Custom Query – src

Description

The CMake build scripts (cbuild_roms.csh and cbuild_roms.sh) were cleaned and made more compact:
- Several macro definitions were moved from the build scripts to the main CMakeLists.txt configuration file for simplicity
- The ROMS executable is now copied to the project directory instead of making a symbolic link. It should work even if ROMS were linked to the shared library (libROMS.{so|dylib}) because CMAKE_BUILD_WITH_INSTALL_RPATH is set to FALSE so that RPATH/RUNPATH are set correctly for both the build tree and installed locations of the ROMS executable.
- The macro definitions in Compilers/roms_compiler_flags.cmake and Compilers/roms_config.cmake were also updated.

The OUTPUT_STATS option is introduced to report the statistics of every output variable into standard output to facilitate debugging. For example, we can have the following report:

 WRT_HIS_NF90     - writing history     fields (Index=1,1) in record = 33
   - zeta:                       Min = -2.53787051E-01,  Max =  2.21499656E-01,  CheckSum = 8935
   - ubar:                       Min = -1.34311554E-01,  Max =  1.93256921E-01,  CheckSum = 8568
   - DU_avg1:                    Min = -2.07583251E+07,  Max =  3.32353876E+07,  CheckSum = 7365
   - DU_avg2:                    Min = -2.07602196E+07,  Max =  3.32406785E+07,  CheckSum = 7461
   - vbar:                       Min = -2.15736568E-01,  Max =  1.94236573E-01,  CheckSum = 8406
   - DV_avg1:                    Min = -3.37735448E+07,  Max =  1.84199170E+07,  CheckSum = 7265
   - DV_avg2:                    Min = -3.37768757E+07,  Max =  1.84168047E+07,  CheckSum = 7277
   - u:                          Min = -3.54280363E-01,  Max =  5.53737927E-01,  CheckSum = 257209
   - v:                          Min = -5.36308150E-01,  Max =  4.26453121E-01,  CheckSum = 251702
   - omega:                      Min = -1.60468150E-03,  Max =  1.36090242E-03,  CheckSum = 255075
   - w:                          Min = -2.31089520E-03,  Max =  1.50154444E-03,  CheckSum = 271803
   - temp:                       Min =  1.11330213E+00,  Max =  1.83344385E+01,  CheckSum = 241650
   - salt:                       Min =  3.19036203E+01,  Max =  3.46896641E+01,  CheckSum = 211601
   - AKv:                        Min =  2.23812185E-05,  Max =  8.12660236E-01,  CheckSum = 272259
   - AKt:                        Min =  1.00000000E-05,  Max =  9.92734690E-01,  CheckSum = 273723
   - AKs:                        Min =  1.00000000E-05,  Max =  9.92734690E-01,  CheckSum = 273723
   - Pair:                       Min =  1.00743285E+03,  Max =  1.02769252E+03,  CheckSum = 6863
   - Tair:                       Min = -2.08358809E+00,  Max =  1.77220951E+01,  CheckSum = 6496
   - Uwind:                      Min = -1.45947707E+01,  Max =  3.82034782E+00,  CheckSum = 8050
   - Vwind:                      Min = -7.43046612E+00,  Max =  1.32450908E+01,  CheckSum = 6425
   - shflux:                     Min = -1.26168950E-04,  Max =  1.21942551E-05,  CheckSum = 8438
   - ssflux:                     Min = -1.55420481E-05,  Max =  2.02108689E-06,  CheckSum = 8850
   - latent:                     Min = -5.21229738E-05,  Max =  5.96354770E-06,  CheckSum = 9261
   - sensible:                   Min = -4.84698719E-05,  Max =  7.84890317E-06,  CheckSum = 8970
   - lwrad:                      Min = -3.46309283E-05,  Max = -1.61819579E-06,  CheckSum = 9208
   - evaporation:                Min = -9.84070050E-06,  Max =  8.59023387E-05,  CheckSum = 8691
   - rain:                       Min = -7.05555578E-07,  Max =  4.68687525E-04,  CheckSum = 8526
   - EminusP:                    Min = -4.72947771E-07,  Max =  6.06640234E-08,  CheckSum = 8707
   - swrad:                      Min =  0.00000000E+00,  Max =  6.02349409E-05,  CheckSum = 8724
   - sustr:                      Min = -5.49541550E-04,  Max =  3.78055345E-05,  CheckSum = 8639
   - svstr:                      Min = -9.05397457E-05,  Max =  3.54286819E-04,  CheckSum = 8133

As a consequence, all the calls to nf_fwrite2d, nfwrite3d, and nf_fwrite4d were modified to include the variable metadata index in its fourth argument:

!
!  Write out tracer type variables.
!
      DO itrc=1,NT(ng)
        IF (Hout(idTvar(itrc),ng)) THEN
          scale=1.0_dp
          gtype=gfactor*r3dvar
          status=nf_fwrite3d(ng, model, HIS(ng)%ncid, idTvar(itrc),     &
     &                       HIS(ng)%Tid(itrc),                         &
     &                       HIS(ng)%Rindex, gtype,                     &
     &                       LBi, UBi, LBj, UBj, 1, N(ng), scale,       &
# ifdef MASKING
     &                       GRID(ng) % rmask,                          &
# endif
     &                       OCEAN(ng) % t(:,:,:,NOUT,itrc))
          IF (FoundError(status, nf90_noerr, __LINE__, MyFile)) THEN
            IF (Master) THEN
              WRITE (stdout,20) TRIM(Vname(1,idTvar(itrc))),            &
     &                          HIS(ng)%Rindex
            END IF
            exit_flag=3
            ioerror=status
            RETURN
          END IF
        END IF
      END DO

WARNING: Notice the additional fourth argument idTvar(itrc) to nf_fwrite3d.

The metadata file varinfo.yaml was updated to include ROMS geometry variables used in def_info.F and wrt_info.F. I should have done this a long time ago. For example, when the file is created, it reports its statistics when OUTPUT_STATS is activated:

DEF_HIS_NF90     - creating history file,            Grid 01: wc13_fwd_20040103_outer0.nc
   - h:                          Min =  7.80292502E+01,  Max =  5.19952300E+03,  CheckSum = 7704
   - f:                          Min =  7.27220522E-05,  Max =  1.08086034E-04,  CheckSum = 8151
   - pm:                         Min =  3.11708295E-05,  Max =  4.03430084E-05,  CheckSum = 7924
   - pn:                         Min =  2.69947206E-05,  Max =  2.69947206E-05,  CheckSum = 9405
   - lon_rho:                    Min = -1.34000000E+02,  Max = -1.16000000E+02,  CheckSum = 4984
   - lat_rho:                    Min =  3.00000000E+01,  Max =  4.80000000E+01,  CheckSum = 5282
   - lon_u:                      Min = -1.33833333E+02,  Max = -1.16166667E+02,  CheckSum = 4914
   - lat_u:                      Min =  3.00000000E+01,  Max =  4.80000000E+01,  CheckSum = 5004
   - lon_v:                      Min = -1.34000000E+02,  Max = -1.16000000E+02,  CheckSum = 4628
   - lat_v:                      Min =  3.01666667E+01,  Max =  4.78333333E+01,  CheckSum = 5206
   - lon_psi:                    Min = -1.33833333E+02,  Max = -1.15833333E+02,  CheckSum = 4563
   - lat_psi:                    Min =  3.01666667E+01,  Max =  4.78333333E+01,  CheckSum = 4932
   - angle:                      Min =  1.45444412E-03,  Max =  2.16172340E-03,  CheckSum = 7606
   - mask_rho:                   Min =  1.00000000E+00,  Max =  1.00000000E+00,  CheckSum = 2660
   - mask_u:                     Min =  1.00000000E+00,  Max =  1.00000000E+00,  CheckSum = 2520
   - mask_v:                     Min =  1.00000000E+00,  Max =  1.00000000E+00,  CheckSum = 2470
   - mask_psi:                   Min =  1.00000000E+00,  Max =  2.00000000E+00,  CheckSum = 2340

WARNING:

All the ROMS test repository's CMake build scripts were updated.

The metadata file varinfo.yaml was updated, and the changes are required for this and future versions of ROMS.

Description

We completed the transition of ROMS to GitHub. We have been working on this for the last couple of months.

The GitHub ROMS repositories are at https://github.com/myroms. For more information and instructions on ROMS framework source code, please visit https://github.com/myroms/roms/wiki.

The GitHub version becomes the official git repository for downloading, updating, improving, and correcting defects/bugs in the ROMS source code. Also, it is the version used in the ROMS-JEDI interface hosted at https://github.com/JCSDA-internal, which is currently private.

We will update the git and svn repositories hosted at https://www.myroms.org for some time, but encourage the User to transition to GitHub, which gives you access to the feature branches.

We still highly recommend users registering at https://www.myroms.org and set up a username and password to access the **ROMS forum**, email notifications for bugs/updates, technical support from the community, trac code maintenance history, tutorials, workshops, and publications. The User's ROMS forum has over 24, 000 posts with helpful information. Technical support is limited to registered users.

We do not provide user technical support, usage, or answers in GitHub.

If you have a GitHub username, we suggest following us by checking on the follow/unfollow button in the myroms repositories, so you are notifiedGitHub dashboard about changes and updates to the GitHub ROMS repositories.

You could also check on the watch/unwatch button to receive notifications about changes to any ROMS repositories. You can customize what type of notification you would like to receive.

Your support will help us secure funding from US funding agencies for continued ROMS framework management and development. It is not much to ask since ROMS is freely distributed.

Description

The state vector indices are used in various algorithms. The numeric order is essential in data assimilation because they are used to associate observations with the type of variables in the state vector:

      isFsur = 1                ! free-surface
      isUbar = 2                ! 2D U-velocity
      isVbar = 3                ! 2D V-velocity
      isUvel = 4                ! 3D U-velocity
      isVvel = 5                ! 3D V-velocity
      ic=5
#ifdef SOLVE3D
      DO i=1,MT
        ic=ic+1
        isTvar(i)=ic            ! Active/Passive tracers
      END DO
#endif
#if defined ADJUST_WSTRESS || defined FORCING_SV     || \
    defined HESSIAN_FSV    || defined SO_SEMI        || \
    defined STOCHASTIC_OPT
      ic=ic+1
      isUstr=ic                 ! surface U-velocity stress
      ic=ic+1
      isVstr=ic                 ! surface V-velocity stress
#endif
#ifdef SOLVE3D
# if defined ADJUST_STFLUX  || defined FORCING_SV     || \
     defined HESSIAN_FSV    || defined SO_SEMI        || \
     defined STOCHASTIC_OPT
      DO i=1,MT
        ic=ic+1
        isTsur(i)=ic            ! surface tracer flux      
      END DO
# endif
#endif
#ifdef WEC
      ic=ic+1
      isU2Sd=ic                 ! 2D Stokes U-velocity 
      ic=ic+1
      isV2Sd=ic                 ! 2D Stokes V-velocity
# if defined SOLVE3D
      ic=ic+1
      isU3Sd=ic                 ! 3D Stokes U-velocity
      ic=ic+1
      isV3Sd=ic                 ! 3D Stokes V-velocity
# endif
#endif
#ifdef SOLVE3D
# if defined GLS_MIXING || defined MY25_MIXING
      ic=ic+1
      isMtke=ic                 ! TKE
# endif
      ic=ic+1
      isWvel=ic                 ! vertical velocity
#endif

Therefore, all the state indices from the zeta to the last Tvar(:) tracer variables cannot be changed.

Updated the GNU make configuration (*.mk) files to include the environmental variable ESMFMKFILE. Thus, now we have:

ifdef USE_ESMF
                     include $(ESMFMKFILE)
          ESMF_OS ?= $(OS)
      ESMF_SUBDIR := $(ESMF_OS).$(ESMF_COMPILER).$(ESMF_ABI).$(ESMF_COMM).$(ESMF_SITE)
      ESMF_MK_DIR ?= $(ESMF_DIR)/lib/lib$(ESMF_BOPT)/$(ESMF_SUBDIR)
           FFLAGS += $(ESMF_F90COMPILEPATHS)
             LIBS += $(ESMF_F90LINKPATHS) $(ESMF_F90ESMFLINKLIBS)
endif

Many thanks to Ufuk Turuncoglu for bringing this issue to my attention.

Made tiny changes to NUOPC cap modules cmeps_roms.F and esmf_roms.F.

Corrected issue in esmf_esm.F (routine ESM_SetRunSequence) that used LocalPET before being assigned.

Ticket	Owner	Reporter	Resolution	Summary
#952		arango	Done	VERY IMPORTANT: CMake build scripts and OUTPUT_STATS
Description	The CMake build scripts (cbuild_roms.csh and cbuild_roms.sh) were cleaned and made more compact: Several macro definitions were moved from the build scripts to the main CMakeLists.txt configuration file for simplicity The ROMS executable is now copied to the project directory instead of making a symbolic link. It should work even if ROMS were linked to the shared library (libROMS.{so\|dylib}) because CMAKE_BUILD_WITH_INSTALL_RPATH is set to FALSE so that RPATH/RUNPATH are set correctly for both the build tree and installed locations of the ROMS executable. The macro definitions in Compilers/roms_compiler_flags.cmake and Compilers/roms_config.cmake were also updated. The OUTPUT_STATS option is introduced to report the statistics of every output variable into standard output to facilitate debugging. For example, we can have the following report: WRT_HIS_NF90 - writing history fields (Index=1,1) in record = 33 - zeta: Min = -2.53787051E-01, Max = 2.21499656E-01, CheckSum = 8935 - ubar: Min = -1.34311554E-01, Max = 1.93256921E-01, CheckSum = 8568 - DU_avg1: Min = -2.07583251E+07, Max = 3.32353876E+07, CheckSum = 7365 - DU_avg2: Min = -2.07602196E+07, Max = 3.32406785E+07, CheckSum = 7461 - vbar: Min = -2.15736568E-01, Max = 1.94236573E-01, CheckSum = 8406 - DV_avg1: Min = -3.37735448E+07, Max = 1.84199170E+07, CheckSum = 7265 - DV_avg2: Min = -3.37768757E+07, Max = 1.84168047E+07, CheckSum = 7277 - u: Min = -3.54280363E-01, Max = 5.53737927E-01, CheckSum = 257209 - v: Min = -5.36308150E-01, Max = 4.26453121E-01, CheckSum = 251702 - omega: Min = -1.60468150E-03, Max = 1.36090242E-03, CheckSum = 255075 - w: Min = -2.31089520E-03, Max = 1.50154444E-03, CheckSum = 271803 - temp: Min = 1.11330213E+00, Max = 1.83344385E+01, CheckSum = 241650 - salt: Min = 3.19036203E+01, Max = 3.46896641E+01, CheckSum = 211601 - AKv: Min = 2.23812185E-05, Max = 8.12660236E-01, CheckSum = 272259 - AKt: Min = 1.00000000E-05, Max = 9.92734690E-01, CheckSum = 273723 - AKs: Min = 1.00000000E-05, Max = 9.92734690E-01, CheckSum = 273723 - Pair: Min = 1.00743285E+03, Max = 1.02769252E+03, CheckSum = 6863 - Tair: Min = -2.08358809E+00, Max = 1.77220951E+01, CheckSum = 6496 - Uwind: Min = -1.45947707E+01, Max = 3.82034782E+00, CheckSum = 8050 - Vwind: Min = -7.43046612E+00, Max = 1.32450908E+01, CheckSum = 6425 - shflux: Min = -1.26168950E-04, Max = 1.21942551E-05, CheckSum = 8438 - ssflux: Min = -1.55420481E-05, Max = 2.02108689E-06, CheckSum = 8850 - latent: Min = -5.21229738E-05, Max = 5.96354770E-06, CheckSum = 9261 - sensible: Min = -4.84698719E-05, Max = 7.84890317E-06, CheckSum = 8970 - lwrad: Min = -3.46309283E-05, Max = -1.61819579E-06, CheckSum = 9208 - evaporation: Min = -9.84070050E-06, Max = 8.59023387E-05, CheckSum = 8691 - rain: Min = -7.05555578E-07, Max = 4.68687525E-04, CheckSum = 8526 - EminusP: Min = -4.72947771E-07, Max = 6.06640234E-08, CheckSum = 8707 - swrad: Min = 0.00000000E+00, Max = 6.02349409E-05, CheckSum = 8724 - sustr: Min = -5.49541550E-04, Max = 3.78055345E-05, CheckSum = 8639 - svstr: Min = -9.05397457E-05, Max = 3.54286819E-04, CheckSum = 8133 As a consequence, all the calls to nf_fwrite2d, nfwrite3d, and nf_fwrite4d were modified to include the variable metadata index in its fourth argument: ! ! Write out tracer type variables. ! DO itrc=1,NT(ng) IF (Hout(idTvar(itrc),ng)) THEN scale=1.0_dp gtype=gfactorr3dvar status=nf_fwrite3d(ng, model, HIS(ng)%ncid, idTvar(itrc), & & HIS(ng)%Tid(itrc), & & HIS(ng)%Rindex, gtype, & & LBi, UBi, LBj, UBj, 1, N(ng), scale, & # ifdef MASKING & GRID(ng) % rmask, & # endif & OCEAN(ng) % t(:,:,:,NOUT,itrc)) IF (FoundError(status, nf90_noerr, __LINE__, MyFile)) THEN IF (Master) THEN WRITE (stdout,20) TRIM(Vname(1,idTvar(itrc))), & & HIS(ng)%Rindex END IF exit_flag=3 ioerror=status RETURN END IF END IF END DO WARNING:* Notice the additional fourth argument idTvar(itrc) to nf_fwrite3d. The metadata file varinfo.yaml was updated to include ROMS geometry variables used in def_info.F and wrt_info.F. I should have done this a long time ago. For example, when the file is created, it reports its statistics when OUTPUT_STATS is activated: DEF_HIS_NF90 - creating history file, Grid 01: wc13_fwd_20040103_outer0.nc - h: Min = 7.80292502E+01, Max = 5.19952300E+03, CheckSum = 7704 - f: Min = 7.27220522E-05, Max = 1.08086034E-04, CheckSum = 8151 - pm: Min = 3.11708295E-05, Max = 4.03430084E-05, CheckSum = 7924 - pn: Min = 2.69947206E-05, Max = 2.69947206E-05, CheckSum = 9405 - lon_rho: Min = -1.34000000E+02, Max = -1.16000000E+02, CheckSum = 4984 - lat_rho: Min = 3.00000000E+01, Max = 4.80000000E+01, CheckSum = 5282 - lon_u: Min = -1.33833333E+02, Max = -1.16166667E+02, CheckSum = 4914 - lat_u: Min = 3.00000000E+01, Max = 4.80000000E+01, CheckSum = 5004 - lon_v: Min = -1.34000000E+02, Max = -1.16000000E+02, CheckSum = 4628 - lat_v: Min = 3.01666667E+01, Max = 4.78333333E+01, CheckSum = 5206 - lon_psi: Min = -1.33833333E+02, Max = -1.15833333E+02, CheckSum = 4563 - lat_psi: Min = 3.01666667E+01, Max = 4.78333333E+01, CheckSum = 4932 - angle: Min = 1.45444412E-03, Max = 2.16172340E-03, CheckSum = 7606 - mask_rho: Min = 1.00000000E+00, Max = 1.00000000E+00, CheckSum = 2660 - mask_u: Min = 1.00000000E+00, Max = 1.00000000E+00, CheckSum = 2520 - mask_v: Min = 1.00000000E+00, Max = 1.00000000E+00, CheckSum = 2470 - mask_psi: Min = 1.00000000E+00, Max = 2.00000000E+00, CheckSum = 2340 WARNING: All the ROMS test repository's CMake build scripts were updated. The metadata file varinfo.yaml was updated, and the changes are required for this and future versions of ROMS.
#953		arango	Done	VERY IMPORTANT: ROMS GitHub Transition
Description	We completed the transition of ROMS to GitHub. We have been working on this for the last couple of months. The GitHub ROMS repositories are at https://github.com/myroms. For more information and instructions on ROMS framework source code, please visit https://github.com/myroms/roms/wiki. The GitHub version becomes the official git repository for downloading, updating, improving, and correcting defects/bugs in the ROMS source code. Also, it is the version used in the ROMS-JEDI interface hosted at https://github.com/JCSDA-internal, which is currently private. We will update the git and svn repositories hosted at https://www.myroms.org for some time, but encourage the User to transition to GitHub, which gives you access to the feature branches. We still highly recommend users registering at https://www.myroms.org and set up a username and password to access the ROMS forum, email notifications for bugs/updates, technical support from the community, trac code maintenance history, tutorials, workshops, and publications. The User's ROMS forum has over 24, 000 posts with helpful information. Technical support is limited to registered users. We do not provide user technical support, usage, or answers in GitHub. If you have a GitHub username, we suggest following us by checking on the follow/unfollow button in the myroms repositories, so you are notifiedGitHub dashboard about changes and updates to the GitHub ROMS repositories. You could also check on the watch/unwatch button to receive notifications about changes to any ROMS repositories. You can customize what type of notification you would like to receive. Your support will help us secure funding from US funding agencies for continued ROMS framework management and development. It is not much to ask since ROMS is freely distributed.
#955		arango	Done	IMPORTANT: Refactored state vector indices
Description	The state vector indices are used in various algorithms. The numeric order is essential in data assimilation because they are used to associate observations with the type of variables in the state vector: isFsur = 1 ! free-surface isUbar = 2 ! 2D U-velocity isVbar = 3 ! 2D V-velocity isUvel = 4 ! 3D U-velocity isVvel = 5 ! 3D V-velocity ic=5 #ifdef SOLVE3D DO i=1,MT ic=ic+1 isTvar(i)=ic ! Active/Passive tracers END DO #endif #if defined ADJUST_WSTRESS \|\| defined FORCING_SV \|\| \ defined HESSIAN_FSV \|\| defined SO_SEMI \|\| \ defined STOCHASTIC_OPT ic=ic+1 isUstr=ic ! surface U-velocity stress ic=ic+1 isVstr=ic ! surface V-velocity stress #endif #ifdef SOLVE3D # if defined ADJUST_STFLUX \|\| defined FORCING_SV \|\| \ defined HESSIAN_FSV \|\| defined SO_SEMI \|\| \ defined STOCHASTIC_OPT DO i=1,MT ic=ic+1 isTsur(i)=ic ! surface tracer flux END DO # endif #endif #ifdef WEC ic=ic+1 isU2Sd=ic ! 2D Stokes U-velocity ic=ic+1 isV2Sd=ic ! 2D Stokes V-velocity # if defined SOLVE3D ic=ic+1 isU3Sd=ic ! 3D Stokes U-velocity ic=ic+1 isV3Sd=ic ! 3D Stokes V-velocity # endif #endif #ifdef SOLVE3D # if defined GLS_MIXING \|\| defined MY25_MIXING ic=ic+1 isMtke=ic ! TKE # endif ic=ic+1 isWvel=ic ! vertical velocity #endif Therefore, all the state indices from the zeta to the last Tvar(:) tracer variables cannot be changed. Updated the GNU make configuration (.mk) files to include the environmental variable ESMFMKFILE. Thus, now we have: ifdef USE_ESMF include $(ESMFMKFILE) ESMF_OS ?= $(OS) ESMF_SUBDIR := $(ESMF_OS).$(ESMF_COMPILER).$(ESMF_ABI).$(ESMF_COMM).$(ESMF_SITE) ESMF_MK_DIR ?= $(ESMF_DIR)/lib/lib$(ESMF_BOPT)/$(ESMF_SUBDIR) FFLAGS += $(ESMF_F90COMPILEPATHS) LIBS += $(ESMF_F90LINKPATHS) $(ESMF_F90ESMFLINKLIBS) endif Many thanks to Ufuk Turuncoglu for bringing this issue to my attention. Made tiny changes to NUOPC* cap modules cmeps_roms.F and esmf_roms.F. Corrected issue in esmf_esm.F (routine ESM_SetRunSequence) that used LocalPET before being assigned.

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