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Modified Makefile to support CCE on titan; and source code changes.
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mgduda
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This is merging PR MPAS-Dev#14 to the code
LarissaReames
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* Update version number to 8.0.2
* * In ./src/core_atmosphere/physics/mpas_atmphys_control.F, the mesoscale-reference suite
uses the nTiedtke (cu_ntiedtke) and not the tiedtke (cu_tiedtke) parameterization of
deep and shallow convection. One motivation of using the cu_ntiedtke option instead of
cu_tiedtke is the scale-aware capability of the nTiedtke parameterization, allowing the
use of nTiedtke iwth variable-resolution meshes.
-> therefore, we decided to rename the package cu_tiedtke_in to cu_ntiedtke_in.
* * In ./src/core_atmosphere/physics/physics_wrf, removed the variables f_qv, f_qr, and
f_qs in module_cu_tiedtke.F and module_cu_ntiedtke.F. Those three variables are not
used in the parameterizations.
* In ./src/core_atmosphere/physics/mpas_atmphys_driver_convection.F, removed f_qv,
f_qr, and f_qs in the calls to cu_tiedtke and cu_ntiedtke.
* * In ./src/core_atmosphere/physics/physics_wrf, removed the variables f_qv and f_qc
in module_cu_kfeta.F. Those two variables are not used in the parameterization.
* In ./src/core_atmosphere/physics/mpas_atmphys_driver_convection.F, removed f_qv
and f_qc in the call to kf_eta_cps.
* * In ./src/core_atmosphere/physics/mpas_atmphys_driver_convection.F, added comments at the
top of module.
* * In ./src/core_atmosphere/physics/physics_wrf, removed the variables f_qv and f_qc
in module_ra_cam.F (subroutine camrad). Those two variables are not used in the
parameterization.
* In ./src/core_atmosphere/physics/mpas_atmphys_driver_radiation_lw(sw).F, removed
f_qv and f_qc in the calls to camrad.
* * In ./src/core_atmosphere/physics/mpas_atmphys_vars.F, removed the variable f_qv
which is not needed in any of the physics parameterizations.
* * In ./src/core_atmosphere/physics:
-> in mpas_atmphys_vars.F, removed the "parameter" definition for f_qc,f_qr,f_qi,
f_qs,f_qg,f_nc,and f_ni. these variables are now simply defined as logicals.
also renamed f_qnc to f_nc, and f_qni to f_ni.
-> in mpas_atmphys_init.F, added subroutine init_physics_flags to initialize f_qc,
f_qr,f_qi,f_qs,f_nc,and f_ni.
-> in mpas_atmphys_driver_pbl.F, changed the call in mynn_bl_driver after renaming
f_qnc to f_nc, and f_qni to f_ni.
* Allow MPAS to use either of 'mpi_f08' or 'mpi' modules
By defining the MPAS_USE_MPI_F08 macro at compile time, MPAS can now use the
more modern 'mpi_f08' module for MPI. If the MPAS_USE_MPI_F08 macro is not
defined, MPAS uses the 'mpi' module as prior to this commit.
With the use of the 'mpi_f08' module, certain MPI types are no longer integers
in Fortran, but are derived types; e.g., MPI_Comm, MPI_Request, MPI_Datatype,
MPI_Info.
In some instances, an integer-typed MPI type is still needed for
interoperability, and the MPI standard permits this to be done through the
'mpi_val' member of all MPI derived types, e.g., MPI_Comm % mpi_val.
* Add logic in top-level Makefile to detect mpi_f08 module availability
By trying to compile a test program that uses the 'mpi_f08' module, the
top-level Makefile can now detect whether the MPI implementation provides an
'mpi_f08' module and, if so, adds a definition of the MPAS_USE_MPI_F08 macro to
the CPPFLAGS used in the build.
* * In ./src/core_atmosphere/physics:
-> renamed module mpas_atmphys_driver_lsm_shared.F to mpas_atmphys_lsm_shared.F.
-> in mpas_atmphys_driver_lsm.F, now use mpas_atmphys_lsm_shared to call subroutine
correct_tsk_over_seaice. removed subroutine correct_tsk_over_seaice at the bottom
of the module.
-> corrected Makefile accordingly.
* Generalize mpas_sphere_angle function to work for non-unit-radius spheres
The methods previously employed in the mpas_sphere_angle function for computing
the side lengths of a spherical triangle were only applicable to unit-radius
spheres. This commit generalizes the computation of these side lengths so that
the mpas_sphere_angle function can be used to compute spherical angles on
spheres of arbitrary radius.
* * In ./src/core_atmosphere/physics/mpas_atmphys_driver_lsm.F, now weigh the local variables
needed in the calculation of t2m, th2m, and q2 prior to updating all LSM variables (see
subroutine lsm_to_MPAS).
* * In ./src/core_atmosphere/physics/mpas_atmphys_driver_lsm.F, moved the call to sfcdiags
from subroutine driver_lsm to subroutine lsm_to_MPAS. This allows t2m, th2m, and q2 to
be correctly computed over seaice points.
* * In ./src/core_atmosphere/physics, added the file mpas_atmphys_driver_seaice.F:
-> mpas_atmphys_driver_seaice.F contains all the sourcecode related to surface
processes over seaice points.
-> in mpas_atmphys_driver_lsm.F, removed all the sourcecode related to surface
processes over seaice points and moved the sourcecode to the seaice driver.
-> changed Makefile accordingly.
* Initialize mvd_r and mvd_c before first use in Thompson microphysics scheme
This commit initializes two local variables, mvd_r and mvd_c, in the mp_thompson
routine to avoid the potential use of uninitialized memory.
Note: Identical changes to those included in this commit have been introduced
into newer versions of the Thompson microphysics scheme, and so the changes here
can be considered a back-port of fixes.
* Remove LIBS from openacc_test in top-level Makefile
Since these OpenACC compilation tests don't depend on NetCDF, GPTL, or
other libraries, problems can be prevented by removing the linking
commands that come from the LIBS variable. For example, the openacc_test
rule will fail and the build will abort if a library the compiler
expects to link against hasn't built yet.
* * In ./src/core_atmosphere/physics/mpas_atmphys_driver_cloudiness.F, corrected the units of
the variable dx_p from meters to kilometers (dx_p is used in the Thompson parameterization
of the cloud fraction).
* * In ./src/core_atmosphere/physics/mpas_atmphys_driver.F, added OpenMP directives around
the loop that calls the seaice driver.
* * In ./src/core_atmosphere/physics/mpas_atmphys_driver_seaice.F, updated the Copyright
at the top of the module.
* Add '-std=f2008' to FFLAGS_DEBUG for the 'gnu' build target
For the 'gnu' target, FFLAGS_OPT contained '-std=f2008' to check for Fortran
2008 conformance, but the debug build flags in FFLAGS_DEBUG lacked this option.
This commit simply adds '-std=f2008' to FFLAGS_DEBUG so that both optimized and
debug builds check that code conforms to the Fortran 2008 standard.
* * In ./src/core_atmosphere/physics, updated the MYNN surface layer scheme using the
sourcecode from WRF version 4.6.
-> in ./physics_mmm, added the CCPP-compliant MYNN surface layer scheme (sf_mynn.F) and
mynn_shared.F that contains functions also shared with the MYNN PBL scheme. Modified
Makefile accordingly.
-> in ./physics_wrf, added the file sf_mynn_pre.F to initialize variables needed in the
surface layer scheme. Modified module_sf_mynn.F which called the MYNN surface layer
scheme. Modified Makefile accordingly.
-> Modified mpas_atmphys_driver_sfclayer.F and mpas_atmphys_vars.F to accomodate updates
to the MYNN surface layer scheme.
* * In ./src/core_atmosphere/physics, very minor corrections to Makefile,
mpas_atmphys_driver_convection.F, and mpas_atmphys_driver_gwdo.F.
* * In ./src/core_atmosphere/physics/physics_mmm, very minor corrections to mp_radar.F
and sf_sfclayrev.F.
* * In ./src/core_atmosphere/physics, updated the MYNN PBL with the sourcecode available
in the WRF version 4.6.
-> in ./physics_mmm, added bl_mynn.F and bl_mynn_subroutines.F modules which are CCPP-
compliant versions of the MYNN PBL scheme. Modified Makefile accordingly.
-> in ./physics_wrf, added bl_mynn_pre.F and bl_mynn_post.F, and modified module_bl_mynn.F
that calls the MYNN PBL scheme. Modified Makefile accordingly.
-> in ./physics:
in mpas_atmphys_vars.F, added (and deleted) variables need to run the updated scheme.
in mpas_atmphys_init.F, initialized the added f_* flags needed to run the updated scheme.
in mpas_atmphys_driver_pbl.F, modified and updated the call to run the updated scheme.
in mpas_atmphys_todynamics.F, added rqsblten to the calculation to tend_scalars(index_qs,.).
-> in ./../Registry.xml, added new variables needed to run the updated MYNN PBL scheme.
* * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, removed extra blank spaces
introduced when updating the sourcecode.
* * In ./src/core_atmosphere/physics, made minor corrections to ./physics_mmm/Makefile
and ./physics_wrf/module_cu_ntiedtke.F.
* * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, commented out
the line:
6537 ! wm2 = wm2 + wm3**twothirds
in subroutine topdown_cloudrad. The variable wm2 is not initialized and not used
anywhere in the subroutine.
* * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn.F, removed the lines:
!JOE-add GRIMS parameters & variables
real(kind=kind_phys),parameter:: d1 = 0.02, d2 = 0.05, d3 = 0.001
real(kind=kind_phys),parameter:: h1 = 0.33333335, h2 = 0.6666667
real(kind=kind_phys):: govrth,sflux,bfx0,wstar3,wm2,wm3,delb
!JOE-end GRIMS
in subroutine bl_mynn_run. The removed GRIMS parameters and variables are
not needed in bl_mynn.F.
* * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, removed the extra
definition of parameters cphm_st, cphm_unst, cphh_st, and cphh_unst.
* * In ./src/core_atmosphere/physics:
-> in ./physics_mmm/bl_mynn.F, added the initialization of the optional variable dqke.
-> in ./physics_wrf/module_bl_mynn.F, made the variables dqke, qwt, qshear, qbuoy, and
qdiss optional variables.
-> in mpas_atmphys_driver_pbl.F, rewrite outputs to logfiles.
* * In ./src/core_atmosphere/Registry.xml, changed the option config_mynn_topdown
from 1 to 0.
* * In ./src/core_atmosphere/physics:
-> in ./physics_wrf/module_bl_mynn.F, added the local logical mynn_tkebudget_l which
is initialized as a function of the input integer variable bl_mynn_tkebudget.
mynn_tkebudget_l == true (false) when bl_mynn_tkebudget == 1 (0). this change is
needed to for CCPP-compliance of the MYNN files in ./physics_mmm.
-> in ./physics_mmm, modified bl_mynn.F and bl_mynn_subroutines.F accordingly.
* * In ./src/core_atmosphere/physics:
-> in physics_wrf/module_bl_mynn.F, added the local logicals mynn_mixclouds_l,
mynn_mixscalars_l, and mynn_mixqt_l which are initialized as functions of the
input integer variables bl_mynn_mixclouds, bl_mynn_mixscalars, and bl_mynn_mixqt.
the local logicals are set to true (false) when their respective input integer
variables are equal to 1 (0). this change is needed for CCPP-compliance of the MYNN
files in ./physics_mmm.
-> in physics_mmm, modified bl_mynn.F and bl_mynn_subroutines.F accordingly.
* * In ./src/core_atmosphere/physics:
-> in physics_wrf/module_bl_mynn.F, added the local logicals mynn_edmf_l and
mynn_edmf_dd_l which are initialized as functions of the input integer variables
bl_mynn_edmf and bl_mynn_edmf_dd. the logicals are set to true (false) when when
their respective input integer variables are equal to 1 (0). this change is needed
for CCPP-compliance of the MYNN files in ./physics_mmm.
-> in physics_mmm, modified bl_mynn.F and bl_mynn_subroutines.F accordingly.
* * In ./src/core_atmosphere/physics:
-> in physics_wrf/module_bl_mynn.F, added the local logicals mynn_edmf_mom_l and
mynn_edmf_tke_l which are initialized as functions of the input integer variables
bl_mynn_edmf_mom and bl_mynn_edmf_tke. the logicals are set to true (false) when
their respective input integer variables are equal to 1 (0). this change is needed
for CCPP-compliance of the MYNN files in ./physics_mmm.
-> in physics_mmm, modified bl_mynn.F and bl_mynn_subroutines.F accordingly.
* * In ./src/core_atmosphere/physics:
-> in physics_wrf/module_bl_mynn.F, added the local logicals mynn_output_l, mynn_dheatopt_l,
mynn_scaleaware_l, and mynn_topdown_l which are initialized as functions of the input integer
variables bl_mynn_output, bl_mynn_dheat_opt, bl_mynn_scaleaware_l, and bl_mynn_topdown. the
logicals are set to true (false) when when their respective input integer variables are equal
to 1 (0). this change is needed for CCPP-compliance of the MYNN files in ./physics_mmm.
-> in physics_mmm, modified bl_mynn.F and bl_mynn_subroutines.F accordingly.
* * In ./src/core_atmosphere/physics/physics_mm/bl_mynn.F, removed extra commented
out lines.
* * In ./src/core_atmosphere/physics/mpas_atmphys_driver_pbl.F, commented out extra
print statements before and after the call to subroutine mynn_bl_driver.
* * In ./src/core_atmosphere/physics/physics_mmm/bl_mynn_subroutines.F, changed all
instances of DOUBLE PRECISION with kind_phys8 where kind_phys8 points to R8KIND.
* Update version number to 8.1.0
* * In ./src/core_atmosphere/physics/physics_mmm/bl_ysu.F, added the initialization
of local variable we.
* Fix memory leaks due to duplicate `allocate` calls on pointers
The `mpas_pool_create_pool` subroutine already allocates the pointer in its arguments.
Therefore, calling `allocate` before `mpas_pool_create_pool` actually causes memory leaks.
* Solution MPAS-Dev#2 for the use of RUC LSM in the MPAS 8.1 (MPAS-Dev#9)
* Updated SOILPARM.TBL and VEGPARM.TBL for RUC LSM.
* Add mpas_atmphys_lsm_shared.o to dirver_lsm section
* RUC LSM and its 2-m diagnostics stay in the LSM driver. It will provide
solutions for land and ice points. Therefore, with RUC LSM, do not do
call to dirver_seaice.
* Added 2-m variables, will be used for RUC LSM diagnostics.
* Removed zero out of frozen and liqid soil water at the first time step.
It has been initialized in ruclsminit.
* Update to Microphysics for HRRRv5 (MPAS-Dev#10)
* 3D Reflectivity (MPAS-Dev#11)
* Set initial value of nc for aerosol-aware microphysics
* Move call to 3D reflectivity to microphysics
* Updated SOILPARM.TBL and VEGPARM.TBL for RUC LSM.
* Add mpas_atmphys_lsm_shared.o to dirver_lsm section
* RUC LSM and its 2-m diagnostics stay in the LSM driver. It will provide
solutions for land and ice points. Therefore, with RUC LSM, do not do
call to dirver_seaice.
* Added 2-m variables, will be used for RUC LSM diagnostics.
* Removed zero out of frozen and liqid soil water at the first time step.
It has been initialized in ruclsminit.
* Initialize clouds (MPAS-Dev#12)
* Set initial value of nc for aerosol-aware microphysics
* Two quick MPAS fixes (MPAS-Dev#10)
* Move call to 3D reflectivity to microphysics
* Add flags for Thompson options
* Move lookup table functions to utils and add flags to initialization
* Clean up microphysics flags for table build and initialization
* Add MPAS code for initialization of cloud number concentration
* Cleanup (MPAS-Dev#13)
* Set initial value of nc for aerosol-aware microphysics
* Two quick MPAS fixes (MPAS-Dev#10)
* Move call to 3D reflectivity to microphysics
* Add flags for Thompson options
* Move lookup table functions to utils and add flags to initialization
* Clean up microphysics flags for table build and initialization
* Add option to built hail-aware or non hail-aware lookup tables
* Update pointer to microphysics submodule commit
* Point to microphysics bugfix
* Update src/core_atmosphere/physics/physics_wrf/module_sf_ruclsm.F
---------
Co-authored-by: Tanya Smirnova <tanya.smirnova@noaa.gov>
Co-authored-by: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
* Updating MYNN-EDMF, cloud-radiation coupling, and surface layer tweaks (MPAS-Dev#12)
* Updating MYNN-EDMF, cloud-radiation coupling, and surface layer tweaks
* Update src/core_atmosphere/Registry.xml
fix typo
---------
Co-authored-by: Janet Derrico <143837053+jderrico-noaa@users.noreply.github.com>
* updated GF for MPAS (MPAS-Dev#13)
* "updated GF for MPAS"
* "clean the print statements"
* Update src/core_atmosphere/physics/physics_wrf/module_sf_ruclsm.F
---------
Co-authored-by: Michael Duda <duda@ucar.edu>
Co-authored-by: Laura Fowler <laura@ucar.edu>
Co-authored-by: G. Dylan Dickerson <gdicker@ucar.edu>
Co-authored-by: Kuan-Chih Wang <kuanchihw@ucar.edu>
Co-authored-by: tanyasmirnova <38667904+tanyasmirnova@users.noreply.github.com>
Co-authored-by: AndersJensen-NOAA <132939212+AndersJensen-NOAA@users.noreply.github.com>
Co-authored-by: Tanya Smirnova <tanya.smirnova@noaa.gov>
Co-authored-by: Joseph Olson <joeolson42@users.noreply.github.com>
Co-authored-by: haiqinli <38666296+haiqinli@users.noreply.github.com>
barlage
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re-implementation of the MYNN-EDMF
MicroTed
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DusanJovic-NOAA
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In the `mpas_io` module, the `MPAS_io_inq_var` subroutine allocates the `dimnames` array and returns it to a calling routine.
In this case, the calling routine is `MPAS_io_def_var`, which has a local pointer array, `inq_dimnames`, that corresponds to
the allocated `dimnames` and must be deallocated before this routine returns.
Direct leak of 152576 byte(s) in 162 object(s) allocated from:
#0 0x7fe7202ef41f in malloc (/lib64/libasan.so.8+0xef41f) (BuildId: 2a7b18228484f7c17d959b022f3ff6aaaf687b3c)
MPAS-Dev#1 0x0000024709b7 in __mpas_io_MOD_mpas_io_inq_var /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/framework/mpas_io.F:1123
MPAS-Dev#2 0x000002468a5b in __mpas_io_MOD_mpas_io_def_var /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/framework/mpas_io.F:1222
MPAS-Dev#3 0x000002613e0a in __mpas_io_streams_MOD_mpas_streamaddfield_generic /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/framework/mpas_io_streams.F:1761
MPAS-Dev#4 0x000002639406 in __mpas_io_streams_MOD_mpas_streamaddfield_1dreal /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/framework/mpas_io_streams.F:959
MPAS-Dev#5 0x0000024a69fa in build_stream /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/framework/mpas_stream_manager.F:4363
MPAS-Dev#6 0x0000024b13d7 in write_stream /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/framework/mpas_stream_manager.F:3251
MPAS-Dev#7 0x0000024b6afd in __mpas_stream_manager_MOD_mpas_stream_mgr_write /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/framework/mpas_stream_manager.F:2858
MPAS-Dev#8 0x00000094afb5 in __atm_core_MOD_atm_core_run /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/core_atmosphere/mpas_atm_core.F:620
MPAS-Dev#9 0x000000406341 in __mpas_subdriver_MOD_mpas_run /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/driver/mpas_subdriver.F:416
MPAS-Dev#10 0x000000402942 in mpas /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/driver/mpas.F:20
MPAS-Dev#11 0x0000004029b2 in main /home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/src/driver/mpas.F:10
MPAS-Dev#12 0x7fe71f208680 in __libc_start_call_main (/lib64/libc.so.6+0x3680) (BuildId: f83cdcaffde35587075ea80e05bcb894963a4bdd)
MPAS-Dev#13 0x7fe71f208797 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3797) (BuildId: f83cdcaffde35587075ea80e05bcb894963a4bdd)
MPAS-Dev#14 0x000000402844 in _start (/home/dusan/sufs/simple-mpas/src/MPAS-Model-develop/build/bin/mpas_atmosphere+0x402844) (BuildId: c0332077ce07f118fef380e98497523209704432)
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Modified Makefile to support CCE on titan; and source code changes.