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add PaHM to build scripts and submodules #57

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111 commits merged into from
Dec 3, 2021
Merged

add PaHM to build scripts and submodules #57

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e02a257
add PaHM as submodule
zacharyburnett May 24, 2021
7cc5d32
updated PaHM submodule to point to newest commit + changed name to PAHM
zacharyburnett Jun 21, 2021
6bbf65a
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
pvelissariou1 Jun 24, 2021
fa468b0
updated PaHM sources to include the nuopc folder
pvelissariou1 Jun 24, 2021
ebefcd3
update modulefile to use stable parallel ESMF build
zacharyburnett Jun 24, 2021
e62388e
modules are under emc-nemspara
zacharyburnett Jun 24, 2021
32d79c1
updated build scripts to fix compilation errors
pvelissariou1 Jun 25, 2021
46027d7
added nuopc/Makefile.in and modified distclean.cmake to not delete th…
pvelissariou1 Jun 25, 2021
4899405
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
pvelissariou1 Jun 25, 2021
b61a7e6
modified the work/cmprflags.mk file for intel
pvelissariou1 Jun 25, 2021
20ac0ba
updated the modulefiles/* files to be more general and mofified the f…
pvelissariou1 Jun 27, 2021
3362622
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
pvelissariou1 Jun 27, 2021
2fe527f
fixed the bug for use_defaults
pvelissariou1 Jun 27, 2021
7835b24
fixed conf/configure.nems* files to set the NETCDF libraries properly
pvelissariou1 Jun 27, 2021
cf18918
fixed orion compiling issues
pvelissariou1 Jun 27, 2021
1f2acab
fixed MACHINE_ID variables
pvelissariou1 Jun 27, 2021
0109000
switched the hera and orion environment modulefiles to theis sys state
pvelissariou1 Jun 27, 2021
0232903
commended out the LICENSE line in the orion cmake file
pvelissariou1 Jun 27, 2021
d5006be
updated submodule
zacharyburnett Jun 28, 2021
b71f5a3
Merge branch 'feature/pahm'
zacharyburnett Jun 28, 2021
dc59ca3
update submodule
zacharyburnett Jun 28, 2021
4d03361
fixed the missing nemsio issue
pvelissariou1 Jun 29, 2021
ff5ee32
deleted the old build scripts
pvelissariou1 Jun 29, 2021
a7b2ef0
updated the modulefile for intel in orion
pvelissariou1 Jun 29, 2021
6e051bc
updated the build and function scripts
pvelissariou1 Jun 29, 2021
753b95f
modified the build script to find the functions_build file; in some s…
pvelissariou1 Jun 29, 2021
f15e3cf
modified PAHM build scripts
pvelissariou1 Jun 29, 2021
5f9211e
updates PaHM build scripts
pvelissariou1 Jun 29, 2021
0b8687d
update modules
zacharyburnett Jun 29, 2021
6182a70
updated submodules
zacharyburnett Jun 29, 2021
31d39ae
fixed the build script to allow the user to define customized names f…
pvelissariou1 Jun 29, 2021
7e9e395
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
pvelissariou1 Jun 29, 2021
6eec406
fixed functions_build to remove NEMS/exe/NEMS*.x if requested
pvelissariou1 Jun 30, 2021
d4ab5ab
modified component_ADCIRC.mk so distclean cleans properly the nuopc …
pvelissariou1 Jun 30, 2021
6cd4aac
updated submodule
zacharyburnett Jun 30, 2021
7be503f
updated ESMF to latest parallel build
zacharyburnett Jun 30, 2021
df4570e
Merge remote-tracking branch 'origin/fix/esmf' into feature/pahm
zacharyburnett Jun 30, 2021
1cd93e4
updated the envmodules_*.linux files to load the proper modules
pvelissariou1 Jul 1, 2021
e68ce42
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
pvelissariou1 Jul 1, 2021
33c172b
fixed the gnu configure file to include the correct compilers and com…
pvelissariou1 Jul 1, 2021
a9e3b6a
fixed make_nuopc.sh to set the compiler variable correctly
pvelissariou1 Jul 1, 2021
4b00454
minor fix of module_EARTH_GRID_COMP.F90 line 2956 to comile with gfor…
pvelissariou1 Jul 1, 2021
8c065d8
fix module_EARTH_GRID_COMP.F90 to compile with gfortran
pvelissariou1 Jul 1, 2021
17d50cb
fix component_ADCIRC.mk to pass the correct compiler option to make_n…
pvelissariou1 Jul 1, 2021
14478a4
fix the find command in functions_build
pvelissariou1 Jul 5, 2021
38726d6
fixed the compiler option to user the NEM_COMPILER variable
pvelissariou1 Jul 5, 2021
c6d21dc
fixed MPI_FINALIZE error in adc_cap.F90 and gnu/intel compile errors …
pvelissariou1 Jul 5, 2021
1c487be
fix gnu/intel/pgi compilation options in estofs_tide_fac/makefile
pvelissariou1 Jul 5, 2021
6da5f12
update submodule to point to merge commit for release/public-v2 on up…
zacharyburnett Jul 6, 2021
0ca4928
fixed work/makefile to delete the util directory on make clean
pvelissariou1 Jul 6, 2021
5b070c0
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
pvelissariou1 Jul 6, 2021
690f97b
updated the control files to include NetCDF file compression
pvelissariou1 Jul 12, 2021
3b15df8
changed file permissions and made some minor format updates in atmesh…
pvelissariou1 Jul 12, 2021
05351dd
modified sources for NUOPC coupling (option NWS=17)
pvelissariou1 Jul 12, 2021
a853999
changed NWS.EQ.17 to ABS(NWS).EQ.17, there is no option NWS=-17
pvelissariou1 Jul 12, 2021
f897d35
modified the modulefiles to account for possible HDF5 access denied e…
pvelissariou1 Jul 12, 2021
9883811
multiple environment modifications
pvelissariou1 Jul 12, 2021
d541297
format modifications
pvelissariou1 Jul 12, 2021
82d0d0b
updated pointer to point to new commits on remote
zacharyburnett Jul 12, 2021
a4e3d24
updated the pointers
pvelissariou1 Jul 12, 2021
ffd7c20
update NEMS pointer to latest in pahm branch
zacharyburnett Jul 13, 2021
f9724c4
update pointer with filename rename
zacharyburnett Jul 13, 2021
ab14b00
renamed ENS_CplComp_ESMFMod_STUB.f90 to ENS_CplComp_ESMFMod_STUB.F90
pvelissariou1 Jul 13, 2021
f969292
renamed ENS_CplComp_ESMFMod_STUB.f90 to ENS_CplComp_ESMFMod_STUB.F90
pvelissariou1 Jul 13, 2021
b3b6abd
renamed ENS_CplComp_ESMFMod_STUB.f90 to ENS_CplComp_ESMFMod_STUB.F90
pvelissariou1 Jul 13, 2021
242dcad
updated PAHM
pvelissariou1 Jul 15, 2021
a7a3a47
updated submodule to point to merge commit
zacharyburnett Jul 19, 2021
5e68d15
updated submodule to use LFS
zacharyburnett Jul 19, 2021
825fbee
updated PAHM to use LFS
zacharyburnett Jul 19, 2021
05767d5
updated submodule pointer
zacharyburnett Jul 21, 2021
86cdcd2
added lfs tracked files
pvelissariou1 Jul 21, 2021
d1bc7d2
added lfs tracked files
pvelissariou1 Jul 21, 2021
9dbc4ab
deleted very large data files
pvelissariou1 Jul 21, 2021
3b6cbb9
Merge branch 'master' into feature/pahm
zacharyburnett Jul 21, 2021
a9373de
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
zacharyburnett Jul 21, 2021
27828cc
Merge branch 'master' into feature/pahm
zacharyburnett Jul 21, 2021
2d51cdc
cleanup of ADCIRC/PAHM components
pvelissariou1 Aug 2, 2021
611513a
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/A…
pvelissariou1 Aug 2, 2021
63baf1b
cleaned top level conf folder
pvelissariou1 Aug 2, 2021
d11d2fb
added new functionality to build other executables
pvelissariou1 Aug 2, 2021
d341b62
cleaned the PAHM/inputs folder
pvelissariou1 Aug 2, 2021
dc794d7
deleted *.rej files
pvelissariou1 Aug 2, 2021
786af16
added functionality to build other executables as well
pvelissariou1 Aug 2, 2021
ce28ba9
add aswip to binaries
zacharyburnett Aug 4, 2021
6b19232
renamed the NUOPC_SRCDIR variables to {MODEL}_NUOPC_SRCDIR
pvelissariou1 Aug 5, 2021
d9eab9c
Merge branch 'feature/pahm' of https://github.com/noaa-ocs-modeling/C…
pvelissariou1 Aug 5, 2021
21faa62
fixed loading the platform modulefile
pvelissariou1 Aug 5, 2021
0154723
modified the pahm_from_file blocks
pvelissariou1 Aug 6, 2021
216b060
added aswip
zacharyburnett Aug 9, 2021
aa36dd4
updated submodule PAHM to commit 6212f2
pvelissariou1 Aug 15, 2021
d9b82cc
updated sources
pvelissariou1 Aug 26, 2021
dd3479b
updated PaHM sources
pvelissariou1 Aug 26, 2021
fdfb7d2
updated pahm cmake file
pvelissariou1 Aug 26, 2021
368a99e
updated orion modulefile to point to the latest stable modules in orion
pvelissariou1 Aug 26, 2021
aa3b70b
updated component_PAHM.mk
pvelissariou1 Aug 26, 2021
b3f1c98
modified the nuopc make files to include aswip
pvelissariou1 Aug 26, 2021
db9593b
updated PAHM sources and the PAHM pointer
pvelissariou1 Aug 29, 2021
36859a3
added aswip program
pvelissariou1 Aug 29, 2021
d90afd1
modified the ADCIRC/PAHM .mk files to use Makefile by default
pvelissariou1 Aug 29, 2021
13bec10
removed the tmp data pointer from the PaHM cap
pvelissariou1 Aug 29, 2021
960b567
removed the tmp data pointer
pvelissariou1 Aug 29, 2021
b2e6120
Fixed the tri, P, uwnd and vwnd variables for NetCDF output
pvelissariou1 Sep 23, 2021
6217a20
Removed the NetCDF atmospheric data inputs functionality
pvelissariou1 Sep 26, 2021
052408c
added doxygen modifications and files to PaHM
pvelissariou1 Nov 8, 2021
30a1d6e
added the doxygen layout file
pvelissariou1 Nov 8, 2021
f461b97
updated the documentation html pages for PaHM
pvelissariou1 Nov 8, 2021
300d5b2
added index.html link in PaHM/doc/
pvelissariou1 Nov 8, 2021
d652fc6
fixed bug in parwind.F90 lines 862 & 890 in converting forecast hours…
pvelissariou1 Nov 12, 2021
f49b37b
set dump to FALSE to avoid MPI_OpenFile errors; will be checked later
pvelissariou1 Nov 12, 2021
d143be6
modified the module file for hera to adapt to the latest system confi…
pvelissariou1 Dec 3, 2021
0c98cb7
modified the cmake module for hera to print a warning when the env. v…
pvelissariou1 Dec 3, 2021
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2 changes: 1 addition & 1 deletion ADCIRC
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Submodule ADCIRC updated from 742873 to 213416
2 changes: 1 addition & 1 deletion NEMS
Open in desktop
Submodule NEMS updated 16 files
+0 −226 src/ENS_Cpl/ENS_CplComp_ESMFMod_STUB.f90
+0 −9 src/ESMFVersionDefine.h
+0 −56 src/conf/configure.nems
+0 −0 src/conf/externals.nems
+0 −0 src/conf/modules.nems
+64 −0 src/incmake/component_PAHM.mk
+16 −0 src/module_EARTH_GRID_COMP.F90
+0 −3,786 src/module_EARTH_GRID_COMP.tmp.f90
+0 −59 src/module_EARTH_INTERNAL_STATE.tmp.f90
+0 −9,214 src/module_MEDIATOR.tmp.f90
+0 −1,440 src/module_MEDIATOR_SpaceWeather.tmp.f90
+0 −359 src/module_MEDIATOR_methods.tmp.f90
+0 −993 src/module_NEMS_GRID_COMP.tmp.f90
+0 −60 src/module_NEMS_INTERNAL_STATE.tmp.f90
+0 −741 src/module_NEMS_Rusage.tmp.f90
+0 −159 src/module_NEMS_UTILS.tmp.f90
2 changes: 1 addition & 1 deletion PAHM
Open in desktop
Submodule PAHM updated 3 files
+3 −3 cmake/Platforms/configure_intel.orion.cmake
+1 −1 cmake/distclean.cmake
+109 −0 nuopc/Makefile.in
6 changes: 4 additions & 2 deletions conf/configure.nems.hera.intel
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Original file line number Diff line number Diff line change
Expand Up @@ -12,8 +12,10 @@ include $(TOP)/conf/configure.nems.NUOPC
################################################################################
## Other settings

NETCDF_INC = -I$(NETCDF)/include
NETCDF_LIB = -L$(NETCDF)/lib -lnetcdf
LIBDIR ?= .

NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
NEMSIO_LIB = -L${LIBDIR} -lnemsio
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12 changes: 8 additions & 4 deletions conf/configure.nems.linux.gnu
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,15 @@ include $(TOP)/conf/configure.nems.NUOPC
################################################################################
## Other settings

NETCDF_INC = -I$(NETCDF_INCDIR)
NETCDF_LIB = -L$(NETCDF_LIBDIR) -lnetcdf
LIBDIR ?= .

NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
NEMSIO_LIB = -L${LIBDIR} -lnemsio
NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

#NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
#NEMSIO_LIB = -L${LIBDIR} -lnemsio
NEMSIO_INC =
NEMSIO_LIB =
SYS_LIB =

EXTLIBS = $(NEMSIO_LIB) \
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12 changes: 8 additions & 4 deletions conf/configure.nems.linux.intel
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,15 @@ include $(TOP)/conf/configure.nems.NUOPC
################################################################################
## Other settings

NETCDF_INC = -I$(NETCDF_INCDIR)
NETCDF_LIB = -L$(NETCDF_LIBDIR) -lnetcdf
LIBDIR ?= .

NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
NEMSIO_LIB = -L${LIBDIR} -lnemsio
NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

#NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
#NEMSIO_LIB = -L${LIBDIR} -lnemsio
NEMSIO_INC =
NEMSIO_LIB =
SYS_LIB =

EXTLIBS = $(NEMSIO_LIB) \
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12 changes: 8 additions & 4 deletions conf/configure.nems.linux.pgi
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,15 @@ include $(TOP)/conf/configure.nems.NUOPC
################################################################################
## Other settings

NETCDF_INC = -I$(NETCDF_INCDIR)
NETCDF_LIB = -L$(NETCDF_LIBDIR) -lnetcdf
LIBDIR ?= .

NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
NEMSIO_LIB = -L${LIBDIR} -lnemsio
NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

#NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
#NEMSIO_LIB = -L${LIBDIR} -lnemsio
NEMSIO_INC =
NEMSIO_LIB =
SYS_LIB =

EXTLIBS = $(NEMSIO_LIB) \
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6 changes: 4 additions & 2 deletions conf/configure.nems.ndcrc.intel
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Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,10 @@ include $(TOP)/conf/configure.nems.NUOPC
################################################################################
## Other settings

NETCDF_INC = -I$(NETCDF)/include
NETCDF_LIB = -L$(NETCDF)/lib -lnetcdff
LIBDIR ?= .

NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
NEMSIO_LIB = -L${LIBDIR} -lnemsio
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61 changes: 61 additions & 0 deletions conf/configure.nems.orion.gnu
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Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
## NEMS configuration file
##
## Platform: Generic/Linux
## Compiler: GNU with MPI --- needs fixing

SHELL = /bin/sh

################################################################################
## Include the common configuration parts
include $(TOP)/conf/configure.nems.NUOPC

################################################################################
## Other settings

LIBDIR ?= .

NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

#NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
#NEMSIO_LIB = -L${LIBDIR} -lnemsio
NEMSIO_INC =
NEMSIO_LIB =
SYS_LIB =

EXTLIBS = $(NEMSIO_LIB) \
$(NETCDF_LIB) \
$(ESMF_LIB) \
$(SYS_LIB) -lm

EXTLIBS_POST = $(NEMSIO_LIB) \
$(ESMF_LIB) \
$(NETCDF_LIB) \
$(SYS_LIB)
###
FC = mpif90 -g -ffree-line-length-none -fno-range-check -fbacktrace
F77 = mpiifort -g -ffree-line-length-none -fno-range-check -fbacktrace
FREE = -free
FIXED = -fixed
R8 = -r8

FINCS = $(ESMF_INC) $(NEMSIO_INC) $(NETCDF_INC)
#TRAPS = ???

#FFLAGS = $(TRAPS) $(FINCS) -fp-model strict
FFLAGS = $(TRAPS) $(FINCS)

OPTS_NMM = -g -ffree-line-length-none -fno-range-check -fbacktrace $(FREE)

FFLAGM_DEBUG =

FFLAGS_NMM = $(MACROS_NWM) $(OPTS_NMM) $(FFLAGS)

FPP = -fpp
CPP = cpp -P -traditional
CPPFLAGS = -DENABLE_SMP -DCHNK_RRTM=8

AR = ar
ARFLAGS = -r

RM = rm
61 changes: 61 additions & 0 deletions conf/configure.nems.orion.intel
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Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
## NEMS configuration file
##
## Platform: Generic/Linux
## Compiler: Intel with IntelMPI

SHELL = /bin/sh

################################################################################
## Include the common configuration parts
include $(TOP)/conf/configure.nems.NUOPC

################################################################################
## Other settings

LIBDIR ?= .

NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

#NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
#NEMSIO_LIB = -L${LIBDIR} -lnemsio
NEMSIO_INC =
NEMSIO_LIB =
SYS_LIB =

EXTLIBS = $(NEMSIO_LIB) \
$(NETCDF_LIB) \
$(ESMF_LIB) \
$(SYS_LIB) -lm

EXTLIBS_POST = $(NEMSIO_LIB) \
$(ESMF_LIB) \
$(NETCDF_LIB) \
$(SYS_LIB)
###
FC = mpiifort -g -qopenmp -mkl=sequential -align array32byte -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -qopenmp -convert big_endian -assume byterecl -mkl=sequential
F77 = mpiifort -g -qopenmp -mkl=sequential -align array32byte -lmkl_intel_lp64 -lmkl_core -lmkl_sequential -lpthread -qopenmp -convert big_endian -assume byterecl -mkl=sequential
FREE = -free
FIXED = -fixed
R8 = -r8

FINCS = $(ESMF_INC) $(NEMSIO_INC) $(NETCDF_INC)
#TRAPS = -g -fno-inline -no-ip -traceback -ftrapuv -fpe0 -ftz -check all -check noarg_temp_created -fp-stack-check

#FFLAGS = $(TRAPS) $(FINCS) -fp-model strict
FFLAGS = $(TRAPS) $(FINCS)

OPTS_NMM = -g -fno-inline -no-ip -traceback -ftrapuv -fpe0 -ftz -check all -check noarg_temp_created -fp-stack-check $(FREE)

FFLAGM_DEBUG =

FFLAGS_NMM = $(MACROS_NWM) $(OPTS_NMM) $(FFLAGS)

FPP = -fpp
CPP = cpp -P -traditional
CPPFLAGS = -DENABLE_SMP -DCHNK_RRTM=8

AR = ar
ARFLAGS = -r

RM = rm
61 changes: 61 additions & 0 deletions conf/configure.nems.orion.pgi
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Original file line number Diff line number Diff line change
@@ -0,0 +1,61 @@
## NEMS configuration file
##
## Platform: Generic/Linux
## Compiler: PGI with MPI --- needs fixing

SHELL = /bin/sh

################################################################################
## Include the common configuration parts
include $(TOP)/conf/configure.nems.NUOPC

################################################################################
## Other settings

LIBDIR ?= .

NETCDF_INC = -I${NETCDF_INCDIR}
NETCDF_LIB = -L${NETCDF_LIBDIR} -lnetcdf

#NEMSIO_INC = -I${LIBDIR}/incmod/nemsio
#NEMSIO_LIB = -L${LIBDIR} -lnemsio
NEMSIO_INC =
NEMSIO_LIB =
SYS_LIB =

EXTLIBS = $(NEMSIO_LIB) \
$(NETCDF_LIB) \
$(ESMF_LIB) \
$(SYS_LIB) -lm

EXTLIBS_POST = $(NEMSIO_LIB) \
$(ESMF_LIB) \
$(NETCDF_LIB) \
$(SYS_LIB)
###
FC = mpif90 -g -Mextend -Minform,inform -Mbounds
F77 = mpif90 -g -Mextend -Minform,inform -Mbounds
FREE = -free
FIXED =
R8 = -r8

FINCS = $(ESMF_INC) $(NEMSIO_INC) $(NETCDF_INC)
#TRAPS = -g -fno-inline -no-ip -traceback -ftrapuv -fpe0 -ftz -check all -check noarg_temp_created -fp-stack-check

#FFLAGS = $(TRAPS) $(FINCS) -fp-model strict
FFLAGS = $(TRAPS) $(FINCS)

OPTS_NMM = -g -Mextend -Minform,inform -Mbounds $(FREE)

FFLAGM_DEBUG =

FFLAGS_NMM = $(MACROS_NWM) $(OPTS_NMM) $(FFLAGS)

FPP = -fpp
CPP = cpp -P -traditional
CPPFLAGS = -DENABLE_SMP -DCHNK_RRTM=8

AR = ar
ARFLAGS = -r

RM = rm
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