###compile GSI in Ubunut 14.04###

1. GSI was tried to compile in Ubuntu 12.04, but ended with failure. GSI requires Gfortran 4.7 and above, but 12.04 repository for up to 4.6, so ubuntu has to upgraded from 12.04 to 14.04 to have gfortran 4.7.
2. Due to this Server was upgraded from Ubuntu 12.04 to 14.04 and compiled WRFV4.3.1 and WPS 4.3.1 in it. It was by Gfortran 4.8.2, Netcdf 4.1.3, and other necessary libraries such as libpng, zlib and jasper as per apt-get method.
3. GSI is required to have OpenMPI for its parallel programming. For this, the installation of OpenMPI was followed from this.

4. OpenMpi was installed by following commands from above-refered page

   wget https://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.1.tar.gz
   tar -xvf openmpi-1.8.1.tar.gz
   cd openmpi-1.8.1.tar.gz    
   ./configure --prefix="/home/$USER/.openmpi"
   make
   do make
   export PATH="$PATH:/home/$USER/.openmpi/bin"
   export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/home/$USER/.openmpi/lib/"
   

   to check the installation by mpirun. Based on the last environment setup the openmpi will become the MPI library instead of mpich used for WRF3V compilation

5. Following environments were set up for GSI configure

   export WRF_DIR=/home/hoopoe/wrfchem341/test/WRFV3
   export NETCDF=/home/hoopoe/wrfchem341/test/netcdf36
   export LAPACK_PATH=/usr/lib
   

   LAPACKPATH environment was setup following [this](http://qiita.com/makenow_just/items/d6e251bbf18f4c141c1d)

6. After the above point, ./configre was executed and configure.gsi was edited to change its line number 43 to consider the difference in gfortaan and its commanding problem mentioned here

7. After this made ./compile > &log.compileA1 and it ends in this error *** Error in `/usr/lib/gcc/x86_64-linux-gnu/4.8/f951': corrupted double-linked list: 0x0000000002b5e5e0 ***. Before getting this error, faced minimal error related with mpif90 command missing etc, easily resolved those issues, need of expert direction for the above error.

8. Based on this error it is decided to use the same compiler and gfortran version mentioned in the user guide. For this, the gfortran version 4.7 is installed by sudo apt-get install gfortran4.7 and gcc version 4.4.5 was tried to install by typing sudo apt-get install gcc-4.4 but it installed version 4.4.7 instead. Attempts such as commands sudo apt-get install gcc-4.4=4.4.5-15ubuntu1 ends but in failure.

9. So based on the available compilers version, gcc-4.4.7 and g++-4.4.7, gfortran-4.7, the wrf will be compiled and tested for its suitability for GSI.

####compiling WRF-CHEM-3.4.1 with gcc-4.4.7, gfortan-4.7.3 and netcdf 3.6.3### 1. Compiling netcdf 3.6.3

*environment setup* **THIS IS WRONG, SEE BELOW**

            export DIR=/home/hoopoe/wrfchem341/test
            export CC=gcc-4.4
            export CXX=g++-4.4
            export FC=gfortran-4.7
            export FCFLAGS=-m64
            export F77=gfortran-4.7
            export FFLAGS=-m64

*compiling*

            cd /home/hoopoe/wrfchem341/test/netcdf-3.6.3
            ./configure --prefix=$DIR/netcdf36g44
            make 
            make install
            make check

but ends in error saying use typeSizes 1 Fatal Error: Wrong module version '10' (expected '9') for file 'typesizes.mod' opened at (1) based on this it might be due to compiler version mismatch. To choose in between different versions of the same program, update-alternatives has to be used, referred by this and based on this. To set up gcc and g++, used following commands

                sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.4 60 --slave /usr/bin/g++ g++ /usr/bin/g++-4.4 
                sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 40 --slave /usr/bin/g++ g++ /usr/bin/g++-4.8 
                sudo update-alternatives --config gcc 

1. To setup gfortran older version 4.7, used following commands,

               which gfortran
     # to knwo the link of current used gfortran
               ls -lh /usr/bin/gfortran
               ls -lh /usr/bin/gfortran*
     #to knwo the list of links for each version
               sudo update-alternatives --install /usr/bin/gfortran gfortran    /usr/bin/gfortran-4.8 60
               sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.7 40
               sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.6 20
               sudo update-alternatives --config gfortran
   

   Based on this required gfortran version may be selected and so the environment setup need not to have the version mentioned as above, so the environment setup is changed as follows

   environment setup

           export DIR=/home/hoopoe/wrfchem341/test
           export CC=gcc
           export CXX=g++
           export FC=gfortran
           export FCFLAGS=-m64
           export F77=gfortran
           export FFLAGS=-m64
   

2. With this setup also, compilation ends with the same error as noted above, so concluded that the gfortran, gcc, and g++ has to be the same version. If it is 4.4, all have to be the same. So install gfortran4.4 by sudo apt-get install gfortran-4.4, this version was added into update-alternatives by

               sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.4 10
   

3. With the above change also faced same Fatal Error: Wrong module version error, from this found that the failure is due to OPENMPI compiled with the wrong gfortran. The gfortran, when doing OPENMPI compilation based on this is 4.8. So OPENMPI has to be compiled with correct gfortran needed by GSI, that is 4.7. So made update-alternatives configuration chosen to gfortran 4.7 and gcc and g++ in 4.4 then proceeded with openmpi compilation as per this.

4. Tried with NetCDF compilation, But got the same error as of former. For a check, tried gcc and gfortran was made into 4.8 and compiled netcdf(NOte here openmpi is made by gfortran4.7), it make check passed without any error. Then again changed the gcc to 4.4 and gfortran to 4.7, this time netcdf make check passed without any error, strange!. Made exporting of compiled netcdf folder by export PATH=$DIR/netcdf36g44/bin:$PATH export NETCDF=$DIR/netcdf36g44

5. So went into testing of netcdf NETCDF testing from here downloaded the testing files and used, mkdir testNET wget http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compile_tutorial/tar_files/Fortran_C_NETCDF_MPI_tests.tar tar -xf FortranCNETCDFMPItests.tar cd testNET cp ${NETCDF}/include/netcdf.inc . gfortran -c 01fortran+c+netcdff.f gcc -c 01fortran+c+netcdfc.c gfortran 01fortran+c+netcdff.o 01fortran+c +netcdfc.o -L${NETCDF}/lib -lnetcdff -lnetcdf
   ./a.out

6. Based on good pass in testing, went into compile wrf with chemistry option as per this, checked the environment setup as per this, checked sudo nano /etc/bash.bashrc for its correctness. Then went into configure and compilation but ends with commenting errors, the log files is this and configure file is this.

7. Based on the last good compilation configure file, the configure file was edited in the line 119 to 120 as per this

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

   from

         FORMAT_FIXED    =       -ffixed-form 
         FORMAT_FEE     =       -ffree-form -ffree-line-length-none
   

8. Then attempted 3 in this regard by ./clean and ./configure then editing line 119 to 120 of configure file, and then doing ./compile em_real >& log.compileA3. This time it took 17 minutes and finished compilation without error and creation of all exe files. This is an advancement in compiling WRF CHEM based on openMPI instead of MPICH.

9. Next started GSI compilations, made sure the environment variable for GSI is correct

         export WRF_DIR=/home/hoopoe/wrfchem341/test/WRFV3
         export NETCDF=/home/hoopoe/wrfchem341/test/netcdf36
         export LAPACK_PATH=/usr/lib    
   

10. Then ./configre was executed and configure.gsi was formed and then given ./compile > &GSIlog.compileA11. This attempt gives error of commending populated in the log file here.

11. Next attempt was made in this regard, given ./clean -a, then ./configure, edited the configure file from line number 43

          CPP_FLAGS      =  -C -P -D_REAL8_ -DWRF -DLINUX -DPGI
    

    to

          CPP_FLAGS      =  -P -D_REAL8_ -DWRF -DLINUX -DPGI
    

    then executed compile by ./compile > &GSIlog.compileA12 Edited to change its line number 43 to consider the difference in gfortaan and its commanding problem mentioned here. With this compile took time and ends with error of no lmkl, indicating no intel mkl, mentioned in the confiugre.gsi file in the line 58 starts with MYLIBsys, in the next attempt this line was eidted from

           MYLIBsys       =  -L$(LAPACK_PATH)/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
    

    to

           MYLIBsys       =  -L$(LAPACK_PATH) 
    

    Also made sure all the package listed here sudo apt-get install libblas3gf sudo apt-get install libblas-doc sudo apt-get install libblas-dev sudo apt-get install liblapack3gf sudo apt-get install liblapack-doc sudo apt-get install liblapack-dev towards LAPCK_PATH was installed in the system.

12. Some of the notes related with advantages of mkl, such as on R and it benchmark is astonishing with OPEN source LAPACK which currently trying to use.

13. Ends with missing file error of ar: plib8b.o: No such file or directory, but less compilation than last attempt 11, log file is here. Makes to speculate problem lies with LAPACK library compilation requirement than just apt-get.

14. LAPCK was compiled based on this, in which the example file for compile make.inc.example used as such by renaming into make.inc and run the command PATH=$PATH:. export PATH; make install blaslib lapacklib tmglib testing blas_testing timing blas_timing but this ended in error of make: *** No rule to make target `make.inc'. Stop.

15. As another attempt related with failure of compiling LAPCK, made a command line search for the actual location of liblapack3 using sudo dpkg -L liblapack3. It showed the place as /usr/lib/lapack and so changed the LPACK_PATH into export LAPACK_PATH=/usr/lib/lapack and redone the compile, to surprise this time compile finished without any error and created the gsi.exe executables, this and this are configured and compile log file.