• HDF5
• Netcdf-4
  • Method 1.
  • Method 2.
• Netcdf4-fortran

HDF5

1. install szip libcurl –prefix=/usr/local

./configure FC=pgf90 CC=gcc CPPFLAGS=-DpgiFortran FFLAGS=-O --prefix=/home/chchoi/x64/hdf5 --with-zlib=/usr/local --with-szlib=/usr/local
 make
 make check
 make install

1. for wrf em , we need –enable-fortran to have -lhdf5_fortran

./configure FC=pgf90 CC=gcc CPPFLAGS=-DpgiFortran FFLAGS=-O --prefix=/home/chchoi/x64/hdf5 --with-zlib=/usr/local --with-szlib=/usr/local --enable-fortran
 make> &make.txt &
 tail -f make.txt
 make check
 make install

2.a. compile with FC=mpif90 CC=mpicc CXX=mpic++

./configure FC=mpif90 CC=mpicc CXX=mpic++ --prefix=/home/chchoi/hdf5 --with-zlib=/usr/local --with-szlib=/usr/local CFLAGS="-O -DNDEBUG -DpgiFortran" CXXFLAGS="-DNDEBUG -DpgiFortran" CPPFLAGS="-DNDEBUG -DpgiFortran"

1. vi ~/.bashrc for HDF5 Path

export HDF5=/home/chchoi/hdf5
export PATH=$PATH:$HDF5/bin

don’t mv lib64 lib for hdf5 beacuse netcdf-4 cannot be compiled

Netcdf-4

Method 1.

Setting LD_LIBRARY_PATH and C_INCLUDE_PATH for the sake of finding hdf5.h when configure netcdf-4 with option –enable-netcdf-4.

Then we can also set CPPFLAGS=-DpgiFortran which is very important to install laps and wrf with pgi

If you have already revised .bashrc and resource ~/.bashrc as following:

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HDF5/lib64
export C_INCLUDE_PATH=$C_INCLUDE_PATH:$HDF5/include

 ./configure FC=pgf90 CC=gcc CPPFLAGS=-DpgiFortran FFLAGS=-O --prefix=/home/chchoi/netcdf4 --with-hdf5=/home/chchoi/hdf5 --with-zlib=/usr/local --with-szlib=/usr/local --enable-netcdf-4
 make> &make.txt &
 tail -f make.txt
 make check (this would be an error in ncgen with SMG Linux Machine)
 make install

Method 2.

Setting equality when configuring netcdf-4

CPPFLAGS=-I$HDF5/include,-DpgiFortran
LDLAGS=-L$HDF5/lib

Hence, the whole configure include LDFLAGS and CPPFLAGS is

./configure FC=pgf90 CC=gcc CPPFLAGS=-I/home/chchoi/x64/hdf5/include,-DpgiFortran FFLAGS=-O --prefix=/home/chchoi/x64/netcdf4 --with-hdf5=/home/chchoi/x64/hdf5 --with-zlib=/usr/local --enable-netcdf-4 LDFLAGS=-L/home/chchoi/x64/hdf5/lib

compile with mpif90 mpicc mpic++

 ./configure --prefix=/home/chchoi/netcdf4 --with-hdf5=/home/chchoi/hdf5 --with-zlib=/usr/local --with-szlib=/usr/local --enable-netcdf-4 CFLAGS="-O -DNDEBUG -DpgiFortran" CXXFLAGS="-DNDEBUG -DpgiFortran" CPPFLAGS="-DNDEBUG -DpgiFortran" CC=mpicc CXX=mpic++ FC=mpif90 LDFLAGS=-L/home/chchoi/hdf5/lib64

Errors for Netcdf-4-C

error "occurlfunctions.c:167: error: 'CURLOPT_USE_SSL' undeclared (first use in this function) "

How to correct it :

add flags   --disable-dap

Ref :link

Netcdf4-fortran

1. vi ~/.bashrc for netcdf-4-C path

    export C_INCLUDE_PATH=/home/chchoi/netcdf4/include:$C_INCLUDE_PATH
    export LD_LIBRARY_PATH=/home/chchoi/netcdf4/lib64:$LD_LIBRARY_PATH
   

   This sets the C include library in order to find netcdf.h when configuring netcdf-fortran-4. Moreover,we can also set CPPFLAGS=-DpgiFortran which is very important to install laps

   Next step is configuring it with the following options:

    ./configure FC=pgf90 CC=gcc CPPLAGS=-DpgiFortran FFLAGS=-O --prefix=/home/chchoi/netcdf4
    make
    make check
    make install
   

2. On the other hand, if you do not set .bashrc about C_INCLUDE_PATH and LD_LIBRARY_PATH, then using the following commands:

    ./configure FC=pgf90 CC=gcc CPPLAGS=-I/home/chchoi/x64/netcdf4/include,-DpgiFortran FFLAGS=-O --prefix=/home/chchoi/x64/netcdf4 LDFLAGS=-L/home/chchoi/x64/netcdf4/lib
    make
    make check
    make install
   

   Remark: LDFLAGS=-L/home/chchoi/netcdf4/lib64 , after compile netcdf-fortran, change lib64 to lib. Otherwise, wrf-em cannot recognize where netcdf lib locate

3. Errors:

   checking netcdf path is the location of netcdf4, not netcdf3, also export to see C_INCLUDE_PATH and LD_LIBRARY_PATH to NOT include netcdf3 path.

   If there are path set in C_INCLUDE_PATH and LD_LIBRARY_PATH, please empty them and source ~/.bashrc again

   cannot compute sizeof (off_t).

   how to correct it : delete LDFLAGS when configuration

4. After complete netcdf4

   • rename lib

   mv $NETCDF/lib64 to $NETCDF/lib
   

   and it is very important to compile wrf-em

   • vi .bashrc for NETCDF PATH

    export NETCDF=/home/chchoi/netcdf4
    export PATH=$NETCDF/bin:$PATH
    export NETCDF_LIB=$NETCDF/lib
    export NETCDF_INC=$NETCDF/include
   

   • How to use netcdf

     i. nc to cdl :#

        cdump netcdf.ncf > netcdf.cdl
     

     ii. cdl to nc :

        ncgen -f netcdf.cdl > netcdf.f
     

     Ref: link