Merge remote-tracking branch 'upstream/support/lisf-557ww-7.6' into f…

…ix/SMAP_DA_soilTemp_bug_fix

.github/scripts/appimage/AppRun

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+#!/bin/bash
+
+SELF=$(readlink -f "${0}")
+HERE=${SELF%/*}
+
+LISF_LIBS_OPENJPEG=${HERE}/usr/lib/openjpeg/2.4.0_gnu-11.2.0
+LISF_LIBS_ECCODES=${HERE}/usr/lib/eccodes/2.22.0_gnu-11.2.0
+LISF_LIBS_NETCDF=${HERE}/usr/lib/netcdf/4.7.4_gnu-11.2.0
+LISF_LIBS_HDF4=${HERE}/usr/lib/hdf4/4.2.15_gnu-11.2.0
+LISF_LIBS_HDFEOS=${HERE}/usr/lib/hdfeos2/3.0_gnu-11.2.0
+LISF_LIBS_HDF5=${HERE}/usr/lib/hdf5/1.12.0_gnu-11.2.0
+LISF_LIBS_ESMF=${HERE}/usr/lib/esmf/8.1.1_gnu-11.2.0_mpich-3.4
+LISF_LIBS_GDAL=${HERE}/usr/lib/gdal/3.5.2_gnu-11.2.0
+LISF_LIBS_FORTRANGIS=${HERE}/usr/lib/fortrangis/2.6-6_gnu-11.2.0
+LISF_LIBS_LIBGEOTIFF=${HERE}/usr/lib/geotiff/1.7.0_gnu-11.2.0
+LISF_LIBS_PROJ=${HERE}/usr/lib/proj/9.1.0_gnu-11.2.0
+LISF_LIBS_TIFF=${HERE}/usr/lib/tiff/4.0.9_gnu-11.2.0
+
+LISF_LIBS_PATH=""
+LISF_LIBS_PATH+=":${LISF_LIBS_ECCODES}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_NETCDF}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_ESMF}/lib/libO/Linux.gfortran.64.mpich3.default"
+LISF_LIBS_PATH+=":${LISF_LIBS_HDF5}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_HDF4}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_GDAL}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_LIBGEOTIFF}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_FORTRANGIS}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_OPENJPEG}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_PROJ}/lib"
+LISF_LIBS_PATH+=":${LISF_LIBS_TIFF}/lib"
+export LISF_LIBS_PATH
+
+export LANG=C
+export LD_LIBRARY_PATH=${LISF_LIBS_PATH}:${LD_LIBRARY_PATH}
+export ECCODES_DEFINITION_PATH=${LISF_LIBS_ECCODES}/share/eccodes/definitions
+export ECCODES_SAMPLES_PATH=${LISF_LIBS_ECCODES}/share/eccodes/samples
+
+export PATH=${HERE}/usr/bin:${PATH}
+
+function lisf_usage {
+   NAME="LISF-x86_64.AppImage"
+   echo "Usage: $NAME [options] [-- LISF options]"
+   echo ""
+   echo "   where [options] are:"
+   echo "   -h               show this help message"
+   echo "   -v               show revision info about LISF"
+   echo "   -i               show configuration info about LISF"
+   echo "   -a <LDT|LIS|LVT> specify which app to run"
+   echo ""
+   echo "   where [LISF options] are options to pass to LISF;"
+   echo "   these must be preceeded by --"
+   echo ""
+   echo "   Examples:"
+   echo "      $NAME -a LDT ldt.config"
+   echo "      mpirun -n N $NAME -a LIS -- --file lis.config"
+   echo "      $NAME -a LVT lvt.config"
+}
+
+function lisf_version {
+   echo "## Revision info"
+   echo ""
+   cat "${HERE}/info/revision.log"
+}
+
+function lisf_info {
+   lisf_version
+   echo ""
+   echo "## LDT info"
+   echo ""
+   echo "### LDT_NetCDF_inc.h"
+   cat "${HERE}/info/ldt/LDT_NetCDF_inc.h"
+   echo ""
+   echo "### LDT_misc.h"
+   cat "${HERE}/info/ldt/LDT_misc.h"
+   echo ""
+   echo "### configure.ldt"
+   cat "${HERE}/info/ldt/configure.ldt"
+   echo ""
+   echo "## LIS info"
+   echo ""
+   echo "### LIS_NetCDF_inc.h"
+   cat "${HERE}/info/lis/LIS_NetCDF_inc.h"
+   echo ""
+   echo "### LIS_misc.h"
+   cat "${HERE}/info/lis/LIS_misc.h"
+   echo ""
+   echo "### LIS_plugins.h"
+   cat "${HERE}/info/lis/LIS_plugins.h"
+   echo ""
+   echo "### configure.lis"
+   cat "${HERE}/info/lis/configure.lis"
+   echo ""
+   echo "## LVT info"
+   echo ""
+   echo "### LVT_misc.h"
+   cat "${HERE}/info/lvt/LVT_NetCDF_inc.h"
+   echo ""
+   echo "### LVT_misc.h"
+   cat "${HERE}/info/lvt/LVT_misc.h"
+   echo ""
+   echo "### configure.lvt"
+   cat "${HERE}/info/lvt/configure.lvt"
+}
+
+if [[ ${#} -eq 0 ]]
+then
+   lisf_usage
+fi
+
+optstring=":hvia:"
+while getopts ${optstring} arg
+do
+   case ${arg} in
+      h)
+         lisf_usage
+         exit 0
+         ;;
+      v)
+         lisf_version
+         exit 0
+         ;;
+      i)
+         lisf_info
+         exit 0
+         ;;
+      a)
+         APP="${OPTARG}"
+         ;;
+      ?)
+         echo "Invalid option: -${OPTARG}"
+         echo ""
+         lisf_usage
+         exit 1
+         ;;
+   esac
+done
+
+shift $((${OPTIND} - 1))
+exec "${HERE}/usr/bin/${APP}" "${@}"

.github/scripts/appimage/Dockerfile

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+FROM lisf_libraries
+
+# LISF {{{
+WORKDIR /home/workdir
+COPY  LISF ./LISF
+RUN cp ./LISF/.github/scripts/appimage/lisf.env .
+RUN cp ./LISF/.github/scripts/appimage/compile_lisf .
+RUN ./compile_lisf
+# }}}
+
+# AppImage {{{
+WORKDIR /home/workdir
+COPY ./LISF/.github/scripts/appimage/AppRun .
+COPY ./LISF/.github/scripts/appimage/LISF.png .
+COPY ./LISF/.github/scripts/appimage/LISF.desktop .
+COPY ./LISF/.github/scripts/appimage/prep_appdir .
+RUN ./prep_appdir
+# }}}

.github/scripts/appimage/LISF.desktop

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+[Desktop Entry]
+Name=LISF
+Exec=LISF
+Icon=LISF
+Type=Application
+Categories=Utility;

.github/scripts/appimage/compile_lisf

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+#!/usr/bin/env bash
+
+source lisf.env
+cd LISF
+
+#
+# Revision
+#
+
+git log -n 1 --oneline --decorate >revision.log
+
+#
+# LDT
+#
+
+# Parallelism (0-serial, 1-dmpar, default=0): 0
+# Optimization level (-3=strict checks with warnings, -2=strict checks, -1=debug, 0,1,2,3, default=2): 2
+# Assume little/big_endian data format (1-little, 2-big, default=2): 2
+# Use GRIBAPI/ECCODES? (0-neither, 1-gribapi, 2-eccodes, default=2): 2
+# NETCDF version (3 or 4, default=4)?: 4
+# NETCDF use shuffle filter? (1-yes, 0-no, default = 1): 1
+# NETCDF use deflate filter? (1-yes, 0-no, default = 1): 1
+# NETCDF use deflate level? (1 to 9-yes, 0-no, default = 9): 1
+# Use HDF4? (1-yes, 0-no, default=1): 1
+# Use HDF5? (1-yes, 0-no, default=1): 1
+# Use HDFEOS? (1-yes, 0-no, default=1): 1
+# Enable GeoTIFF support? (1-yes, 0-no, default=1): 1
+# Enable LIBGEOTIFF support? (1-yes, 0-no, default=1): 1
+# Include date/time stamp history? (1-yes, 0-no, default=1): 1
+
+cd ldt
+printf '%s\n' "0" "2" "2" "2" "4" "1" "1" "1" "1" "1" "1" "1" "1" "1" | ./configure
+./compile -j 2
+
+#
+# LIS
+#
+
+# Parallelism (0-serial, 1-dmpar, default=1): 1
+# Optimization level (-3=strict checks with warnings, -2=strict checks, -1=debug, 0,1,2,3, default=2): 2
+# Assume little/big_endian data format (1-little, 2-big, default=2): 2
+# Use GRIBAPI/ECCODES? (0-neither, 1-gribapi, 2-eccodes, default=2): 2
+# Enable AFWA-specific grib configuration settings? (1-yes, 0-no, default=0): 0
+# Use NETCDF? (1-yes, 0-no, default=1): 1
+# NETCDF version (3 or 4, default=4): 4
+# NETCDF use shuffle filter? (1-yes, 0-no, default = 1): 1
+# NETCDF use deflate filter? (1-yes, 0-no, default = 1): 1
+# NETCDF use deflate level? (1 to 9-yes, 0-no, default = 9): 1
+# Use HDF4? (1-yes, 0-no, default=1): 1
+# Use HDF5? (1-yes, 0-no, default=1): 1
+# Use HDFEOS? (1-yes, 0-no, default=1): 1
+# Use MINPACK? (1-yes, 0-no, default=0): 0
+# Use LIS-CRTM? (1-yes, 0-no, default=0): 0
+# Use LIS-CMEM? (1-yes, 0-no, default=0): 0
+# Use LIS-LAPACK? (0-no, 1-mkl, 2-lapack/blas, 3-lapack/refblas, default=0): 0
+# Use PETSc? (1-yes, 0-no, default=0): 0
+
+cd ../lis
+printf '%s\n' "1" "2" "2" "2" "0" "1" "4" "1" "1" "1" "1" "1" "1" "0" "0" "0" "0" "0" | ./configure
+./compile -j 2
+
+#
+# LVT
+#
+
+# Optimization level (-3=strict checks with warnings, -2=strict checks, -1=debug, 0,1,2,3, default=2): 2
+# Assume little/big_endian data format (1-little, 2-big, default=2): 2
+# Use GRIBAPI/ECCODES? (1-gribapi, 2-eccodes, default=2): 2
+# Use NETCDF? (1-yes, 0-no, default=1): 1
+# NETCDF version (3 or 4, default=4): 4
+# NETCDF use shuffle filter? (1-yes, 0-no, default = 1): 1
+# NETCDF use deflate filter? (1-yes, 0-no, default = 1): 1
+# NETCDF use deflate level? (1 to 9-yes, 0-no, default = 9): 1
+# Use HDF4? (1-yes, 0-no, default=1): 1
+# Use HDF5? (1-yes, 0-no, default=1): 1
+# Use HDFEOS? (1-yes, 0-no, default=1): 1
+# Enable AFWA-specific grib configuration settings? (1-yes, 0-no, default=0): 0
+# Enable GeoTIFF support? (1-yes, 0-no, default=1): 1
+# Use MATLAB support? (1-yes, 0-no, default=0): 0
+
+cd ../lvt
+printf '%s\n' "2" "2" "2" "1" "4" "1" "1" "1" "1" "1" "1" "0" "1" "0" | ./configure
+./compile -j 2

.github/scripts/appimage/lisf.env

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+LISF_LIBS_MPICH=/home/workdir/lib/mpich/3.4_gnu-11.2.0
+LISF_LIBS_OPENJPEG=/home/workdir/lib/openjpeg/2.4.0_gnu-11.2.0
+LISF_LIBS_ECCODES=/home/workdir/lib/eccodes/2.22.0_gnu-11.2.0
+LISF_LIBS_NETCDF=/home/workdir/lib/netcdf/4.7.4_gnu-11.2.0
+LISF_LIBS_HDF4=/home/workdir/lib/hdf4/4.2.15_gnu-11.2.0
+LISF_LIBS_HDFEOS=/home/workdir/lib/hdfeos2/3.0_gnu-11.2.0
+LISF_LIBS_HDF5=/home/workdir/lib/hdf5/1.12.0_gnu-11.2.0
+LISF_LIBS_ESMF=/home/workdir/lib/esmf/8.1.1_gnu-11.2.0_mpich-3.4
+LISF_LIBS_PROJ=/home/workdir/lib/proj/9.1.0_gnu-11.2.0
+LISF_LIBS_GDAL=/home/workdir/lib/gdal/3.5.2_gnu-11.2.0
+LISF_LIBS_FORTRANGIS=/home/workdir/lib/fortrangis/2.6-6_gnu-11.2.0
+LISF_LIBS_LIBGEOTIFF=/home/workdir/lib/geotiff/1.7.0_gnu-11.2.0
+LISF_LIBS_TIFF=/home/workdir/lib/tiff/4.0.9_gnu-11.2.0
+LISF_LIBS_LAPACK=/home/workdir/lib/blaslapack/3.11.0_gnu-11.2.0
+LISF_LIBS_PETSC=/home/workdir/lib/petsc/3.16.1_gnu-11.2.0
+
+LISF_LIBS_PATH="$LISF_LIBS_MPICH/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_ECCODES/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_NETCDF/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_ESMF/lib/libO/Linux.gfortran.64.mpich3.default"
+LISF_LIBS_PATH+=":$LISF_LIBS_HDF5/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_HDF4/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_PROJ/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_GDAL/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_LIBGEOTIFF/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_OPENJPEG/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_TIFF/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_LAPACK/lib"
+LISF_LIBS_PATH+=":$LISF_LIBS_PETSC/lib"
+export LISF_LIBS_PATH
+
+def_lis_jpeg=""
+def_lis_openjpeg=$LISF_LIBS_OPENJPEG
+def_lis_eccodes=$LISF_LIBS_ECCODES
+def_lis_netcdf=$LISF_LIBS_NETCDF
+def_lis_hdf4=$LISF_LIBS_HDF4
+def_lis_hdfeos=$LISF_LIBS_HDFEOS
+def_lis_hdf5=$LISF_LIBS_HDF5
+def_lis_modesmf=$LISF_LIBS_ESMF/mod/modO/Linux.gfortran.64.mpich3.default
+def_lis_libesmf=$LISF_LIBS_ESMF/lib/libO/Linux.gfortran.64.mpich3.default
+def_lis_minpack=""
+def_lis_crtm=""
+def_lis_crtm_prof=""
+def_lis_cmem=""
+def_lis_lapack=$LISF_LIBS_LAPACK/lib
+def_lis_petsc=$LISF_LIBS_PETSC
+def_lvt_gdal=$LISF_LIBS_GDAL
+def_lvt_fortrangis=$LISF_LIBS_FORTRANGIS
+def_ldt_libgeotiff=$LISF_LIBS_LIBGEOTIFF
+
+export LIS_ARCH=linux_gfortran
+export LIS_SPMD=parallel
+export LIS_FC=mpif90
+export LIS_CC=mpicc
+export LIS_CPPC=mpiCC
+export LIS_JPEG=$def_lis_jpeg
+export LIS_OPENJPEG=$def_lis_openjpeg
+export LIS_ECCODES=$def_lis_eccodes
+export LIS_NETCDF=$def_lis_netcdf
+export LIS_HDF4=$def_lis_hdf4
+export LIS_HDFEOS=$def_lis_hdfeos
+export LIS_HDF5=$def_lis_hdf5
+export LIS_MODESMF=$def_lis_modesmf
+export LIS_LIBESMF=$def_lis_libesmf
+export LIS_MINPACK=$def_lis_minpack
+export LIS_CRTM=$def_lis_crtm
+export LIS_CRTM_PROF=$def_lis_crtm_prof
+export LIS_CMEM=$def_lis_cmem
+export LIS_PETSC=$def_lis_petsc
+export LIS_LAPACK=$def_lis_lapack
+
+export LDT_ARCH=linux_gfortran
+export LDT_FC=mpif90
+export LDT_CC=mpicc
+export LDT_JPEG=$def_lis_jpeg
+export LDT_OPENJPEG=$def_lis_openjpeg
+export LDT_ECCODES=$def_lis_eccodes
+export LDT_NETCDF=$def_lis_netcdf
+export LDT_HDF4=$def_lis_hdf4
+export LDT_HDFEOS=$def_lis_hdfeos
+export LDT_HDF5=$def_lis_hdf5
+export LDT_MODESMF=$def_lis_modesmf
+export LDT_LIBESMF=$def_lis_libesmf
+export LDT_GDAL=$def_lvt_gdal
+export LDT_FORTRANGIS=$def_lvt_fortrangis
+export LDT_LIBGEOTIFF=$def_ldt_libgeotiff
+
+export LVT_ARCH=linux_gfortran
+export LVT_FC=mpif90
+export LVT_CC=mpicc
+export LVT_JPEG=$def_lis_jpeg
+export LVT_OPENJPEG=$def_lis_openjpeg
+export LVT_ECCODES=$def_lis_eccodes
+export LVT_NETCDF=$def_lis_netcdf
+export LVT_HDF4=$def_lis_hdf4
+export LVT_HDFEOS=$def_lis_hdfeos
+export LVT_HDF5=$def_lis_hdf5
+export LVT_MODESMF=$def_lis_modesmf
+export LVT_LIBESMF=$def_lis_libesmf
+export LVT_GDAL=$def_lvt_gdal
+export LVT_FORTRANGIS=$def_lvt_fortrangis
+
+export LANG=C
+export PATH=$LISF_LIBS_MPICH/bin:$PATH
+export LD_LIBRARY_PATH=$LISF_LIBS_PATH:$LD_LIBRARY_PATH
+
+unset def_lis_jpeg
+unset def_lis_openjpeg
+unset def_lis_eccodes
+unset def_lis_netcdf
+unset def_lis_hdf4
+unset def_lis_hdfeos
+unset def_lis_hdf5
+unset def_lis_modesmf
+unset def_lis_libesmf
+unset def_lis_minpack
+unset def_lis_crtm
+unset def_lis_crtm_prof
+unset def_lis_cmem
+unset def_lis_lapack
+unset def_lis_petsc
+unset def_lvt_gdal
+unset def_lvt_fortrangis
+unset def_ldt_libgeotiff
+unset LISF_LIBS_MPICH
+unset LISF_LIBS_OPENJPEG
+unset LISF_LIBS_ECCODES
+unset LISF_LIBS_NETCDF
+unset LISF_LIBS_HDF4
+unset LISF_LIBS_HDFEOS
+unset LISF_LIBS_HDF5
+unset LISF_LIBS_ESMF
+unset LISF_LIBS_PROJ
+unset LISF_LIBS_GDAL
+unset LISF_LIBS_FORTRANGIS
+unset LISF_LIBS_LIBGEOTIFF
+unset LISF_LIBS_TIFF
+unset LISF_LIBS_LAPACK
+unset LISF_LIBS_PETSC

.github/scripts/appimage/make_appimage

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+#!/usr/bin/env bash
+
+sudo docker create --name dummy lisf_appdir
+sudo docker cp dummy:/home/workdir/LISF.AppDir .
+sudo docker rm -f dummy
+
+sudo appimagetool LISF.AppDir