Development Web
-- DavidOvens - 18 Mar 2008
good documentation also at:
http://www.dtcenter.org/wrf-nmm/users/docs/presentations/index.php
# installing WRF 2.2 on oldsage Jan 2007 (see also ~ovens/notes/wps.notes):
cd wrf2007
set MAINDIR = $PWD
setenv NETCDF /usr/local/netcdf-ifort
if (`uname -m` == "x86_64") setenv NETCDF /usr
setenv NCARG_ROOT /usr/local/ncarg-ifort
setenv WRF_EM_CORE 1
source /usr/local/gempak/Gemenviron
echo $GEMEXE | grep 5.8
if ($status == 0) then
# GEMPAK 5.9 and 5.8 settings differ
# these are 5.8 settings
setenv JASPERLIB $NAWIPS/jasper/linux/lib
setenv JASPERINC $NAWIPS/jasper/linux/include
setenv PNGLIB $NAWIPS/lib/linux
setenv ZLIB $NAWIPS/lib/linux
setenv ZLIBINC $NAWIPS/gempak/include
else
# these are 5.9 settings
setenv JASPERLIB $GEMLIB
setenv JASPERINC $NAWIPS/extlibs/JasPer/v1.701.0/src/libjasper/include
setenv PNGLIB $GEMLIB
setenv ZLIB $GEMLIB
## not sure about this next one
setenv ZLIBINC $NAWIPS/gempak/include
endif
##
## one time only:
tar zxvf geog.tar.gz
##
## for each new WPS and WRFV2
tar zxvf ~/code_repository/WPSV2.2.TAR.gz
tar zxvf ~/code_repository/WRFV2.2.TAR.gz
##
## for each new domain
set GEOG = /home/disk/sage2/mm5rt/wps/geog
set DOMAIN = $MAINDIR/domains/may06
mkdir -p $DOMAIN
##
## compile WRF first
cd WRFV2
ifort -v
if (`uname -m` == "x86_64") then
## use option 9 on tahoma/rainier x86_64 machines
## (option 7 does not allow nesting,
## option 8 allows nesting, and seems to want to try to do multiple
## threads, but it really only uses 1.4 CPU... lame)
./configure <<EOF
9
EOF
else
## oldsage cluster
./configure <<EOF
12
EOF
endif
emacs configure.wrf &
## KEY MISSING ITEM: -P in
## CPP = /lib/cpp -traditional
## CPP = /lib/cpp -P -traditional
## ALSO ADD:
## LINUX_MPIHOME = /usr/local/mpich-ifort-1.2.5.2
## ALSO CHANGE TO:
## FC = $(LINUX_MPIHOME)/bin/mpif90 -f90=ifort
## LD = $(LINUX_MPIHOME)/bin/mpif90 -f90=ifort
## CC = $(LINUX_MPIHOME)/bin/mpicc -cc=gcc -DMPI2_SUPPORT -DFSEEKO64_OK
## FCOPTIM = -O2 -xW -tpp7
## FCBASEOPTS = -FR -cm -w -I. $(FCDEBUG) -convert big_endian
## KEY MISSING ITEM: -P in
## CPP = /lib/cpp -traditional
## CPP = /lib/cpp -P -traditional
## ALSO ADD:
## LINUX_MPIHOME = /usr/local/mpich-ifort-1.2.5.2
##
## did not make the wrfio_grib2 changes that I had to do with the
## pre-release. If problems appear due to GRIB2, bacio, g2lib, see
## the ~ovens/notes/wps.notes file for info on what I had to do with
## the pre-release.
##
## compile the code
./compile em_real | & tee make.out
## --> took 3 hours!!!!!!!!!!!!!!!!
## --> took 3 hours!!!!!!!!!!!!!!!!
##
## now compile WPS
cd ../WPS
if (! -e arch/preamble.orig) then
cp -p arch/preamble arch/preamble.orig
emacs arch/preamble
##
## I add LINUX_MPIHOME stuff right before SUFFIXES line:
LINUX_MPIHOME = /usr/local/mpich-ifort-1.2.5.2
## new tahoma one is this:
LINUX_MPIHOME = /usr/local/mpich-ifort-2.1.0.4p1
##
## MUST change hard-coded:
COMPRESSION_LIBS = -L/data3a/mp/gill/WPS_LIBS/local/lib \
-ljasper -lpng12 -lpng -lz
COMPRESSION_INC = -I/data3a/mp/gill/WPS_LIBS/local/include
## to
COMPRESSION_LIBS = -L$(JASPERLIB) -L$(PNGLIB) \
-ljasper -lpng12 -lpng -lz
COMPRESSION_INC = -I$(JASPERINC)
endif
if (! -e arch/configure.defaults.orig) then
cp -p arch/configure.defaults arch/configure.defaults.orig
emacs arch/configure.defaults
## on oldsage, look for and edit the
#ARCH PC Linux i486 i586 i686, Intel compiler DM parallel
# section as follows:
##
## I also do add LINUX_MPIHOME stuff:
FC = mpif90 -f90=ifort
## -->
FC = $(LINUX_MPIHOME)/bin/mpif90 -f90=ifort
## and
CC = mpicc -cc=icc
## -->
CC = $(LINUX_MPIHOME)/bin/mpicc -cc=gcc
## and I add NCARG stuff for using pgf90 instead of ifort
NCARGFC = pgf90
NCARGLDFLAGS = -byteswapio
## on tahoma, rainier, look for and edit the
#ARCH PC Linux x86_64 (IA64 and Opteron), PGI compiler 5.2 or higher, serial
# section as follows:
##
## change
COMPRESSION_LIBS = -L/contrib/zlib/lib -lz \
-L/contrib/jasper/lib -ljasper \
-L/contrib/libpng/lib -lpng
COMPRESSION_INC = -I/contrib/zlib/include \
-I/contrib/jasper/include \
-I/contrib/libpng/include
FC = pgf90
SFC = pgf90
FFLAGS = -Mfree -byteswapio -O
F77FLAGS = -byteswapio -O
FNGFLAGS = $(FFLAGS)
LDFLAGS =
CC = pgcc
SCC = pgcc
CFLAGS = -O
CPP = /lib/cpp -C -P -traditional
CPPFLAGS = -D_UNDERSCORE -DBYTESWAP -DLINUX -DIO_NETCDF -DIO_BINARY -DIO_GRIB1 -DBIT32
NCARG_LIBS2 = -L${PGI}/linux86-64/5.2/lib -lpgftnrtl -lpgc \
-L/usr/lib64 -lg2c
##
## to
FC = $(LINUX_MPIHOME)/bin/mpif90 -f90=ifort
SFC = ifort
FFLAGS = -FR -convert big_endian
F77FLAGS = -convert big_endian
FNGFLAGS = $(FFLAGS)
LDFLAGS =
CC = $(LINUX_MPIHOME)/bin/mpicc -cc=gcc
SCC = gcc
CFLAGS = -w
CPP = /lib/cpp -C -P -traditional
CPPFLAGS = -D_UNDERSCORE -DBYTESWAP -DLINUX -DIO_NETCDF -DIO_BINARY -DIO_GRIB1 -D_MPI -DBIT32
endif
if (`uname -m` == "x86_64") then
## use option 2 on tahoma/rainier x86_64 machines
./configure <<EOF
2
EOF
else
## use option 8 on oldsage cluster
./configure <<EOF
8
EOF
endif
if (! -e geogrid/src/parallel_module.F90.bad) then
cp -p geogrid/src/parallel_module.F90 geogrid/src/parallel_module.F90.bad
emacs geogrid/src/parallel_module.F90
## MUST delete MPI_Bcast calls for MPI_CHARACTER in
## geogrid/src/parallel_module.F90 with this:
if (present(from_whom)) then
! call MPI_Bcast(cval, n, MPI_CHARACTER, from_whom, comm, mpi_ierr)
else
! call MPI_Bcast(cval, n, MPI_CHARACTER, IO_NODE, comm, mpi_ierr)
end if
print *,'cannot run mpi_bcast on char...'
call exit(1)
endif
if (! -e ungrib/src/Makefile.orig) then
cp -p ungrib/src/Makefile ungrib/src/Makefile.orig
emacs ungrib/src/Makefile
##
## MUST CHANGE:
##
g2print.exe: gridinfo.o g2print.o
$(FC) -o $(@) $(LDFLAGS) g2print.o \
## to
g2print.exe: gridinfo.o g2print.o filelist.o gridinfo.o
$(FC) -o $(@) $(LDFLAGS) g2print.o filelist.o gridinfo.o \
endif
./compile |& tee make.out
pushd $DOMAIN
emacs $MAINDIR/WPS/namelist.wps &
cp $MAINDIR/WPS/namelist.wps .
set WPSDIR = $MAINDIR/WPS
##
## one time only
## NOTE that the opt_output_from_geogrid_path value setting of ./ will
## put the output into a path relative to the path to executable!
## if the the executable is not the current directory, ./ will not be
## the current directory, but the directory where the executable is
## located.
ln -s $WPSDIR/geogrid.exe .
./geogrid.exe |& tee geogrid.out
setenv RIP_ROOT $ms/rt/postprocess/RIP4
########################################################################
## Run ungrib
## edit share and ungrib sections of namelist.wps file
set date = 2006090712
set ym = `echo $date | cut -c1-6`
mkdir $ms2/wrf/$date.wps3
cd $ms2/wrf/$date.wps3
cp $WPSDIR/namelist.wps .
emacs namelist.wps&
## after setting start and end dates and confirming output format,
## we must supply a Vtable and the GRIB files must be linked to
## the filenames that are expected by ungrib. Many Vtables are
## already supplied and can just be linked in as 'Vtable'.
## e.g. ln -s ungrib/Vtable.GFS Vtable
##
## Wants files named GRIBFILE.AAA..., so use link_grib.csh to do this:
cp $WPSDIR/ungrib/Variable_Tables/Vtable.GFS Vtable
## past case
mkdir input.grids
cd input.grids
cp $ms/data/input.grids/$ym/$date/*gfs* .
gunzip *gz; bunzip2 *bz2
cd ..
set inputdir = $PWD/input.grids
## normal case
set inputdir = $ms/data/input.grids
$WPSDIR/link_grib.csh $inputdir/$date*gfs.grb
$WPSDIR/ungrib.exe
ls -l FIL*
rm GRIBFILE*
#In the final step of running WPS, the meteorological data extracted
# by ungrib are horizontally interpolated to the simulation grids
# defined by geogrid. In order to run metgrid, the namelist.wps file
# must be edited. In particular, the share and
# metgrid namelist sections are of relevance to the metgrid
# program. Examples of these sections are shown below.
# note that for metgrid, the opt_output_from_geogrid_path value setting
# of ./ will look for the output from geogrid in current directory
# --> needed to change that to a full path
# Also, metgrid needed to have this set:
# opt_metgrid_tbl_path = '/home/disk/sage2/mm5rt/wps/WPS/metgrid/',
# Also, if
# opt_output_from_metgrid_path = './',
# is set -- the default -- and you run the command as $path/metgrid.exe,
# the output does not go to ./ but to $path.
## Then created namelist.input and ran real.exe and wrf.exe off of that.
ln -s $WPSDIR/metgrid.exe .
./metgrid.exe |& tee metgrid.out
## run real.exe
#create a namelist.input file
cp $MAINDIR/WRFV2/run/namelist.input .
emacs namelist.input &
## set up the fdda stuff here, before real.exe
##
&fdda
grid_fdda = 1, 0,
gfdda_inname = "wrffdda_d<domain>"
gfdda_interval_m = 180, 0,
gfdda_end_h = 180, 0,
io_form_gfdda = 2
fgdt = 0, 0,
if_no_pbl_nudging_uv = 0
if_no_pbl_nudging_t = 1
if_no_pbl_nudging_q = 1
if_zfac_uv = 1, 0
k_zfac_uv = 10, 10
if_zfac_t = 0, 0
k_zfac_t = 10, 10
if_zfac_q = 0, 0
k_zfac_q = 10, 10
guv = 0.0001, 0.0001
gt = 0.0001, 0.0001
gq = 0.000001
if_ramping = 0
dtramp_min = 0.0
/
if (`uname -m` == "x86_64") then
/usr/local/mpich-ifort-2.1.0.4p1/bin/mpiexec -np 4 $MAINDIR/WRFV2/main/real.exe
else
/usr/local/mpich-ifort-1.2.5.2/bin/mpirun -np 1 $MAINDIR/WRFV2/main/real.exe
endif
ncdump -v Times wrfbdy*
ncdump -v Times wrfinput_d01
ncdump -v Times wrffdda_d01
cp $MAINDIR/WRFV2/run/[C-V]* .
cp $MAINDIR/WRFV2/run/{grib,ozone,tr,urban}* .
cp $MAINDIR/WRFV2/run/wrf.exe .
if (`uname -m` == "x86_64") then
time /usr/local/mpich-ifort-2.1.0.4p1/bin/mpiexec -np 4 $MAINDIR/WRFV2/main/wrf.exe
else
/usr/local/mpich-ifort-1.2.5.2/bin/mpirun -np 1 $PWD/wrf.exe
endif
========================================================================
installing WRF 2.0.2 on sage:
references:
http://www.mmm.ucar.edu/wrf/users/docs/user_guide/users_guide_chap2.html#Introduction
cd $ms3/wrf_tests
gunzip -c ../WRFV2.0.2.TAR.gz | tar xvf -
setenv NETCDF /usr/local
setenv WRF_EM_CORE 1
limit stacksize 480M
setenv MP_STACK_SIZE 64000000
setenv MPICH_F90 pgf90
setenv OMP_NUM_THREADS 1 # for now...
cd WRFV2/
##
## Note, the single-processor wrf.exe which I compiled first
## does not work with nests. Need to use my configure.wrf.mpi.
./configure
1
time ./compile em_real ## this took 14:06
ls -ls main/*.exe
## Now, attempt wrfsi
for 200603 build, see /home/disk/sage2/mm5rt/wrf2006/wrfsi/commands
references:
http://www.mmm.ucar.edu/wrf/users/docs/user_guide/users_guide_chap2.html#Introduction
http://www.mmm.ucar.edu/wrf/users/docs/user_guide/users_guide_chap3.html#Introduction
wrfsi/INSTALL:
http://www.wrf-model.org/si/wrfsiREADME.html
gunzip -c ../../wrfsi_v2.0.1.tar.gz | tar xvf -
cd wrfsi
setenv NETCDF /usr/local
setenv MPICH /usr/local/mpich-1.2.5.bad
mkdir /home/disk/sage2/mm5rt/wrf_tests/domains
mkdir /home/disk/sage2/mm5rt/wrf_tests/input.grids
##
## check for updates to global terrain, landuse, soil at
## ftp://aftp.fsl.noaa.gov/divisions/frd-laps/WRFSI/Geog_Data/
## and place into /home/disk/sage2/mm5rt/wrf_tests/terrain
perl -d install_wrfsi.pl \
--source_root=/home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi \
--installroot=/home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi \
--dataroot=/home/disk/sage2/mm5rt/wrf_tests/domains \
--ext_dataroot=/home/disk/sage2/mm5rt/wrf_tests/input.grids \
--geog_dataroot=/home/disk/sage2/mm5rt/wrf_tests/terrain \
--templates=/home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi/templates \
--path_to_netcdf=/usr/local
## paths output to:
## $INSTALLROOT/config_paths
##
## Instructions then say to:
##
## -- Set up grib_prep to ingest your GRIB data sets:
## a. cd /home/disk/sage2/mm5rt/wrf_tests/input.grids/static
## b. Edit grib_prep.nl and/or the Vtables
## -- See /home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi/HOW_TO_RUN.txt for more info
setenv INSTALLROOT /home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi
setenv SOURCE_ROOT /home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi
setenv DATAROOT /home/disk/sage2/mm5rt/wrf_tests/domains
setenv EXT_DATAROOT /home/disk/sage2/mm5rt/wrf_tests/input.grids
setenv GEOG_DATAROOT /home/disk/sage2/mm5rt/wrf_tests/terrain
setenv TEMPLATES /home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi/templates
##
## Step 1: Localize the simulation domain and create static fields - window_domain_rt.pl
##setenv MOAD_DATAROOT is a new case directory
setenv MOAD_DATAROOT /home/disk/sage2/mm5rt/wrf_tests/domains/dec03
cd $INSTALLROOT/templates
cp -r default $MOAD_DATAROOT:t
chmod -R ug+w $MOAD_DATAROOT:t
emacs $MOAD_DATAROOT:t/wrfsi.nl
## paid particular attention, as User's Guide Chap. 3 Step 1 (for
## window_domain_rt.pl) tells me, to the &hgridspec section
$INSTALLROOT/etc/window_domain_rt.pl -w wrfsi -c -t $TEMPLATES/$MOAD_DATAROOT:t
## this in turn, runs this:
## $INSTALLROOT/etc/localize_domain.pl --dataroot=/home/disk/sage2/mm5rt/wrf_tests/domains/dec03 --srcroot=/home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi --install_root=/home/disk/sage2/mm5rt/wrf_tests/WRFV2/wrfsi --which_type=wrfsi > /home/disk/sage2/mm5rt/wrf_tests/domains/dec03/log/localize_domain.log
##
## this did not work at all with '-t $TEMPLATES'. It created a
## single domain over the midwest! some stupid default, 144x144
## grid. They have now updated the User's Guide to the CRUCIAL
## '-t $TEMPLATES/$MOAD_DATAROOT:t'.
##
## Step 2: Debrib GRIB files - grib_prep.exe
emacs $EXT_DATAROOT/static/grib_prep.nl ## edit &gpinput_defs section
! The grib_prep.nl namelist is used to control execution of grib_prep, the
! program WRFSI uses to decode GRIB files into the binary intermediate format
! used by hinterp. It is composed of two namelist sections, "filetimespec"
! and "gpinputdefs". The grib_prep.exe executable expects to find this
! file in the working directory from which it is executed, along with
! a series of GRIB files to process named "GRIBFILE.AA", "GRIBFILE.AB",
! etc. The grib_prep.exe program only uses the filetimespec section of the
! namelist. The gpinputdefs section is used by the perl script "grib_prep.pl"
! to set up the EXT_DATA_ROOT/work/SOURCE subdirectory from which to run
! the executable. If you are not using grib_prep.pl to run grib_prep.exe, then
! you will need to manually set up everything that the script takes care of.
##
## Since I have gone to so much trouble to create pregrid.pl, I am going
## to skip their grib_prep.pl and use my own in the future.
perl -d $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 72 \
-t 3 -f '^2004092812_0[0-7]\d_gfs.grb' GFS
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092712 -l 0 \
-t 24 -f '^2004092\d12.sea_temp' OTISSST
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 0 \
-t 24 -f '^20040928\d\d_221.t.grb' ETA221
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 0 \
-t 24 -f '^20040928\d\d_221.t.grb' ETA221SOIL
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 0 \
-t 24 -f '^20040928(00|12)_000_ruc20soil.grb' RUC20
##trial
cd $EXT_DATAROOT/extprd
cat ETA221SOIL:2004-09-28_12 OTISSST:2004-09-27_12 > ETA221.SNOW_SOIL_OTIS.SST_FILE:2004-09-28_12
##
## NOTE: Vtables are slightly different than those used in MM5's
## pregrid -- the soil parameter output names have changed
##
## NOTE: $INSTALLROOT/src/grib_prep/grib.misc/grib_prep.F is
## $MM5/rt/preprocess/REGRID/pregrid/grib.misc/pregrid_grib.F
## differences are in output.F, add map%source, map%startloc
## rd_grib.F -- will want to modify/update
## to handle UKMO, thinned grids, etc.
##
## Step 3: Interpolating meteorological data - wrfprep.pl
## runs hinterp and vinterp
##
## make MOAD_DATAROOT/static/wrfsi.nl consistent with
## $TEMPLATES/$MOAD_DATAROOT:t/wrfsi.nl
## pay attention here to &interp_control section
emacs $MOAD_DATAROOT/static/wrfsi.nl
##
perl -d $INSTALLROOT/etc/wrfprep.pl -s 2004092812 -f 72
--> trying:
cp $MOAD_DATAROOT/static/wrfsi.nl.0hour $MOAD_DATAROOT/static/wrfsi.nl
perl -d $INSTALLROOT/etc/wrfprep.pl -s 2004092812 -f 0
b 926
system('pwd') tells us running in $MOAD_DATAROOT/siprd
hinterp fails for domain 2 with a segmentation fault on the SST
field... but this does work for GFS
--> trying:
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 0 \
-t 24 -f '^20040928\d\d_221.t.grb' ETA221FULL
cp $MOAD_DATAROOT/static/wrfsi.nl.0hour.eta221full $MOAD_DATAROOT/static/wrfsi.nl
perl -d $INSTALLROOT/etc/wrfprep.pl -s 2004092812 -f 0
## THIS WORKED !!!!!
## THIS WORKED !!!!!
--> trying:
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 0 \
-t 24 -f '^20040928\d\d_221.t.grb' ETA221LSM
cp $MOAD_DATAROOT/static/wrfsi.nl.allhours.gfs.eta221lsm $MOAD_DATAROOT/static/wrfsi.nl
## cp $MOAD_DATAROOT/static/wrfsi.nl.0hour.gfs.eta221lsm $MOAD_DATAROOT/static/wrfsi.nl
cd $MOAD_DATAROOT/siprd
ln -s $EXT_DATAROOT/extprd/{GFS,OTISSST,ETA221LSM}* .
$INSTALLROOT/bin/hinterp.exe |& tee WRFHELP.hinterp.out
foreach i (hinterp*)
cp $i WRFHELP.$i
end
$INSTALLROOT/bin/vinterp.exe |& tee WRFHELP.vinterp.out
foreach i (wrf_real*)
cp $i WRFHELP.$i
end
11/23
I am wondering, is my meshing just putting temperature into T when it
is really supposed to be potential temperature? A look at a single,
standard run should be able to confirm that it's potential
temperature. A my siprd.eta221otis/wrf_real* files have T not THETA,
but siprd.mesh2/wrf_real* have THETA. Which is correct?
11/23 tried:
:: cp $MOAD_DATAROOT/static/wrfsi.nl.fulltimerange.mixedconstants $MOAD_DATAROOT/static/wrfsi.nl
mkdir $MOAD_DATAROOT/siprd.mixedconstants
cd $MOAD_DATAROOT/siprd.mixedconstants
ln -s $EXT_DATAROOT/extprd/{GFS,ETA221.SNOW}* .
$INSTALLROOT/bin/hinterp.exe |& tee MIXEDCONST.hinterp.out
AGAIN, THIS CRASHED WITH SEGMENTATION FAULT. The mixed constants
approach does not work!
:: now, try spoofing ETA221LSM files (internal dates will be the start
time, but file name dates will look like forecast times):
cp $MOAD_DATAROOT/static/wrfsi.nl.allhours.gfs.eta221lsm $MOAD_DATAROOT/static/wrfsi.nl
mkdir siprd.multihourlsm
cd siprd.multihourlsm
ln -s $EXT_DATAROOT/extprd/{GFS,OTISSST,ETA221LSM}* .
set date = 2004092812
while ($date <= 2004100112)
set date = `time-increment "${date}0000" yy 0 10800 YYYYMMDDHH`
set fdate = `time-increment "${date}0000" yy 0 0 "YYYY-MM-DD_HH"`
echo "ln -s ETA221LSM:2004-09-28_12 ETA221LSM:$fdate"
ln -s ETA221LSM:2004-09-28_12 ETA221LSM:$fdate
end
$INSTALLROOT/bin/hinterp.exe |& tee MULTIHOURLSM.hinterp.out
==> FAILED, spoofed external date didn't fool it. The internal date
overruled.
Now, I think I should try testing a quick modification to MM5 PREGRID
to output into wrfsi format. Then, I can go back to the previous
test with the constants file and see if that works. Hmm...or should
I just use my mesh code on all GFS:FILE* files? result should be the
same...
:: 11/24 after talking with Rick, I think that the LSM approach is
actually very close to doing what I want. He also has used multiple
files in the CONSTANTS in MM5, so this may work for WRF.
. created Vtable.GFS2, Vtable.ETA221LSM2, Vtable.ETA221CONSTANT in
$EXT_DATAROOT/static/
. edited $EXT_DATAROOT/static/grib_prep.pl
. ran grib prep
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 0 -t 24 -f \
'^20040928\d\d_221.t.grb' ETA221CONSTANT
perl $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 0 -t 24 -f \
'^20040928\d\d_221.t.grb' ETA221LSM2
perl -d $INSTALLROOT/etc/grib_prep.pl -s 2004092812 -l 72 \
-t 3 -f '^2004092812_0[0-7]\d_gfs.grb' GFS
. now go for it..
cp $MOAD_DATAROOT/static/wrfsi.nl.allhours.gfs2.lsm2.constant $MOAD_DATAROOT/static/wrfsi.nl
mkdir $MOAD_DATAROOT/siprd.gfs2lsm2constant
cd $MOAD_DATAROOT/siprd.gfs2lsm2constant
ln -s $EXT_DATAROOT/extprd/{GFS2,ETA221LSM2,ETA221CONST,OTIS}* .
$INSTALLROOT/bin/hinterp.exe |& tee GFS2LSM2CONSTANT.hinterp.out
# worked !!
$INSTALLROOT/bin/vinterp.exe |& tee GFS2LSM2CONSTANT.vinterp.out
--- this worked, but output went into ../siprd not PWD !!!!
--- this worked, but output went into ../siprd not PWD !!!!
--- this worked, but output went into ../siprd not PWD !!!!
--- this worked, but output went into ../siprd not PWD !!!!
Answers were identical to WRFHELP because of the siprd problem!!!!
mv siprd siprd.wrfhelp
mv siprd.gfs2lsm2constant siprd
cd siprd
$INSTALLROOT/bin/vinterp.exe |& tee GFS2LSM2CONSTANT.vinterp.out
cd ..
mv siprd siprd.gfs2lsm2constant
mv siprd.wrfhelp siprd
this makes me think that SPECHUMD and SOILHGT need to be dropped via
further refinement of those Vtables... OR, I may just want to see if
the wrfinput and wrfby files actually differ between this and the
WRFHELP version.
##trial
cd $EXT_DATAROOT/extprd
cat ETA221SOIL:2004-09-28_12 OTISSST:2004-09-27_12 > ETA221.SNOW_SOIL_OTIS.SST_FILE:2004-09-28_12
## --> fails vinterp
CONSTANTS_FULL_NAME = 'OTISSST:2004-09-27_12',
works, but anything with ETA221SOIL stuff fails....
##
## hinterp notes from User's Guide:
## 10. CONSTANTS_FULL_NAME: Specifies a list of file names to look
## for in "CONSTANTS_PATH". Data contained in any of these
## files actually found will be used at every output time, and
## will take precedence over duplicate data found in
## LSM_ROOT/INIT_ROOT/LBC_ROOT files.
##
## check output:
$INSTALLROOT/bin/siscan $MOAD_DATAROOT/siprd/hinterp.d02.2004-09-28_12:00:00
## seems to have worked..., $MOAD_DATAROOT/siprd files hinterp*
## wrf_real_input_em* all exist
setenv NCARG_ROOT /usr/local/ncarg
setenv NCL_COMMAND /usr/local/ncarg/bin/ncl
cd $INSTALLROOT/graphics/ncl
./generate_images.pl ## puts images in $MOAD_DATAROOT/static/*cgm
##
## Preparing nested wrf input files using real.exe:
I created $MOAD_DATAROOT/setenv.csh
cd $INSTALLROOT/../test/em_real
ln -s $MOAD_DATAROOT/siprd/wrf_real_input_em.d02* .
rename . "wrf_real_input_em.d02*" d02 d01
emacs namelist.input
## only need one time and only first column matters
./real.exe
/bin/cp namelist.input namelist.d02.input
/bin/cp namelist.d01.input namelist.input
./real.exe
##
## I recompiled wrf.exe with -tp p7 instead of -tp p6 (the default)
## and I still got the error.
./wrf.exe
--> leads to a 'Floating Exception' really early on -- at the first
## time step -- so I need to examine the input data. What about
##TSK?? I saw problems in real.exe about that didn't I?
########################################################################
Ryan's scripts:
/home/disk/ridge/torn/wrf_scripts
Ryan's real-time:
/home/disk/ridge/torn/real_time_dom
Terrain info:
. as with 8/29/2003, I investigated the aug02/terrain.matchwrf
files. The WRF terrain values, found in
/home/sage2/mm5rt/wrf_tests/dataroot/mm5d1aug02/static are at MM5
cross points with one extra in the i and j locations. Hence, to
see the match up, look at the second to last entries in WRF (MM5
has **** in the last entries for the cross points, but WRF gives
real numbers).
. generated TERRAIN for MM5 to be used in WRF comparisons
-- aug02/terrain.matchwrf/TERRAIN_DOMAIN2 is the file that matches
/home/disk/wrf1/mm5rt/wrf_tests/dataroot/mm5d1aug02/static/static.wrfsi
as best as I can do it. This was generated in /ensm/TERRAIN on
wrf18 by modifying src/setup.F changing A/6370./ to A/6371.2/.
some more links from training:
http://box.mmm.ucar.edu/mm5/mpp/wrfbrowser
http://www.mmm.ucar.edu/wrf/users/WRF_arch_03.doc
trying to install new wrfsi
make WRF code
cd WRFV1.3/wrfsi-1.3.2/
setenv NETCDF /usr/local
setenv GEOG_DATAROOT /home/disk/sage2/mm5rt/wrf_tests/terrain
unsetenv EXT_DATAROOT
perl install_wrfsi.pl
Setting up a new domain:
setenv INSTALLROOT /home/disk/wrf1/mm5rt/wrf_tests/WRFV1/wrfsi
setenv MOAD_DATAROOT /home/disk/wrf1/mm5rt/wrf_tests/dataroot/torn
cd $INSTALLROOT/templates
cp -r default $MOAD_DATAROOT:t
chmod -R u+w $MOAD_DATAROOT:t
emacs $MOAD_DATAROOT:t/wrfsi.nl
cd $INSTALLROOT/etc
./window_domain_rt.pl -w wrfsi -t \
$INSTALLROOT/templates/$MOAD_DATAROOT:t -c -s $INSTALLROOT
cd $INSTALLROOT/etc
./wrfsi.pl -h
SRCPATH in
/home/disk/wrf1/mm5rt/wrf_tests/extdataroot/static/grib_prep.nl
shows where programs will look for input data
pushd /home/disk/wrf1/mm5rt/wrf_tests/dataroot/mm5d1aug02/gfs
ln -s /home/disk/mm5rt/data/input.grids/2003081200_*avn.grb .
cd $INSTALLROOT/etc
./wrfsi.pl 2003081200 24 GFS
grib_prep.pl (now run by wrfsi.pl) ==== PREGRID output format is
slightly different, files are bigger
-rw-rw-r-- 1 mm5rt rmm5rt 35210160 Sep 3 22:10 GFS.FILE:2003-08-29_12
-rw-rw-rw- 1 mm5rt rmm5rt 37824120 Sep 3 22:02 GFS:2003-08-29_12
wrfprep.pl (now run by wrfsi.pl) ==== REGRIDDER
problems:
x) what is the difference between
WRFV1/wrfsi/templates/mm5d1aug02/wrfsi.nl
($INSTALLROOT/templates/mm5d1aug02/wrfsi.nl)
and
dataroot/mm5d1aug02/static/wrfsi.nl
($MOAD_DATAROOT/static/wrfsi.nl) ?
1) README.namelist in test/em_real/ (../../run/README.namelist) needs
updating. Specifically, io_form_initial is now io_form_input.
2) wrfsi.nl in $INSTALLROOT/templates/default needs to be updated
there are very large portions which are missing
x) All logging should be to STDOUT by default, a user should specify
"-log logfile" on the command line to redirect STDOUT and STDERR
to a logfile. Here's how I do it:
while ($ARGV[0] ne "") {
if .. {
} elsif($ARGV[0] =~ /^-log/) {
$logfile = $ARGV[1];
shift; shift;
}
...
if ($logfile) {
close(STDOUT);
close(STDERR);
open (STDOUT,">>$logfile");
open(STDERR, ">&STDOUT");
}
x) where are the grib_prep filters specified? Mine always return
nothing.
x) in wrfprep.pl the workdir is $MOAD_DATAROOT/siprd and it cleans
this directory -- obviously you cannot have 2 of these running at
a time!!! Working directory MUST BE cwd!
x) why do GFS:* files show up in EXT_DATAROOT/extprd? shouldn't that
be an external data directory? Output should go to cwd.
x) in $MOAD_DATAROOT/static/wrfsi.nl the ANALPATH, LBCPATH, LSMPATH,
CONSTANTS_PATH environment variables are used to point to paths
for the input GRIB data -- in my case they are pointing to
EXT_DATAROOT/extprd. At no point do you specify that the Vtables
are in EXT_DATAROOT/static or that you will be running in
EXT_DATAROOT/work or that logging will go into EXT_DATAROOT/log.
You are using a hard-coded directory structure rather than being
explicit. For my part, I want EXT_DATAROOT/work to be local to
whatever machine I am running WRFSI on -- this speeds up program
execution, whereas the GRIB files in EXT_DATAROOT/extprd are links
to a big remote data disk -- definitely a place I do not wish to
run on or attempt to write to. You must be explicit about ALL
paths that you will be using and you really should get rid of most
of these directories anyways. What you really need in terms of
paths are:
1) path to Vtables
2) paths to GRIB data (SST, SOIL, MODEL, etc.)
3) path to working directory
4) path to output directory -- should default to current working
directory unless specified differently on the command line.
Also, do we really want to specify the starting and ending times
of this particular forecast in this file AND in namelist.input AND
to specify our initialization date on the command line? Why not
at least have wrfsi calculate this information based on the
initialization date from the command line?.....<add more>...xs
Also, major flaw in you "work" directory is that you cannot have 2
wrfsi scripts running simultaneously -- they'll try to use the
same directory!
x) ARGH!!!! why are SRCPATHs and filetimespec specified in yet another
namelist file -- EXT_DATAROOT/static/grib_prep.nl why can't this
be as used in wrfsi.nl???? -- Looks like maybe wrfprep.pl and
grib_prep.pl might be somewhat intelligent about dates...
x) why do I have to specify julday in namelist.input -- can't the
code figure this out for me, especially if I have to re-specify
all my run information in namelist_05.
x) Why in blazes is MOAD_DATAROOT/ populated with subdirectories
[cwd = current working directory]
cdl -- important information, get rid of this directory and
put the contents into the new "static" directory
log -- get rid of this and output to cwd
siprd -- what does this stand for? why would I want output to
go to this directory by default? It should go to cwd
static -- important files in here, however, wrfsi.nl contains
&filetimespec information which is definitely not
"static" -- it changes with each new forecast.
wrfprd -- get rid of this entirely.
3) prior to running wrfsi.pl, it is very difficult to determine how
the code is going to try to find model GRIB files. Where is this
specified? We store GRIB files in one central disk which is
readable but not writable by me. Do I need to create links
somewhere? -- this turns out to be specified in
/home/disk/wrf1/mm5rt/wrf_tests/extdataroot/static/grib_prep.nl is
that written by one of these programs or am I just supposed to know
that I should edit it?
x) A problem with all of WRF SI, input and output should by default
be into the current working directory unless otherwise specified by
options on the command-line. There are way too many directories and
environment variables floating around to keep track of.
Also, namelists that are going to be used by a program should be in
the current directory or specified on the command line.
x) Purging should be done by separate routines. Having wrfsi.pl
purge a directory such as this
Purging /home/disk/wrf1/mm5rt/wrf_tests/extdataroot/extprd/GFS:2003-07-06_12
is not helpful when you are simple trying to set up a run.
x) When some routine dies such as in wrfprep.pl line 474
...
}else{
print WPLOG "No matching files found for initial conditions.\n";
$timenow = `date -u`; chomp $timenow;
print "Died at $timenow\n";
close (WPLOG);
die;
}
...
Not only the log, but stdout should indicate what files could not be
found.
x) work directories, such as $EXT_DATAROOT/work/xx should be local
to the machine on which the code is running. /tmp is ideal for this
on most platforms. At least allow this as an option to wrfsi.pl,
grid_prep.pl, or wrfprep.pl.
see HOW_TO_RUN.txt, README, INSTALL,
in /home/disk/wrf1/mm5rt/wrf_tests/WRFV1/setenv.csh
setenv NETCDF /usr/src/netcdf-3.5.0
setenv DATAROOT /home/disk/wrf1/mm5rt/wrf_tests/dataroot
setenv GEOG_DATAROOT /home/disk/wrf1/mm5rt/wrf_tests/terrain
setenv EXT_DATAROOT /home/disk/wrf1/mm5rt/wrf_tests/extdataroot
setenv INSTALLROOT /home/disk/wrf1/mm5rt/wrf_tests/WRFV1/wrfsi
setenv PERL5OPT -Mblib=/home/disk/wrf1/mm5rt/wrf_tests/WRFV1/wrfsi/gui/perlTk/blib
setenv MOAD_DATAROOT /home/disk/wrf1/mm5rt/wrf_tests/dataroot/mm5d1aug02
7/3/2003: working on wrf:
. got wrfsi and wrf.exe and real.exe compiled
. on my domain, grep floating exception around 19th timestep on wrf18
in /tmp/
. my executable runs fine after running real.exe on Ryan's
real_input* files ---> implication, my wrfsi is fouled up
. next step is to try to run wrfsi to create his domain -- not sure
how to set environment variables to created this new domain
. I am not sure that their OpenMP compiler flags work, you see some
pgf90 lines that definitely do not have "-mp" in them, not sure if
they should be there -- tried one pretty standard version of
their's and got the following for Ryan's domain in /tmp/ryans on wrf18:
INPUT LANDUSE = USGS
LANDUSE TYPE = USGS FOUND 24 CATEGORIES 2 SEASONS
WATER CATEGORY = 16 SNOW CATEGORY = 24
Segmentation fault
Then, I made sure configure.wrf had
FCBASEOPTS = -fastsse -byteswapio -Ktrap=fp -Mfree \
-tp p7 -pc 32 -Mvect=prefetch,cachesize:524288 -mp $(FCDEBUG)
and this resulted in a successful running of the thing but with
Timings showing "0 f0.00000 elapsed seconds" for everthing.
Top showed one wrf.exe but timing was 1:48 vs. 4:12 (no -fastsse)
and 3:11 (with -fastsse and -mp code, but with OMP_NUM_THREADS=1)
.. timing indicates this is working
.. wrfout files are in exact agreement
. Ryan's stuff can be found in:
/home/disk/ridge/torn/wrfsi/data/static/wrfsi.nl
/home/disk/ridge/torn/wrfsi/data/siprd/ -- daily real_input* files
/home/disk/ridge/torn/WRFV1/test/em_real/ -- his run directory, namelist.input
/home/disk/ridge/torn/wrf_scripts/WRF_RT.OUT -- stdout from his run
. Ran the 2-d squall line case seemingly fine on wrf16 even though
the output showed:
Timing for main: time step # 1199 on domain 1: 0.00000 elapsed seconds.
Timing for main: time step # 1200 on domain 1: 0.00000 elapsed seconds.
Timing for main: time step # 1200 on domain 1: 0.00000 elapsed seconds.
Timing for Writing output for domain 1: 0.00000 elapsed seconds.
setting up a non-centered domain:
> I have a couple of questions about using the wrfsi GUI.
>
> #1 Since there is no nesting capability, it looks like I cannot set up
> a 36-km domain to match our current MM5 real-time 36-km domain
> (http://www.atmos.washington.edu/mm5rt/36kmterrain.gif) which was
> created by running MM5 TERRAIN and using a bigger outer 36-km
> domain that is never used. We chose to do this so that the
> longitude line over Washington would be vertical and not skewed.
> Since WRF seems to keep that requirement of center lat/lon being in
> the center of the mother domain and there are no nests, I am stuck
> creating a single bigger domain or a skewed version. Is that
> correct?
Actually SI allows you to define a off-centered grid. The variables you
need to define are
MOAD_KNOWN_LAT and MOAD_KNOWN_LON: these are the
lat and long of your center grid point (in your case, the 36 km domain's
center value);
MOAD_STAND_LATS: these are the true lats as you would
use it in MM5;
MOAD_STAND_LONS: this is the center longitude
from the MM5 definition (and this doesn't have to be the same as the
longitude of your center grid point).
So what you need to find are the values of lat and long in your center 36 km domain.
>
> #2 I am on the "Initialization Controls" tab of the wrfsi GUI and I
> really want to know what all of the NUM_DOMAINS, DOMAIN_ID_LIST,
> HINTERP_METHOD, etc. mean and what my choices are. Where can I
> find out about these?
There is a README.wrfsi_nl in the top wrfsi directory, and that has explanation
of the namelist variables used for SI.
>
here's how some people have compiled WRF with ifort Intel fortran
compiler:
From: "Hara, Masayuki" <hara.masayuki@jamstec.go.jp>
I compiled WRFSI with ifort v8.1 on i686/Redhat 7.3.
When you compile WRFSI using ifort, NetCDF libraries should be compiled
with gcc/ifort, too.
#--------------------------------------------------
CC=gcc
DEFS=-Di686 -DDEC -DBIT32 -DF90 -DFORTRANUNDERSCORE -DDYNAMIC
CFLAGS= $(DEFS)
DBCFLAGS= -g -DDEBUG=1 $(DEFS)
FC = ifort
NCARGFC = /usr/local/ncarg/bin/ncargf77
FFLAGS = $(INC) -O2 -convert big_endian
DBFLAGS = $(INC) -g -C -convert big_endian
FIXED=-fixed
FREE=-free
LDFLAGS=
CPP = ifort -E -free
CPPFLAGS = $(INC) $(DEFS)
USECPP=1
MACHTYPE = pc
#--------------------------------------------------
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