Modeling Aerosol Dust: WRF Model installation,running and error log

Running

High Profile Computer Commands

qstat : shows all jobs in the Queue.
quota -s
showq : shows the state of the Queue.
showstart JOBID : Gives an indication of Start and Completion Times ...
NOTE: showstart is very unreliable and can give misleading results.

ssh bigmem1024-1

sudo openvpn --config /home/homo/Dropbox/vpn/newyork.ovpn

Running commands

ncl util/plotgrids_new.ncl

rm met_em.d01.*
rm geogrid.log ungrib.log metgrid.log

ln -sf /home/users/halbadi/wrf/parwrf/WPS/geogrid/GEOGRID.TBL.ARW_CHEM GEOGRID.TBL

./geogrid.exe

ln -sf ungrib/Variable_Tables/Vtable.GFS Vtable

./link_grib.csh /home/homo/Model_IO_data/Case_data/WPS_input/WRF-CHEM_GFS/10*
./link_grib.csh /home/users/halbadi/cases/WRF-CHEM_GFS/10*

./ungrib.exe >& ungrib.log

./metgrid.exe

cd test/em_real

ln -sf /home/homo/model/WPS/met_em.d01.2010* .
ln -sf /home/users/halbadi/wrf/WPS/met_em.d01.2010* .
ln -sf /home/users/halbadi/wrf/parwrf/WPS/met_em.d01.2010-07* .
ln -sf /scratch/halbadi/20100714_3km/met_em.d01.2010-07* .

./real.exe

./wrf.exe

Resources

http://www.goes-r.gov/users/comet/mesoprim/dust/navmenu.php_tab_1_page_8.4.2.htm

WRF online tutorial

WRF Administration site

WRF modeling system source codes download page

User’s Guide for the Advanced Research WRF (ARW) Modeling System Version 3.5 ucar.edu

WRF : WORKING GROUP 11: ATMOSPHERIC CHEMISTRY

EUROPEAN OPERATIONAL AIR QUALITY FORECASTS: WRF/CHEM-EMIMO by Universidad Politécnica

WRF user forums

Exercises with WRF in Dust and Climate Change

Installation :

Main Rules - Install WRF first then WPS

Instullation Resources

-Installing WRF model in Zepheyr
- Build Flex from source :difficulty installing flex-2.5.33.tar.gz on linux (debian)
- http://www2.mmm.ucar.edu/wrf/OnLineTutorial/Class/cases/find_the_bugs.php

To instal HDF5

./configure --prefix=/usr/local/hdf5 --enable-fortran --with-zlib=/usr/local/zlib-1.2.8/include,/usr/local/zlib-1.2.8/lib --with-szlib=/usr/local/szip-2.1
to install netCDF

./configure --prefix=/usr/local/netcdf CPPFLAGS='-I/usr/local/hdf5/include -I/usr/local/zlib-1.2.8/include -I/usr/local/szip-2.1/include' LDFLAGS='-L/usr/local/hdf5/lib -L/usr/local/zlib-1.2.8/lib -L/usr/local/szip-2.1/lib'

or
./configure --prefix=/usr/local CPPFLAGS='-I/usr/local/include' LDFLAGS='-L/usr/local/lib'

netCDF-FORTRAN needed to Install libtool form source due incompatibility
ftp://ftp.gnu.org/gnu/libtool/

netCDF -FORTRAN

To avoid lib-tool problem use only
export LD_LIBRARY_PATH=/usr/local/netcdf/lib:${LD_LIBRARY_PATH}
export CPPFLAGS='-I/usr/local/netcdf/include'
export LDFLAGS='-L/usr/local/netcdf/lib'
./configure --prefix=/usr/local/netcdf

To install YACC

sudo apt-get install byacc

Jasper Error:
configure:2538: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.
solution
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:'/home/users/halbadi/wrf/lib/libpng/lib'

Installing WRF

For version 3.6 and gfortran 4.6 the following changes are necessary to changes to
DM_CC = mpicc -DMPI2_SUPPORT
CPP = /lib/cpp -C -P

(Not Applicable version for 3.6 and gfortran 4.6 and above ) To fix the GFORTRAN compiler compatibility that triggerred warning during compilation: generate the file configure.wrf as usual and before compile anything change manually those two lines by adding -cpp :

FORMAT_FIXED    =       -ffixed-form -cpp
FORMAT_FREE     =       -ffree-form -ffree-line-length-none -cpp


more details in WRF user forum (

gfortran treating comments as code )

The same compiler option should be set in configure.wps file before compiling WPS as follows:

FFLAGS = -ffree-form -O -fconvert=big-endian -frecord-marker=4 -cpp
F77FLAGS = -ffixed-form -O -fconvert=big-endian -frecord-marker=4 -cpp

WPS Running Errors

ERROR: The mandatory field TT was not found in any input data.Solution : Run-out of Hard Disk memory caused corruption in ungrib output file
other : here

Utilities Errors
ARWpost
ERROR :input_module.o: In function `__input_module_MOD_arw_get_next_time':
input_module.f:(.text+0x41): undefined reference to `nf_inq_varid_'
input_module.f:(.text+0x80): undefined reference to `nf_inq_var_'
input_module.f:(.text+0x130): undefined reference to `nf_get_vara_text_'
input_module.o: In function `__input_module_MOD_input_close':
input_module.f:(.text+0x1bc): undefined reference to `nf_close_'

Solution :
open up the ARWpost file src/Makefile you will see a section that looks as below

Code:

ARWpost.exe: $(OBJS)
  $(FC) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS)  \
    -L$(NETCDF)/lib -I$(NETCDF)/include  -lnetcdf

You need to add -l netcdff linking to this so it now looks like below

Code:

ARWpost.exe: $(OBJS)
  $(FC) $(FFLAGS) $(LDFLAGS) -o $@ $(OBJS)  \
    -L$(NETCDF)/lib -I$(NETCDF)/include  -lnetcdf  -lnetcdff

WRF Model installation,running and error log

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