####Compile wrf chem: QUICK NOTE####

1. It is based on the NCAR wrf chem compile complete process and note on wrf chem compile by this
2. Basic environemtn testl, passes all the tests which checks libs such as, gcc, gfortran, gcc+gfortran, perl, csh.
3. Made sure the gcc and gfortran versions are matching, current case version is 4.8.2 for both gcc and gfortran
4. Basic library compile MPICh and NETCDF

For setting up PATH for NETCDF

export DIR=/home/ubuntu/wrf/libs/ export CC=gcc export CXX=g++ export FC=gfortran export FCFLAGS=-m64 export F77=gfortran export FFLAGS=-m64

./configure –prefix=$DIR/netcdf –disable-dap
–disable-netcdf-4 –disable-shared

make (this command ends in error related to documentation, there is a patch for this error) make install

export PATH=$DIR/netcdf/bin:$PATH export NETCDF=$DIR/netcdf

#setting up PATH for mpich and compileing tar xzvf mpich-3.0.4.tar.gz #or just .tar if no .gz present cd mpich-3.0.4 ./configure –prefix=$DIR/mpich make make install export PATH=$DIR/mpich/bin:$PATH 1. Remianing requiered librries were installed by normal sudo apt-get command, libs requiered were of sudo apt-get install m4 sudo apt-get install libjasper-dev sudo apt-get install libpng-dev sudo apt-get install libnetcdf-dev sudo apt-get install zlib1g-dev sudo apt-get install build-essential sudo apt-get install libcloog-ppl-dev sudo apt-get install tcsh sudo apt-get install libcloog-ppl0

1. Basic library check was undergone, which checks netcdf and mpich , this test was passed good. ######compiling WRF######

2. Edited the file sudo nano /etc/bash.bashrc, added following lines in it

           export NETCDF=/home/ubuntu/wrf/libs/netcdf
           export JASPERLIB=/usr/lib
           export JASPERINC=/usr/include
           export WRF_EM_CORE=1
           export WRF_NMM_CORE=0
           export WRF_CHEM=1
           export WRF_KPP=0
           export WRFIO_NCD_LARGE_FILE_SUPPORT=1
   

3. Inside the wrf chem folder in whcih the chem folder already copy pasted, run following commands

           cd /home/hoopoe/wrfchem341/WRFV3_mpichA4/WRFV3/
   ./configure
   

4. The configure.wrf file has to be edited since the groftran and gcc used is of 4.8.2 version. The lines starting with has to be as below

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

5. Then execute the command, ./compile emreal and ./compile emiconv. This completes WRF CHEM compilation

6. For compiling WPS, unzip the wps folder and run the command ./configure and choose serial based wps, it ends in creation of file configure.wps.

7. Edit the file configure.wps and change the line starting with exactly as below

               #### Architecture specific settings ####
   
               COMPRESSION_LIBS    = -L/usr/lib -ljasper -lpng -lz
               COMPRESSION_INC     = -I/usr/include
   
               #
               #   Settings for Linux x86_64, gfortran    (serial) 
               #
               #
               COMPRESSION_LIBS    = -L/usr/lib -ljasper -lpng -lz
               COMPRESSION_INC     = -I/usr/include
   

8. Chnage the line in wps due to gformartn version used 4.8.2 as, CPP = /usr/bin/cpp -P -traditional

9. Then execute the command, ./compile, and it will generate the exe required for WPS.

10. Changed the lopcation of wrf compiled folder ######compiling PREPCHEMSRC######

11. compiling zlib1.7.2, inside the source directory, given follwoing command, FC=gfortran CC=gcc ./configure –prefix=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/zlib make make install

12. compiling hdf5-1.8.4, inside the source directory, given following command,

                FC=gfortran CC=gcc CXX=gc++ ./configure  \
                --prefix=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/hdf \
                --with-zlib=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/zlib  \
                --disable-shared \
                --enable-fortran
      make
      make install
    

13. Then editing the prepchmesrc fconfigure file, include.mk.opt.gfortran, with lines

                NETCDF=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/netcdf
                HDF5=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/hdf
                HDF5_LIB=-L$(HDF5)/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -L/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/zlib/lib/ -lz
    

14. Made sure that the line contain wording for big endian memory as F_OPTS= -Xpreprocessor -D$(CHEM) -O2 -fconvert=big-endian -frecord-marker=4

15. Then saved the configure file and given the command

                cd /home/hoopoe/wrfchem341/WRFV3_mpichA3/PREP-CHEM-SRC-1.4/bin/build/
      make OPT=gfortran.wrf CHEM=RACM
    

16. This ends in error saying

                H5PL.c:(.text+0xa7): undefined reference to `dlclose'
                /home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/hdf/         lib/libhdf5.a(H5PL.o): In function `H5PL_load':
                H5PL.c:(.text+0x319): undefined reference to `dlsym'
                H5PL.c:(.text+0x45c): undefined reference to `dlopen'
                H5PL.c:(.text+0x475): undefined reference to `dlsym'
                H5PL.c:(.text+0x5a4): undefined reference to `dlclose'
                H5PL.c:(.text+0x629): undefined reference to `dlerror'
                H5PL.c:(.text+0x83c): undefined reference to `dlclose'
                collect2: error: ld returned 1 exit status
                make: *** [../prep_chem_sources_RACM.exe] Error 1
    

17. So made another attmept of compiling HDF librar alone as follows, inside the source directory of compiling hdf5-1.8.4, given following command,

                FC=gfortran CC=gcc CXX=gc++ ./configure  \
                --prefix=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/hdfA2 \
                --with-zlib=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/zlib  \
                --enable-shared --enable-hl\
                --enable-fortran
      make -j 3
      make install
    

18. This new location of HDF compiled by enabling shared library and hl is linked in prepchemsrc soure and it made exe without any error.

19. But running the wrf chem with prepchemsrcRACM ends in same end of file error. It is supected that the compilation command has to give make OPT=gfortran.wrf CHEM=RADMWRFFIM instead of make OPT=gfortran.wrf CHEM=RACM, for a proper run. While compileing with make OPT=gfortran.wrf CHEM=RADMWRF_FIM, it ends in error of no hdf5.mod avilable in directory. It seems the disable -shared compilation does created the hdf5.mod, but ends in earlier error of undefined reference to `dlclose’.

20. So recompile the hdf with out any enable-fortran as done earlier. Inside the source directory of compiling hdf5-1.8.4, given following command,

                FC=gfortran CC=gcc CXX=gc++ ./configure  \
                --prefix=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/hdfA3 \
                --with-zlib=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/zlib  \
                --enable-shared --enable-hl
      make -j 3
      make install
    

    This also doesn’t created the hdf5.mod file proving that the mod file creation is by shared library variable.

21. One more trial with Inside the source directory of compiling hdf5-1.8.4, given following command,

                FC=gfortran CC=gcc CXX=gc++ ./configure  \
                --prefix=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/hdfAA4 \
                --with-zlib=/home/hoopoe/wrfchem341/WRFV3_mpichA3/libs/zlib  \
                --disable-shared --enable-fortran --enable-parallel
    

which ends in error of checking whether a simple MPI-IO program can be linked… no configure: error: unable to link a simple MPI-IO application 1. Based on this zlib also has to be compiled specific to enable-parallel

FC=gfortran CC=gcc ./configure –prefix=/home/hoopoe/wrfchem341/WRFV3mpichA3/libs/zlib125A1 make make install

FC=gfortran CC=/home/hoopoe/wrfchem341/WRFV3mpichA3/libs/mpich/bin/mpicc CXX=gc++ ./configure
–prefix=/home/hoopoe/wrfchem341/WRFV3mpichA3/libs/hdfAA5 –enable-parallel
–with-zlib=/home/hoopoe/wrfchem341/WRFV3mpichA3/libs/zlib125A1
–enable-shared –enable-hl –enable-fortran

1. So go back to the readme of the prepchemsrc, follow its version spcifications.

to donwload hdf1.8.8 from http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.8/src/hdf5-1.8.8.tar.gz

to downlaod zlib1.2.5 http://sourceforge.net/projects/libpng/files/zlib/1.2.5/zlib-1.2.5.tar.gz/download

to donwload the netcdf 4.1.1, wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.1.1.tar.gz

FC=gfortran CC=gcc CXX=gc++ ./configure -prefix=/home/hoopoe/wrfchem341/WRFV3mpichA4/libs/hdfA1 –with-zlib=/home/hoopoe/wrfchem341/WRFV3mpichA3/libs/zlib –enable-shared –enable-fortran

1. It is found that the prepchmesrc compilaiton as make OPT=gfortran.wrf CHEM=RADM_WRF_FIM. is problamatic due to netcdf. so go for with netcdf 4.1.1 for wrf chem starting itsefl. But trying to compile hdf1.8.8 with zlib 1.2.5 ends in error of make[2]: *** [h5diff.lo] Error 1. So going with hdf1.8.14 and zlib 1.2.7.
2. The libraries hdf1.8.14 and zlib1.2.7 was compiled smoothly and then compiled PREPCHEMSRC using the gfortran.wrf and removing the -lnetcdff comments in it which ends the compilaiotn of prepchemsrc also.
3. Output from this compialtion is correctly read by wrf convert_emiss.exe system and thus ends the compilaiton of wrf chem and its auxillary compontnets.

FC=gfortran CC=gcc ./configure –prefix=/home/hoopoe/wrfchem341/WRFV3_mpichA4/libs/zlib make make install

FC=gfortran CC=gcc CXX=gc++ ./configure -prefix=/home/hoopoe/wrfchem341/WRFV3mpichA4/libs/hdfA1 –with-zlib=/home/hoopoe/wrfchem341/WRFV3mpichA4/libs/zlib –enable-shared –enable-fortran

wget http://www2.mmm.ucar.edu/wrf/src/WRFV3.4.1.TAR.gz wget http://www2.mmm.ucar.edu/wrf/src/WPSV3.4.1.TAR.gz wget http://www2.mmm.ucar.edu/wrf/src/WRFV3-Chem-3.4.1.TAR.gz

wget http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/mpich-3.0.4.tar.gz

wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.1.1.tar.gz

tar xzvf netcdf-4.1.1.tar.gz cd

wget http://zlib.net/fossils/zlib-1.2.7.tar.gz

wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.14.tar

gunzip WPSV3.4.1.TAR.gz tar -xf WPSV3.4.1.TAR

• To start a screen with name screen -S wrfems
• To view running screen screen -r
• to get into particular screen screen -xr pid(of the screen)
• to get out of screen CTRL+A+D

chmod a+x emsinstall.pl perl emsinstall.pl –install

ssh -i /home/swl-sacon-dst/Desktop/gssa.pem ubuntu@ec2-54-255-173-125.ap-southeast-1.compute.amazonaws.com

ssh -i /home/swl-sacon-dst/Desktop/wrfa.pem ubuntu@ec2-54-224-94-144.compute-1.amazonaws.com

FC=gfortran CC=gcc ./configure –prefix=/home/ubuntu/wrf/libs/zlib make make install

tar xvf hdf5-1.8.14.tar FC=gfortran CC=gcc CXX=gc++ ./configure -prefix=/home/ubuntu/wrf/libs/hdfA1 –with-zlib=/home/ubuntu/wrf/libs/zlib –disable-shared –enable-fortran

./configure -prefix=/home/hoopoe/wrfchem341/WRFV3_mpichA4/libs/hdfA2 –with-zlib=/home/ubuntu/wrf/libs/zlib –enable-shared –enable-fortran

./configure –prefix=/usr/local –enable-shared –enable-hl –with-zlib=/home/ubuntu/wrf/libs/zlib –enable-fortran make sudo checkinstall

ftp://aftp.fsl.noaa.gov/divisions/taq/global_emissions/prep_chem_sources_v1.4_08aug2013.tar.gz

tar xzvf prepchemsourcesv1.408aug2013.tar.gz

make OPT=gfortran.wrf CHEM=RADMWRFFIM

dpkg -L hdf5 sudo dpkg -r hdf5 #addressing the issue of hdf5 file missing in prepchemsrc.exe

./configure –prefix=/usr/local –enable-shared –enable-hl –with-zlib=/home/hoopoe/wrfchem341/WRFV3_mpichA4/libs/zlib127 –enable-fortran make sudo checkinstall

#BIG overcome, ldconfig, solve the compile exe not found link

make OPT=gfortran.wrf CHEM=RADMWRFFIM #no missing file was reported in this compile, indicating for prepchemsrc, the locaiton of hdf5 is hardcoded in /usr/local/, so has to be compiled for /usr/local

For server export DIR=/home/hoopoe/wrfchem341/WRFV3_mpichA4/libs export PATH=$DIR/netcdf/bin:$PATH export NETCDF=$DIR/netcdf export PATH=$DIR/mpich/bin:$PATH