoother works in MPI * Doxygen for CALGUST (NOAA-EMC#451) * Doxygen for CALDRG.f * This is part of Issue NOAA-EMC#392 Fixes the doxygen warnings in CALGUST.f Please review this subroutine. Thank you. * The fix in CALUPDHEL.f (NOAA-EMC#458) * Modify CALUPDHEL.f for restricting undefined grids in computation. * Update VERSION to 10.0.12. * Bug fix for SLLEVEL bound issue when not RUC LSM (NOAA-EMC#463) Co-authored-by: Tracy <tracy.hertneky@noaa.gov> * Doxygen caldrg caldwcp calgust refinement (NOAA-EMC#464) * Further refinement to the tables and logs. * Further refinement to the tables and logs. (NOAA-EMC#455) * This is part of Issue NOAA-EMC#392 (NOAA-EMC#460) Fixes the doxygen warnings in CALHEL.f CALHEL2.f CALHEL3.f Please review this subroutine. Thank you. * Unify global and regional FV3 read interfaces (NOAA-EMC#453) * Unify the interfaces for reading FV3 outputs in netcdf. * Remove interface INITPOST_GFS_NETCDF_PARA. * Remove INITPOST_GFS_NETCDF.f. * Remove the capability of serial netcdf reading FV3 outputs. * Correct reading rswinc. * Remove duplication in CLDRAD.f. * Remove duplicated avgalbedo reading * Add changes for reading pwat from model. * Clean up commented out code * Clean up duplicated lines * Add ability to compile script to use non-intel compilers; add Cheyenne modulefiles for gnu and intel (NOAA-EMC#468) * Add cheyenne modulefile * Intel 19 --> 2021 * Add ability to specify compiler; move all existing modulefiles to ${name}_intel since they are all for intel compilers; add "cheyenne_gnu" modulefile * Revert move of intel modulefiles; now the implicit default for a modulefile is intel, only gnu and other compilers will have the compiler name appended to the modulefile * Allow for lua modulefiles with ".lua" appended * This is part of Issue NOAA-EMC#392 (NOAA-EMC#465) Fixes the doxygen warnings in CALLCL.f CALMCVG.f CALMICT.f * This is part of Issue NOAA-EMC#392 (NOAA-EMC#466) Fixes the doxygen warnings in CALPBL.f CALPBLREGIME.f CALPOT.f CALPW.f. * Doxygen in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. (NOAA-EMC#467) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. * Fixed typo. * Update to PR NOAA-EMC#458. * Doxygen in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f (NOAA-EMC#469) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f. * Fixed minor bug in CALVOR.f. * Update to PR#453. * More updates. * Doxygen in EXCH.f, FDLVL.f, FILL_PSETFLD.f, FRZLVL.f, and FRZLVL2.f. (NOAA-EMC#470) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in EXCH.f, FDLVL.f, FILL_PSETFLD.f, FRZLVL.f, and FRZLVL2.f. * Minor fix and Added new features from Ed's comments. * Format enhancement from Edward's comments. * Updated documentation. * Doxygen in GFSPOSTSIG.F NGMFLD.f OTLFT.f OTLIFT.f PARA_RANGE.f PROCESS.f and retrieve_index.f. (NOAA-EMC#477) * This is part of Issue NOAA-EMC#392. Fix the doxygen warnings in GFSPOSTSIG.F NGMFLD.f OTLFT.f OTLIFT.f PARA_RANGE.f PROCESS.f and retrieve_index.f. * Minor fix. * Update table for NGMFLD.f. * Doxygen in GET_BITS.f, GPVS.f, LFMFLD.f, LFMFLD_GFS.f, MDL2P.f, MDL2STD_P.f, MDL2THANDPV.f, and MSFPS.f. (NOAA-EMC#474) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in GET_BITS.f, GPVS.f, LFMFLD.f, LFMFLD_GFS.f, MDL2P.f, MDL2STD_P.f, MDL2THANDPV.f, and MSFPS.f. * Minor fix. * Doxygen in kinds_mod.F, native_endianness.f, UPP_MATH.f and UPP_PHYSICS.f. (NOAA-EMC#479) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in kinds_mod.F, native_endianness.f, UPP_MATH.f and UPP_PHYSICS.f. * Further enhancement from Ed's comment. * Bug fix in UPP build script on Catcus (NOAA-EMC#481) * Doxygen in SCLFLD.f SELECT_CHANNELS.f SET_OUTFLDS.f SETUP_SERVERS.f SMOOTH.f TRPAUS.f TRPAUS_NAM.f WETFRZLV.f WRFPOST.f and ZENSUN.f (NOAA-EMC#480) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in SCLFLD.f SELECT_CHANNELS.f SET_OUTFLDS.f SETUP_SERVERS.f SMOOTH.f TRPAUS.f TRPAUS_NAM.f WETFRZLV.f WRFPOST.f ZENSUN.f * Further enhancement from Ed's comment. * Update readme (NOAA-EMC#486) * Starting UPP version numbers with 10.0.0 for develop branch * Add codeowners file to develop * Update README * Formatting updates * update inline post supported applications * Additional updates to supported models Co-authored-by: Kate Fossell <you@example.com> * Doxygen in GFSPOST.F (NOAA-EMC#476) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in GFSPOST.F and GFSPOSTSIG.F. * Testing:revert GFSPOST.F * Testing: Revert GFSPOSTSIG.F and test GFSPOST.F only. * Convert list to a table. * Add more document. * Add more document. * Add more document. * Fixed indentation. * Minor fixes. * Further refinement from Ed's comment. * Doxygen in INITPOST.F, INITPOST_GFS_NEMS_MPIIO, INITPOST_NEMS.f and INITPOST_NETCDF.f. (NOAA-EMC#473) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in INITPOST.F, INITPOST_GFS_NEMS_MPIIO, INITPOST_NEMS.f and INITPOST_NETCDF.f. * Minor fix. * Minor fix. * Further refinement from Ed's comments. * Minor bug fix. * This is part of Issue NOAA-EMC#392. (NOAA-EMC#487) Fixes the doxygen warnings in BOUND.f. * fix a bug in AOD calculation (NOAA-EMC#489) * fixed a bug in AOD calculation * add mie aod and surface dust pm10 * remove enddo in line 5211 in CLDRAD.f * parm updates for dust pm10 * increment version of develop (NOAA-EMC#502) Co-authored-by: Kate Fossell <you@example.com> * Add camshe to codeowners for public docs and run script (NOAA-EMC#506) Co-authored-by: Kate Fossell <you@example.com> * Update gfs itag files for in-line post. (NOAA-EMC#508) * Merge release/public-v3 (NOAA-EMC#509) * run_upp script got the following updates: -updated directory name -updated executable path -added error message for binarynemsiompiio option -added netcdfpara option * Further refinement from Tracy's comment. * Minor fix. * More minor change from Tracy. * Link update from Tracy. * Documentation updates for release * minor updates based on comments * minor revisions to documentation * Increment version for public release * update informat - only netcdfpara * Removed netcdf option and rename GFS input file names. * Minor change. Co-authored-by: kayee <kayee.wong@noaa.gov> Co-authored-by: Tracy <hertneky@ucar.edu> Co-authored-by: Kate Fossell <you@example.com> * Documentation changes (NOAA-EMC#511) * Remove mention of Guassian grid for FV3 * Fix latest change to table * Remove app-specific tables * 2D Decomposition (NOAA-EMC#339) * Changes to support 2D Decomposition shape changes. Full I dimension remains in all arrays bu t SURFCE is altered to use isx:iex bounds which are equivalent to IM which is equivalent to 1:IM * test of commit only added one comment to PROCESS.f * comment test 2 * Added more routines to 2D decomposition * Changed isx and iex to ISTA and IEND in listed routines. ISTA had prior use in MDL2P.f and that needed changing. IEND had prior use in PARA_CONFIG, changed to IENDJ in PARA_CONFIG2 where needed PARA_CONFIG did not need changing * test commit of new base into clone * repair of a bunch of changed routines somehow corrupted by a merge 5/3/2021 * fixed 5/25 problem * added ctlblk change to support ista and iend partial I dimensons * added para_range2 to PARA_RANGE.f to support 2D decomposition * Modified MPI_FIRST.f to support a 2D decomposition but the actual numbers used remain the 1D special case and the changes just add two more indices for start and end I domains and logic to convert scatter counts and displacements to the product of the I and J subdomain sizes rather than I full domain x J subdomain. * Added support for halo settings of 2D boundaries i.e ista_2l to match the 1D analogs long present in the source 6/1/2021 * Added definitions for ista_2u, and ista_2u in MPI_FIRST.f * Reshaped arrays in MDL2FLD.f to support 2D decomposition. Modified TWO (only) loops to try thie * Remove TIMEF.f. * 20210702 JesseMeng modify MPI_FIRST.f MDLFLD.f for 2D decomposition * 20210706 BoCui modify INITPOST_GFS_NETCDF_PARA.f * 20210707 JesseMeng modified grib2_module.f for 2d decomposition * test version INITPOST_GFS_NETCDF_PARA.f * test version INITPOST_GFS_NETCDF_PARA.f and MPI_FIRST.f * 20210713 BoCui test INITPOST_GFS_NETCDF_PARA.f, MPI_FIRST.f and ALLOCATE_ALL.f * 20210713 BoCui test INITPOST_GFS_NETCDF_PARA.f, MPI_FIRST.f and ALLOCATE_ALL.f * 20210719 BoCui Modified CLDRAD.f for 2d decomposition * 20210816 Jesse Meng commit George's EXCH update for 1 layer 2D halos transforming * 20210816 Jesse Meng remove ifcore in EXCH * 20210903 Bo Cui update ALLOCATE_ALL.f after new merge from 'upstream/develop' * 20210903 Bo Cui Added new routines to 2D decomposition * 20210903 Jesse Meng fixed the ieql allocation bug in ALLOCATE_ALL.f * 20210904 Bo Cui fixed CLDRAD.f * 20210913 Jesse Meng commit progress of 2D decomposition * 20210917 Bo Cui add new routines to 2D decomposition * 20210917 Jesse Meng remove 4 legacy files * 20210917 Jesse Meng remove legacy code SLP_NMM EXCH2 * 20210917 Jesse Meng remove legacy code INITPOST_GFS_SIGIO.f INITPOST_GFS_NEMS.f * 20210917 Jesse Meng add INITPOST_GFS_NEMS.f back to avoid compiling error. * 20210930 Jesse Meng add George's itag/numx entry and progress on 2D decompose * 20211015 Jesse Meng progress on 2D DECOMPOSITION * 20211017 Bo Cui add new subroutines to UPP 2D decomposition * 20211026 Jesse Meng commit progress in 2D DECOMPOSITION * 20211026 Jesse Meng fix INITPOST_GFS_NETCDF_PARA.f for 2D DECOMPOSITION * 20211026 Jesse Meng update SURFCE.f for 2D DECOMPOSITION * 20211103 Jesse Meng commit progress of 2D DECOMPOSITION * 20211106 Bo Cui commit progress of 2D decomposition * 20211109 Jesse Meng updates for 2D DECOMPOSITION * 20211110 Jesse Meng updates in 2D DECOMPOSITION * 20211112 Jesse Meng updates for 2D DECOMPOSITION * 20211115 Jesse Meng updates for 2D DECOMPOSITION * 20211119 Jesse Meng updates for 2D DECOMPOSITION * 20211201 Jesse Meng move CALVOR to UPP_PHYSICS module; implement fullpole in MPI_FIRST * 20211202 Jesse Meng minor update of MPI_FIRST using mpi_allgatherv * 20211203 Jesse Meng implement fullpole in MDL2THANDPV and CALDIV * 20211207 Jesse Meng update MISCLN.f SURFCE.f * 20211208 Jesse Meng add parm/hafs_nosat files * 20211213 Bo Cui updates for 2D decomposition * 20211213 Jesse Meng update the merged 'upstream/develop' and 'post_2d_decomp' branch to 2d_decomp style * 20211215 Jesse Meng use i=0:im+1 for GFS in MPI_FIRST and EXCH * 20211216 Jesse Meng minor update UPP_PHYSICS for i=0:im+1 expansion * 20220104 Jesse Meng add George's minor fix in EXHC.f * 20220118 Jesse Meng commit George's cleaned up code. * 20220203 Jesse Meng - update MAPSSLP.f to be consistent with develop branch. * 20220222 Jesse Meng add checkcoords flag in EXCH.f to move around George's debug code. * 20220302 Jesse Meng Restrict computation from undefined grids * 20220304 Bo Cui Add a reset of numx=1 if remainder of num_procs/numx is not 0 * 20220310 Jesse Meng Add a reset of numx=1 if(numx>num_procs/2) * 20220322 Jesse Meng mpi_allgatherv change communicator to MPI_COMM_COMP * 20220328 Jesse Meng bug fix for passing 2d subarrays between subroutines * 20220328 Jesse Meng minor fix for CLDRAD call BOUND variable array size * 20220330 Jesse Meng fix cloud cover variabes full field collection in 2d decomp * 20220401 Jesse Meng minor fix for CALMCVG.f and update CALUPDHEL.f with develop * 20220414 BoCui sync and merge UPP/develop into post_2d_decomp (#7) * Added lambert conformal projection for FV3SAR and handled composite reflectivity correctly (#14) (#2) * exec is selectable for executable directory (NOAA-EMC#448) * Doxygen for CALGUST (NOAA-EMC#451) * Doxygen for CALDRG.f * This is part of Issue NOAA-EMC#392 Fixes the doxygen warnings in CALGUST.f Please review this subroutine. Thank you. * The fix in CALUPDHEL.f (NOAA-EMC#458) * Modify CALUPDHEL.f for restricting undefined grids in computation. * Update VERSION to 10.0.12. * Bug fix for SLLEVEL bound issue when not RUC LSM (NOAA-EMC#463) Co-authored-by: Tracy <tracy.hertneky@noaa.gov> * Doxygen caldrg caldwcp calgust refinement (NOAA-EMC#464) * Further refinement to the tables and logs. * Further refinement to the tables and logs. (NOAA-EMC#455) * This is part of Issue NOAA-EMC#392 (NOAA-EMC#460) Fixes the doxygen warnings in CALHEL.f CALHEL2.f CALHEL3.f Please review this subroutine. Thank you. * Unify global and regional FV3 read interfaces (NOAA-EMC#453) * Unify the interfaces for reading FV3 outputs in netcdf. * Remove interface INITPOST_GFS_NETCDF_PARA. * Remove INITPOST_GFS_NETCDF.f. * Remove the capability of serial netcdf reading FV3 outputs. * Correct reading rswinc. * Remove duplication in CLDRAD.f. * Remove duplicated avgalbedo reading * Add changes for reading pwat from model. * Clean up commented out code * Clean up duplicated lines * Add ability to compile script to use non-intel compilers; add Cheyenne modulefiles for gnu and intel (NOAA-EMC#468) * Add cheyenne modulefile * Intel 19 --> 2021 * Add ability to specify compiler; move all existing modulefiles to ${name}_intel since they are all for intel compilers; add "cheyenne_gnu" modulefile * Revert move of intel modulefiles; now the implicit default for a modulefile is intel, only gnu and other compilers will have the compiler name appended to the modulefile * Allow for lua modulefiles with ".lua" appended * This is part of Issue NOAA-EMC#392 (NOAA-EMC#465) Fixes the doxygen warnings in CALLCL.f CALMCVG.f CALMICT.f * This is part of Issue NOAA-EMC#392 (NOAA-EMC#466) Fixes the doxygen warnings in CALPBL.f CALPBLREGIME.f CALPOT.f CALPW.f. * Doxygen in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. (NOAA-EMC#467) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALRAD_WCLOUD_newcrtm.f CALRCH.f CALSTRM.f CALTAU.f CALTHTE.f CALUPDHEL.f. * Fixed typo. * Update to PR NOAA-EMC#458. * Doxygen in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f (NOAA-EMC#469) * This is part of Issue NOAA-EMC#392. Fixes the doxygen warnings in CALVOR.f, CALWXT_BOURG.f, CLDRAD.f, COLLECT.f, COLLECT_LOC.f, DEALLOCATE.f, and DEALLOCATE.f. * Fixed minor bug in CALVOR.f. * Update to PR#453. * More updates. * 20220411 Bo Cui 2D decompositio CALVOR.f and INITPOST_NETCDF.f * 20220411 Bo Cui update doxgen and global and regional FV3 read interface * 20220414 Bo Cui: remove read_netcdf_2d_scatter and read_netcdf_3d_scatter from INITPOST_NETCDF.f * 20220415 Bo Cui delete CALVOR.f, add exch of gdlon in INITPOST_NETCDF.f * 20220421 Bo Cui Doxygen in UPP_PHYSICS.f,add restriction run 2D decomp only for GFS/FV3R in WRFPOST.f Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: Wen Meng <wen.meng@noaa.gov> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: kayeekayee <kayee.wong@noaa.gov> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> * 20220502 Bo Cui code cleanup * 20220512 Jesse Meng minor fix for INITPOST_GFS_NEMS_MPIIO.f calling EXCH * 20220525 Jesse Meng minor fix to 2d_decomp syntax * Update VERSION to 11.0.0 * 20220607 Jesse Meng add variable declaration block in PARA_RANGE.f * 20220608 Jesse Meng remove blank spaces in sorc/ncep_post.fd/AllGETHERV_GSD.f * Add 2D decomp overview documentation (#6) * Add 2D decomp overview documentation * Update 2D overview Co-authored-by: George Vandenberghe <George.Vandenberghe@noaa.gov> Co-authored-by: wx15gv <George.Vandenberghe@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a1.ncep.noaa.gov> Co-authored-by: Bo Cui <Bo.Cui@noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a2.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a2.ncep.noaa.gov> Co-authored-by: Jesse.Meng <Jesse.Meng@noaa.gov> Co-authored-by: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: kayeekayee <kayee.wong@noaa.gov> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> Co-authored-by: Jesse Meng <jmeng@Orion-login-4.HPC.MsState.Edu> Co-authored-by: Kate Fossell <fossell@ucar.edu> * Fix for absv computation in RRFS (NOAA-EMC#516) * read in dx/dy instead of calculating them (NOAA-EMC#523) * read in dx/dy instead of caculating them * add the change log for dxdy code change * change 2011 to 2022 in the change log * Upgrade intel/impi version to 2022.1.2 on Hera and Orion (NOAA-EMC#527) * Update modulefiles on hera. * tweaking hera.lua * Update modulefile on orion * add spack-based ci. (NOAA-EMC#528) * add spack-based ci. replace dependency on w3nco with w3emc. Update w3emc to 2.9.2 on all machines (wcoss2 is already at 2.9.2) * remove deprecated hera and orion env. modulefiles * update nemsio version to 2.5.4. Flush cache * Without IFI, output missing values for IFI fields. If IFI is requested and missing, build anyway. * delete old file RQSTFLD.F * bug fixes to get IFI to run * First attempt to add RRFS_dev development on top of latest EMC develop branch * Geting rid of unnecesary changes in MISCLN.f * Making reading in of wet1 consistent with new netcdf parallel read. * Output lat/lon on four corner points of rotated lat-lon grids in text file (NOAA-EMC#531) * Output lat/lon on four corner points of rotated lat-lon grids in text file. * Further modification * add forecast hour in file name convention * read model top outgoing longwave (NOAA-EMC#534) * Updating fix files. * IFI works 2D * Missing value in ifi debug files & some logging * missing EXCH_c_float.f file * double-specified access specification * fix two syntax errors (missing <0) * Build with IFI by default, if it is present. * bug fixes for build and namelist reporting * disable ifi by default * Add c++ linker flags * current rrfs parallel xml from eric * Make sam_fv3lam_rrfs.xml and sam_post_avblflds.xml copies of eric_fv3lam_rrfs.xml and eric_post_avblflds.xml with IFI fields. * Remove some # lines that confuse intel * try 2 at an rrfs txt * Deallocate all allocated arrays (NOAA-EMC#538) * Bug fix in tcdc on isobaric levels (NOAA-EMC#540) * Restrict undefined points involved in rounding cloud faction uppper and lower bounds * tweaking changes * add a change for underground points * Remove comment line * Move ifi fields to fv3lam_post_avblflds.xml&fv3lam_rrfs.xml * txt version of fv3lam rrfs file * switch to post_avblflds.xml for making postxconfig-NT-fv3lam_rrfs.txt * correct name of ifi grib file * calculate CAPE&CIN when only outputting IFI fields * Bug fixes to allow IFI fields to be generated when nothing else is requested * add ifi fields to fv3lam xml & txt files * remove cpp directives from a file that is not passed through cpp * -i flag to compile ifi * Missing IGET(ient)>0 check in IFI.F caused crashes * Bug fixes for when IFI is completely or partially disabled * safeguard against out-of-bounds access in UPP_PHYSICS.f * compile_upp.sh -i can compile with libIFI on hera * Fix an out-of-bounds access in CALCAPE2 (NOAA-EMC#555) * Eliminate out-of-bounds access in CALCAPE2 with extreme atmospheric conditions * Author note update for CALCAPE2 * out-of-bounds access in interpolation in MDL2SIGMA * add intel compiler checks in debug mode: bounds, pointers, shape, stack, uninit * IFI bug fixes and remove "continue"-ended do loops * update ifi version on jet and add -i option to compile_upp.sh * many bug fixes * update ifi module version on hera * Fix out-of-bounds accesses and modernize some line-number do loops (NOAA-EMC#559) * Fix out-of-bounds accesses and modernize some line-number do loops * add comments * update modulefile * remove unused variable * add a missing allocate() * update ifi module version on jet * Updating fix files to include new GOESS-16 simulated satellite brightness temps * Updated fix file. * Updated fix files. Co-authored-by: EricJames-NOAA <eric.james@noaa.gov> Co-authored-by: Ming.Hu <Ming.Hu@noaa.gov> Co-authored-by: Christina Holt <56881914+christinaholtNOAA@users.noreply.github.com> Co-authored-by: Christina Holt <Christina.Holt@noaa.gov> Co-authored-by: Jaymes Kenyon <jaymes.kenyon@noaa.gov> Co-authored-by: kayee <kayee.wong@noaa.gov> Co-authored-by: WenMeng-NOAA <48260754+WenMeng-NOAA@users.noreply.github.com> Co-authored-by: Rahul Mahajan <aerorahul@users.noreply.github.com> Co-authored-by: lgannoaa <37596169+lgannoaa@users.noreply.github.com> Co-authored-by: Tracy Hertneky <39317287+hertneky@users.noreply.github.com> Co-authored-by: Chan-Hoo.Jeon-NOAA <60152248+chan-hoo@users.noreply.github.com> Co-authored-by: Tracy <tracy.hertneky@noaa.gov> Co-authored-by: Michael Kavulich <kavulich@ucar.edu> Co-authored-by: Kate Fossell <fossell@ucar.edu> Co-authored-by: Kate Fossell <you@example.com> Co-authored-by: lipan-NOAA <li.pan@noaa.gov> Co-authored-by: Tracy <hertneky@ucar.edu> Co-authored-by: George Vandenberghe <George.Vandenberghe@noaa.gov> Co-authored-by: wx15gv <George.Vandenberghe@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a1.ncep.noaa.gov> Co-authored-by: Bo Cui <Bo.Cui@noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a2.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@m71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v72a1.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a3.ncep.noaa.gov> Co-authored-by: wx22mj <Jesse.Meng@v71a2.ncep.noaa.gov> Co-authored-by: Jesse.Meng <Jesse.Meng@noaa.gov> Co-authored-by: BoCui-NOAA <53531984+BoCui-NOAA@users.noreply.github.com> Co-authored-by: Jesse Meng <jmeng@Orion-login-4.HPC.MsState.Edu> Co-authored-by: LinZhu-NOAA <lin.l.zhu@noaa.gov> Co-authored-by: Dusan Jovic <48258889+DusanJovic-NOAA@users.noreply.github.com>
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WenMeng-NOAA
assigned gspetro-NOAA and WenMeng-NOAA and unassigned gspetro-NOAA, camshe and WenMeng-NOAA
This was referenced Mar 14, 2023
This was referenced Apr 24, 2023
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Doxygen gives warnings when things aren't quite right. I've added the current list of warnings, they can also be seen in the CI runs (after #390 is merged).
Once all these warnings are fixed, we can turn on the WARN_AS_ERROR flag, and that will cause the CI build to break if someone commits code without proper doxygen documentation. This is very worthwhile as it enforces some documentation standards automatically.
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