Setup_E3SM_Windows.md

Setup E3SM in Centos-7 of Win-10

1. Install Centos-7 on the Windows Subversion System for Linux

refer to https://docs.microsoft.com/en-us/windows/wsl/install-win10

2. Install Packages with yum

export MainDir=/usr/bin

1. gcc:

   sudo yum group install "Development Tools"

   sudo wget https://ftp.gnu.org/gnu/gcc/gcc-8.3.0/gcc-8.3.0.tar.gz

   sudo tar -zxvf gcc-8.3.0.tar.gz

   ./contrib/download_prerequisites

   sudo ./configure --enable-languages=c,c++,fortran --disable-multilib

   sudo make

   sudo make install

   scl enable devtoolset-6 bash

   scl enable devtoolset-8 bash

2. cmake: wget https://cmake.org/files/v3.12/cmake-3.12.3.tar.gz tar zxvf cmake-3.* cd cmake-3.*

    ./bootstrap --prefix=/home/dalei/cmake
   
    make -j$(nproc)
   
    make install
    
    add cmake-path to ./bash_profile PATH=/home/dalei/cmake/bin:$PATH:$HOME/.local/bin:$HOME/bin
   

3. mpich cd /usr/local

   sudo wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz

   sudo tar -zxvf mpich-3.3.2.tar.gz

   cd mpich-3.3.2

   sudo ./configure --prefix=$MainDir

   sudo make

   sudo make install

   https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz

4. zlib export MainDir=/home/dalei

   cd /home/dalei

   wget https://zlib.net/fossils/zlib-1.2.11.tar.gz

   tar -zxvf zlib-1.2.11.tar.gz

   cd zlib-1.2.11

   ./configure --prefix=${MainDir}/zlib

   make

   make install

5. hdf5

   export CC=/usr/bin/bin/mpicc

   export CXX=/usr/bin/bin/mpicxx

   export FC=/usr/bin/bin/mpif90

   export F77=/usr/bin/bin/mpif77

   cd ~/install

   wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.20/src/hdf5-1.8.20.tar.gz

   tar -zxvf hdf5-1.8.20.tar.gz

   cd hdf5-1.8.20

   ./configure --prefix=${MainDir}/hdf5 --with-zlib=${MainDir}/zlib --enable-fortran --enable-fortran2003 --with-pic

   make

   make install

   6. pnetcdf(optional) cd ~ mkdir netcdf-install cd netcdf-install wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz tar -zxvf pnetcdf-1.12.1.tar.gz cd pnetcdf-1.12.1 ./configure --prefix=/home/dalei/pnetcdf make make install

6. netcdf-c

   cd ~/netcdf-install

   wget https://github.com/Unidata/netcdf-c/archive/v4.6.2.tar.gz

   tar -zxvf v4.6.2.tar.gz

   cd netcdf-c-4.6.2

   export CPPFLAGS="-I/home/dalei/zlib/include -I/home/dalei/hdf5/include -I/home/dalei/pnetcdf/include"

   export CFLAGS="-I/home/dalei/zlib/include -I/home/dalei/hdf5/include -I/home/dalei/pnetcdf/include"

   export LDFLAGS="-L/home/dalei/zlib/lib -L/home/dalei/hdf5/lib -lhdf5 -lhdf5_hl -lz -L/home/dalei/pnetcdf/lib"

   export LD_LIBRARY_PATH="/home/dalei/hdf5/lib:/home/dalei/zlib/lib:$LD_LIBRARY_PATH"

   ./configure --prefix=/home/dalei/netcdf_all --disable-shared --disable-dap --enable-pnetcdf

   make

   make install

7. netcdf-fortran cd ~/netcdf-install wget https://github.com/Unidata/netcdf-fortran/archive/v4.4.3.tar.gz

tar xzvf v4.4.3.tar.gz cd netcdf-fortran-4.4.3 export CPPFLAGS="-I/home/dalei/zlib/include -I/home/dalei/hdf5/include -I/home/dalei/netcdf_all/include -I/home/dalei/pnetcdf/include"

export CFLAGS="-I/home/dalei/zlib/include -I/home/dalei/hdf5/include -I/home/dalei/netcdf_all/include -I/home/dalei/pnetcdf/include"

export LDFLAGS="-L/home/dalei/zlib/lib -L/home/dalei/hdf5/lib -L/home/dalei/netcdf_all/lib -lhdf5 -lhdf5_hl -lz -L/home/dalei/pnetcdf/lib"

./configure --prefix=/home/dalei/netcdf_all --disable-shared --enable-pnetcdf

make

make check

make install

8. LibXML sudo yum install "perl(XML::LibXML)"

9. BLAS & LAPACK yum install atlas atlas-devel lapack-devel blas-devel -llapack -lblas

3. setup E3SM

scl enable devtoolset-8 bash

cd ~/model1/e3sm/cime/config/ export LD_LIBRARY_PATH="/home/dalei/hdf5/lib:/home/dalei/zlib/lib::/home/dalei/netcdf/lib:$LD_LIBRARY_PATH" chmod -R 700 .

cd ../script

export RES=1x1_brazil

export COMPSET=ICLM45

export COMPILER=gnu

export MACH=WE39911

export CASE_NAME=test42

cd ~/model1/e3sm/cime/scripts

./create_newcase
-case ${CASE_NAME}
-compset ${COMPSET}
-res ${RES}
-compiler ${COMPILER}
-mach ${MACH}

cd $CASE_NAME

./xmlchange STOP_N=1,STOP_OPTION=nyears

./xmlchange PIO_VERSION=1

./case.setup

./case.build

Install packages in Cygwin (Windows 10)

1. Install Cygwin

including some packages (git, wget, c++, c++g++, etc.)

2. Install Package Management Tool: apt-cyg

link: https://www.ccammack.com/posts/install-cygwin-and-apt-cyg/   https://github.com/transcode-open/apt-cyg
wget rawgit.com/transcode-open/apt-cyg/master/apt-cyg
install apt-cyg /bin
rm apt-cyg

3. Install necessary packages via apt-cyg

gcc cmake netcdf perl-XML-LibXML gcc-fortune via apt-cyg
mpich: http://people.cs.uchicago.edu/~asiegel/courses/cspp51085/quick-ref/mpich-install.txt (new version mpich-3.3.2.tar.gz)
gmake:  Use make    % cd /bin
                    % ln -s make gmake

4. Clone E3SM code from github

5. Test Case

sudo apt install libxml2-utils

essential

netcdf libxml-libxml-perl

sudo ln -s /usr/bin/make /usr/bin/gmake

cmake

hdf5

https://www.wbhatti.org/notes/hdf5-with-cpp-support-debian.html

net-cdf-c

sudo ./configure --prefix=$ID/netcdf
--enable-shared --enable-static
--enable-netcdf-4 --disable-dap
CPPFLAGS="-I$ID/hdf5/include -I$ID/zlib/include"
LDFLAGS="-L$ID/hdf5/lib -Wl,-rpath=$ID/hdf5/lib
-L$ID/zlib/lib -Wl,-rpath=$ID/zlib/lib"

Centos 7

sudo yum group install "Development Tools": gcc g++ make
sudo yum install cmake
cd /usr/local
sudo mkdir mpich
cd mpich
sudo wget http://www.mpich.org/static/downloads/3.1.3/mpich-3.1.3.tar.gz
sudo tar -xf mpich-3.1.3.tar.gz 
cd mpich-3.2.2
sudo ./configure -prefix=/usr/bin |& tee c.txt
sudo make 2>&1 | tee m.txt
sudo make install 2>&1 | tee mi.txt

sudo yum install "perl(XML::LibXML)"

# Where to install libraries

export LIBBASE=/usr/bin

Compilers

export SERIAL_FC=gfortran export SERIAL_F77=gfortran export SERIAL_CC=gcc export SERIAL_CXX=g++ export MPI_FC=mpif90 export MPI_F77=mpif77 export MPI_CC=mpicc export MPI_CXX=mpicxx

/usr/local/

zlib hdf5 netcdf

cmake sudo wget https://src.fedoraproject.org/lookaside/extras/cmake/cmake-3.4.0-rc3.tar.gz/b949c919e82d5fe70cfd9e799f1da3a6/cmake-3.4.0-rc3.tar.gz

• zlib cd /usr/local sudo mkdir zlib cd zlib sudo wget https://zlib.net/fossils/zlib-1.2.8.tar.gz sudo tar xzvf zlib-1.2.8.tar.gz cd zlib-1.2.8 sudo ./configure --prefix=/usr/bin/zlib sudo make sudo make install

• hdf5

  Compilers

  export SERIAL_FC=gfortran export SERIAL_F77=gfortran export SERIAL_CC=gcc export SERIAL_CXX=g++ export MPI_FC=mpif90 export MPI_F77=mpif77 export MPI_CC=mpicc export MPI_CXX=mpicxx cd /usr/local sudo mkdir hdf5 cd hdf5 sudo wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/hdf5-1.8.14/src/hdf5-1.8.14.tar.bz2 sudo tar xjvf hdf5-1.8.14.tar.bz2 cd hdf5-1.8.14 export FC=$MPI_FC export CC=$MPI_CC export CXX=$MPI_CXX sudo ./configure --prefix=/usr/bin --enable-parallel --with-zlib=/usr/bin --enable-fortran sudo make sudo make check sudo make install

• netcdf-c ${LIBBASE} = /usr/bin

cd /usr/local sudo mkdir netcdf cd netcdf sudo wget https://github.com/Unidata/netcdf-c/archive/v4.4.0.tar.gz sudo tar xzvf v4.4.0.tar.gz cd netcdf-c-4.4.0 export CPPFLAGS="-I${LIBBASE}/include" export LDFLAGS="-L${LIBBASE}/lib" export LIBS="-lhdf5_hl -lhdf5 -lz -ldl" export LD_LIBRARY_PATH=${LIBBASE}/lib:$LD_LIBRARY_PATH export CC=$MPI_CC sudo ./configure --prefix=${LIBBASE} --disable-dap --enable-netcdf4 --enable-pnetcdf --enable-parallel-tests --disable-shared make make check make install export NETCDF=${LIBBASE}

netcdf-fortran sudo wget https://github.com/Unidata/netcdf-fortran/archive/v4.4.3.tar.gz

tar xzvf v4.4.3.tar.gz cd netcdf-fortran-4.4.3 export FC=$MPI_FC export F77=$MPI_F77 export LIBS="-lnetcdf ${LIBS}" ./configure --prefix=${LIBBASE} --enable-parallel-tests --disable-shared make make check make install

https://modules.readthedocs.io/en/latest/INSTALL.html
install environmental modules:
sudo yum install tcl
sudo yum install tcl-devel