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release/public-v1: documentation, license, modulefiles, build.sh (#74)
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* Final touches: documentation, license, modulefiles
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@DusanJovic-NOAA
DusanJovic-NOAA authored Mar 5, 2020
1 parent 9d95a2b commit 52c13e4
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Showing 16 changed files with 9,642 additions and 10,248 deletions.
2 changes: 1 addition & 1 deletion FV3
Submodule FV3 updated 2 files
+5 −153 LICENSE.md
+26 −17 atmos_model.F90
637 changes: 19 additions & 618 deletions LICENSE.md
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2 changes: 1 addition & 1 deletion NEMS
Submodule NEMS updated 14 files
+3 −0 .gitignore
+10 −0 LICENSE.md
+2,445 −0 doc/Doxyfile.IN
+64 −0 doc/Makefile
+48 −0 doc/architecture.md
+15 −0 doc/cap-doc.md
+95 −0 doc/configuring.md
+12 −0 doc/documentation.dox
+76 −0 doc/introduction.md
+3 −0 doc/make-images-fit.css
+239 −0 doc/mediator.md
+21 −0 doc/nemsmain.md
+234 −0 doc/prep_inputs.py
+34 −0 doc/scan_repo.pl
7 changes: 6 additions & 1 deletion build.sh
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@@ -1,7 +1,12 @@
#!/bin/bash
set -eu

MYDIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
# Find date command
if [[ $(uname -s) == Darwin ]]; then
MYDIR=$(cd "$(dirname "$(greadlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
else
MYDIR=$(cd "$(dirname "$(readlink -f -n "${BASH_SOURCE[0]}" )" )" && pwd -P)
fi

export CMAKE_Platform=${CMAKE_Platform:?"Please set the CMAKE_Platform environment variable, e.g. [macosx.gnu|linux.gnu|linux.intel|hera.intel|...]"}
export CMAKE_C_COMPILER=${CMAKE_C_COMPILER:-mpicc}
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2 changes: 1 addition & 1 deletion modulefiles/cheyenne.gnu/fv3
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Expand Up @@ -25,7 +25,7 @@ module load netcdf/4.7.3
## use pre-compiled EMSF library and NCEP libraries for above compiler / MPI combination
##
module use -a /glade/p/ral/jntp/GMTB/tools/modulefiles/gnu-8.3.0/mpt-2.19
module load NCEPlibs/1.0.0beta02
module load NCEPlibs/1.0.0

##
## set cmake compilers
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2 changes: 1 addition & 1 deletion modulefiles/cheyenne.intel/fv3
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Expand Up @@ -25,7 +25,7 @@ module load netcdf/4.7.3
## use pre-compiled EMSF library and NCEP libraries for above compiler / MPI combination
##
module use -a /glade/p/ral/jntp/GMTB/tools/modulefiles/intel-19.0.5/mpt-2.19
module load NCEPlibs/1.0.0beta02
module load NCEPlibs/1.0.0

##
## set cmake compilers
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20 changes: 9 additions & 11 deletions modulefiles/gaea.intel/fv3
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Expand Up @@ -18,26 +18,24 @@ module-whatis "loads NEMS FV3 prerequisites for Gaea/Intel"
module load PrgEnv-intel/6.0.3
module rm intel
module load intel/18.0.3.222
module load cray-netcdf
module unload cray-mpich/7.4.0
module load cray-mpich/7.7.3
module unload cray-netcdf

module use -a /lustre/f2/pdata/esrl/gsd/ufs/modules/modulefiles/intel-18.0.3.222

##
## NCEP libraries (download and build manually for the time being; https://github.com/NCAR/NCEPlibs)
##
module load NCEPlibs/9.9.9

##
## use pre-compiled EMSF library for above compiler / MPI combination
## use pre-compiled EMSF library and NCEP libraries for above compiler / MPI combination
##
module load esmf/8.0.0
module use -a /lustre/f2/pdata/esrl/gsd/ufs/modules/modulefiles/intel-18.0.3.222
module load NCEPlibs/1.0.0

# Needed at runtime:
## Needed at runtime:
module load alps

##
## load cmake
##
module use -a /lustre/f2/pdata/esrl/gsd/ufs/modules/modulefiles/generic
module load cmake/3.16.4
setenv CMAKE_C_COMPILER cc
setenv CMAKE_CXX_COMPILER CC
setenv CMAKE_Fortran_COMPILER ftn
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2 changes: 1 addition & 1 deletion modulefiles/hera.intel/fv3
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Expand Up @@ -29,7 +29,7 @@ module load netcdf/4.7.0
## use pre-compiled EMSF library and NCEP libraries for above compiler / MPI combination
##
module use -a /scratch1/BMC/gmtb/software/modulefiles/intel-18.0.5.274/impi-2018.0.4
module load NCEPlibs/1.0.0beta02
module load NCEPlibs/1.0.0

##
## load cmake
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18 changes: 6 additions & 12 deletions modulefiles/jet.intel/fv3
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Expand Up @@ -14,27 +14,21 @@ module purge
## load slurm utils (arbitrary.pl layout.pl)
##
module load contrib sutils

module load intel/18.0.5.274
module load impi/2018.4.274
module load hdf5/1.10.4
module load netcdf/4.6.1

module use -a /lfs3/projects/hfv3gfs/GMTB/modulefiles/intel-18.0.5.274

##
### NCEP libraries (download and build manually for the time being; https://github.com/NCAR/NCEPlibs)
###
module load NCEPlibs/9.9.9
module load netcdf/4.7.0

##
### use pre-compiled EMSF library for above compiler / MPI combination
## use pre-compiled EMSF library and NCEP libraries for above compiler / MPI combination
##
module load esmf/8.0.0
module use -a /lfs3/projects/hfv3gfs/GMTB/modulefiles/intel-18.0.5.274/impi-2018.4.274
module load NCEPlibs/1.0.0

##
## load cmake
##
module use -a /lfs3/projects/hfv3gfs/GMTB/modulefiles/generic
module load cmake/3.16.4
setenv CMAKE_C_COMPILER mpiicc
setenv CMAKE_CXX_COMPILER mpiicpc
setenv CMAKE_Fortran_COMPILER mpiifort
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2 changes: 1 addition & 1 deletion stochastic_physics
Submodule stochastic_physics updated from e41f5e to 8accd3
16,376 changes: 8,182 additions & 8,194 deletions tests/Compile_cheyenne.gnu.log
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1,188 changes: 594 additions & 594 deletions tests/Compile_cheyenne.intel.log
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1,502 changes: 755 additions & 747 deletions tests/Compile_hera.intel.log
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38 changes: 19 additions & 19 deletions tests/RegressionTests_cheyenne.gnu.log
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@@ -1,9 +1,9 @@
Mon Feb 24 15:26:13 MST 2020
Wed Mar 4 17:27:13 MST 2020
Start Regression test


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_prod
Checking test 001 fv3_ccpp_gfs_v15p2 results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -95,7 +95,7 @@ Test 001 fv3_ccpp_gfs_v15p2 PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_coldstart_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_coldstart_prod
Checking test 002 fv3_ccpp_gfs_v15p2_coldstart results ....
Comparing phyf000.tile1.nc .........OK
Comparing phyf000.tile2.nc .........OK
Expand Down Expand Up @@ -125,7 +125,7 @@ Test 002 fv3_ccpp_gfs_v15p2_coldstart PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_restart_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_restart_prod
Checking test 003 fv3_ccpp_gfs_v15p2_restart results ....
Comparing phyf027.tile1.nc .........OK
Comparing phyf027.tile2.nc .........OK
Expand Down Expand Up @@ -187,7 +187,7 @@ Test 003 fv3_ccpp_gfs_v15p2_restart PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_no_nsst_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_no_nsst_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_no_nsst_prod
Checking test 004 fv3_ccpp_gfs_v15p2_no_nsst results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -279,7 +279,7 @@ Test 004 fv3_ccpp_gfs_v15p2_no_nsst PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_prod
Checking test 005 fv3_ccpp_gfs_v16beta results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -371,7 +371,7 @@ Test 005 fv3_ccpp_gfs_v16beta PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_coldstart_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_coldstart_prod
Checking test 006 fv3_ccpp_gfs_v16beta_coldstart results ....
Comparing phyf000.tile1.nc .........OK
Comparing phyf000.tile2.nc .........OK
Expand Down Expand Up @@ -401,7 +401,7 @@ Test 006 fv3_ccpp_gfs_v16beta_coldstart PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_restart_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_restart_prod
Checking test 007 fv3_ccpp_gfs_v16beta_restart results ....
Comparing phyf027.tile1.nc .........OK
Comparing phyf027.tile2.nc .........OK
Expand Down Expand Up @@ -463,7 +463,7 @@ Test 007 fv3_ccpp_gfs_v16beta_restart PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_no_nsst_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_no_nsst_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_no_nsst_prod
Checking test 008 fv3_ccpp_gfs_v16beta_no_nsst results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -555,7 +555,7 @@ Test 008 fv3_ccpp_gfs_v16beta_no_nsst PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_debug_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_debug_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_debug_prod
Checking test 009 fv3_ccpp_gfs_v15p2_debug results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -623,7 +623,7 @@ Test 009 fv3_ccpp_gfs_v15p2_debug PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_no_nsst_debug_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_no_nsst_debug_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_no_nsst_debug_prod
Checking test 010 fv3_ccpp_gfs_v15p2_no_nsst_debug results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -691,7 +691,7 @@ Test 010 fv3_ccpp_gfs_v15p2_no_nsst_debug PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_debug_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_debug_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_debug_prod
Checking test 011 fv3_ccpp_gfs_v16beta_debug results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -759,7 +759,7 @@ Test 011 fv3_ccpp_gfs_v16beta_debug PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_no_nsst_debug_ccpp
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_no_nsst_debug_prod
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_no_nsst_debug_prod
Checking test 012 fv3_ccpp_gfs_v16beta_no_nsst_debug results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -827,7 +827,7 @@ Test 012 fv3_ccpp_gfs_v16beta_no_nsst_debug PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_repro
Checking test 013 fv3_ccpp_gfs_v15p2 results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -919,7 +919,7 @@ Test 013 fv3_ccpp_gfs_v15p2 PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v15p2_no_nsst_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v15p2_no_nsst_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v15p2_no_nsst_repro
Checking test 014 fv3_ccpp_gfs_v15p2_no_nsst results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -1011,7 +1011,7 @@ Test 014 fv3_ccpp_gfs_v15p2_no_nsst PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_repro
Checking test 015 fv3_ccpp_gfs_v16beta results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -1103,7 +1103,7 @@ Test 015 fv3_ccpp_gfs_v16beta PASS


baseline dir = /glade/p/ral/jntp/GMTB/NEMSfv3gfs/RT/ufs-public-release-20200224/GNU/fv3_gfs_v16beta_no_nsst_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_3077/fv3_ccpp_gfs_v16beta_no_nsst_repro
working dir = /glade/scratch/heinzell/FV3_RT/rt_51249/fv3_ccpp_gfs_v16beta_no_nsst_repro
Checking test 016 fv3_ccpp_gfs_v16beta_no_nsst results ....
Comparing atmos_4xdaily.tile1.nc .........OK
Comparing atmos_4xdaily.tile2.nc .........OK
Expand Down Expand Up @@ -1195,5 +1195,5 @@ Test 016 fv3_ccpp_gfs_v16beta_no_nsst PASS


REGRESSION TEST WAS SUCCESSFUL
Mon Feb 24 16:29:33 MST 2020
Elapsed time: 01h:03m:20s. Have a nice day!
Wed Mar 4 18:33:10 MST 2020
Elapsed time: 01h:05m:57s. Have a nice day!
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