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Merged
fossell merged 5 commits into from
May 10, 2022
Merged

Update community run script #491

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f5b2d71
run_upp script got the following updates:
kayeekayee May 5, 2022
b74250b
Further refinement from Tracy's comment.
kayeekayee May 5, 2022
8b76d29
Minor fix.
kayeekayee May 5, 2022
ec11e6b
More minor change from Tracy.
kayeekayee May 6, 2022
1b6d0d4
Link update from Tracy.
kayeekayee May 10, 2022
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50 changes: 24 additions & 26 deletions scripts/run_upp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,10 @@ set -x
# October 2020: Modified to remove WRF and grib1; Add FV3LAM
# Updates for cmake build, Change exec name
#
# May 2022: Modified to remove binarynemsiompiio;
# Added netcdfpara;
# Changed UPP directory name and path
#
#--------------------------------------------------------
#
# This script runs the stand-alone community version of UPP
Expand All @@ -31,11 +35,11 @@ set -x
#----------------------------------------------------------------------------------
#--- USER EDIT DESCIPTIONS --------------------------------------------------------
# See UPP User's Guide for more information
# https://upp.readthedocs.io/en/ufs-v2.0.0/
# https://upp.readthedocs.io/en/latest/
#----------------------------------------------------------------------------------
Comment thread
kayeekayee marked this conversation as resolved.
# TOP_DIR : Top level directory for building and running UPP
# DOMAINPATH : Working directory for this run.
# UNIPOST_HOME : Location of the EMC-post directory
# UPP_HOME : Location of the UPP directory
# POSTEXEC : Location of the UPP executable
# modelDataPath : Location of the model output data files to be post-processed
# txtCntrlFile : Name and location of the flat text file that lists desired fields for output
Expand All @@ -44,8 +48,8 @@ set -x
# LAM (Limited Area Model): postxconfig-NT-fv3lam.txt
# model : What model is used? GFS or LAM (Limited Area Model)
# inFormat : Format of the model data
# GFS - "binarynemsiompiio" or "netcdf"
# LAM - "netcdf"
# GFS - "netcdf" or "netcdfpara"
# LAM - "netcdf" or "netcdfpara"
# outFormat : Format of output from UPP
# grib2
# startdate : Forecast start date (YYYYMMDDHH)
Expand All @@ -64,8 +68,8 @@ set -x
# as recommended in the users guide where UPP will output.
export TOP_DIR=/home/username
export DOMAINPATH=${TOP_DIR}/test_case
export UNIPOST_HOME=${TOP_DIR}/EMC_post
export POSTEXEC=${UNIPOST_HOME}/bin
export UPP_HOME=${TOP_DIR}/UPP
export POSTEXEC=${UPP_HOME}/tests/install/bin
export modelDataPath=/path/to/model/data
export txtCntrlFile=${DOMAINPATH}/parm/postxconfig-NT-GFS.txt

Expand All @@ -92,9 +96,6 @@ export RUN_COMMAND="mpirun -np 1 ${POSTEXEC}/upp.x "
#export RUN_COMMAND="mpirun.lsf ${POSTEXEC}/upp.x "
#export RUN_COMMAND="mpiexec_mpt ${POSTEXEC}/upp.x "

# DEBUG command example found further below, search "DEBUG"


# Shouldn't need to edit these.
# tmmark is an variable used as the file extention of the output
# filename .GrbF is used if this variable is not set
Expand Down Expand Up @@ -135,17 +136,17 @@ else
fi

if [ ${model} == "GFS" ]; then
if [[ ${inFormat} == "binarynemsiompiio" ]]; then
echo "Check: You are using 'model' 'inFormat'!"
elif [[ ${inFormat} == "netcdf" ]]; then
if [[ ${inFormat} == "netcdf" || ${inFormat} == "netcdfpara" ]]; then
echo "Check: You are using 'model' 'inFormat'!"
else
echo "ERROR: 'inFormat' must be 'binarynemsiompiio' or 'netcdf' for GFS model output. Exiting... "
echo "ERROR: 'inFormat' must be 'netcdf' or 'netcdfpara' for GFS model output. Exiting... "
exit 1
fi
elif [[ ${model} == "LAM" ]]; then
Comment thread
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if [[ ${inFormat} != "netcdf" ]]; then
echo "ERROR: 'inFormat' must be 'netcdf' for LAM model output. Exiting... "
if [[ ${inFormat} == "netcdf" || ${inFormat} == "netcdfpara" ]]; then
echo "Check: You are using 'model' 'inFormat'!"
else
echo "ERROR: 'inFormat' must be 'netcdf' or 'netcdfpara' for LAM model output. Exiting... "
exit 1
fi
fi
Expand Down Expand Up @@ -194,17 +195,17 @@ fi
# file which defines the GRIB2 table values
if [[ ${outFormat} == "grib2" ]]; then
ln -fs ${txtCntrlFile} postxconfig-NT.txt
ln -fs ${UNIPOST_HOME}/parm/post_avblflds.xml post_avblflds.xml
ln -fs ${UNIPOST_HOME}/parm/params_grib2_tbl_new params_grib2_tbl_new
ln -fs ${UPP_HOME}/parm/post_avblflds.xml post_avblflds.xml
ln -fs ${UPP_HOME}/parm/params_grib2_tbl_new params_grib2_tbl_new
fi

# Link microphysics tables - code will use based on mp_physics option
# found in data
ln -fs ${UNIPOST_HOME}/parm/nam_micro_lookup.dat .
ln -fs ${UNIPOST_HOME}/parm/hires_micro_lookup.dat .
ln -fs ${UPP_HOME}/parm/nam_micro_lookup.dat .
ln -fs ${UPP_HOME}/parm/hires_micro_lookup.dat .

# link coefficients for crtm2 (simulated synthetic satellites)
CRTMDIR=${UNIPOST_HOME}/crtm/fix
CRTMDIR=${UPP_HOME}/crtm/fix
ln -fs $CRTMDIR/EmisCoeff/IR_Water/Big_Endian/Nalli.IRwater.EmisCoeff.bin ./
ln -fs $CRTMDIR/EmisCoeff/MW_Water/Big_Endian/FASTEM4.MWwater.EmisCoeff.bin ./
ln -fs $CRTMDIR/EmisCoeff/MW_Water/Big_Endian/FASTEM5.MWwater.EmisCoeff.bin ./
Expand Down Expand Up @@ -289,17 +290,14 @@ echo 'YY' $YY

# Create model file name (inFileName)
if [ ${model} == "GFS" ]; then
if [[ ${inFormat} == "binarynemsiompiio" ]]; then
inFileName=${modelDataPath}/atmf${fhour}.nemsio
flxFileName=${modelDataPath}/sfcf${fhour}.nemsio
elif [ ${inFormat} == "netcdf" ]; then
if [[ ${inFormat} == "netcdf" || ${inFormat} == "netcdfpara" ]]; then
inFileName=${modelDataPath}/atmf${fhour}.nc
flxFileName=${modelDataPath}/sfcf${fhour}.nc
fi
elif [ ${model} == "LAM" ]; then
if [ ${inFormat} == "netcdf" ]; then
if [[ ${inFormat} == "netcdf" || ${inFormat} == "netcdfpara" ]]; then
inFileName=${modelDataPath}/dynf${fhour}.nc
flxFileName=${modelDataPath}/dynf${fhour}.nc
flxFileName=${modelDataPath}/phyf${fhour}.nc
fi
fi

Expand Down