Update regional FV3 read interface with parallel netcdf read #441
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WenMeng-NOAA
added
RRFS
HAFS
No Baseline Change
There was a problem hiding this comment.
Look good.
@WenMeng-NOAA thank you for helping RRFS team speed up their post processing
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@EricRogers-NOAA, @BinLiu-NOAA, @EricJames-NOAA, |
EricRogers-NOAA
approved these changes
Feb 9, 2022
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@WenMeng-NOAA - Should we consider renaming INITPOST_NETCDF to more adequately describe what it will be doing now? e.g. INITPOST_REG_NETCDF_PARA, like was done for GFS? Or maybe it won't matter since there is effort to unify these routines anyway? |
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@fossell Since our upcoming goal is unifying global and regional FV3 read interfaces, I would prefer to not rename regional FV3 |
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@WenMeng-NOAA - sounds good to me. |
BinLiu-NOAA
approved these changes
Feb 11, 2022
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The UPP regression tests were conducted on WCOSS1-Dell, WCOSS-Cray and Hera. No changed results were found. This update will speed up offline posts for RRFS and HAFS more than 40% runtime. The PR is ready for merging. |
EricJames-NOAA
added a commit
to NOAA-GSL/UPP
that referenced
this pull request
Aug 5, 2022
* 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
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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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Update regional Fv3 read interface with parallel netcdf read.