CMAQ v5.0.2 installation tutorial on Ubuntu 15.04 with GCC 4.6

lrxwisdom

It is the the translation of my previous post： http://bbs.06climate.com/forum.p ... 7293&extra=page%3D1
I hope it could help non-Chinese reader

• Downgrade GCC to version 4.6.2
  

Because compiling IOAPI with GCC 4.7 or higher version would cause
Error: 'runspec' of module 'm3utilio', importedat....

I don't know how to solve it. If you know please let me know. Thank you!





Install some neccessary plug-ins

1. sudo apt-get install tcsh samba cpp m4 quota cvs

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Install gcc g++ gfortran 4.6

1. sudo apt-get install gfortran gfortran-multilib gcc-4.6 gcc-4.6-multilib g++-4.6 g++-4.6-multilib gfortran-4.6 gfortran-4.6-multilib

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adjust priorities among versions

1. sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.6 50
   
2. sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 40
   
3. sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.6 50
   
4. sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 40
   
5. sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.6 50
   
6. sudo update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-4.9 40

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Check working gcc version, make sure it is 4.6 now

1. gcc --version
   
2. g++ --version
   
3. gfortran --version

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• Install libraries
  

Here I install zlib hdf5 netcdf-c netcdf-c++ netcdf- fortran in same directory to avoid error like NO zlib found

zlib

1. wget http://zlib.net/zlib-1.2.8.tar.gz
   
2. tar xf zlib-1.2.8.tar.gz
   
3. cd zlib-1.2.8
   
4. ./configure --prefix=/usr/local/netcdf
   
5. make
   
6. make check
   
7. sudo make install
   
8. cd ..

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hdf5

1. wget https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.14/src/hdf5-1.8.14.tar.gz
   
2. tar xf hdf5-1.8.14.tar.gz
   
3. cd hdf5-1.8.14
   
4. ./configure --prefix=/usr/local/netcdf --enable-shared --enable-hl --with-zlib=/usr/local/netcdf
   
5. make -j 4
   
6. make -j 4 check
   
7. sudo make -j 4 install
   
8. cd ..

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-j 4 is used to speed up compiling by using multi-cores.


netcdf-c

1. wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.1.tar.gz
   
2. tar xf netcdf-4.3.3.1.tar.gz
   
3. cd netcdf-4.3.3.1
   
4. LDFLAGS=-L/usr/local/netcdf/lib CPPFLAGS=-I/usr/local/netcdf/include ./configure --enable-netcdf-4 --enable-dap --enable-shared --prefix=/usr/local/netcdf
   
5. make
   
6. make check
   
7. sudo make install
   
8. cd ..

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Do not use -j 4 here! Error may reported!

netcdf-c++  #Many tutorial does not mention this maybe since they use the verison before 4.1.3 in which netcdf-c++ defaultly included.

1. wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-cxx-4.2.tar.gz
   
2. tar xf netcdf-cxx-4.2.tar.gz
   
3. cd netcdf-cxx-4.2
   
4. LDFLAGS=-L/usr/local/netcdf/lib CPPFLAGS=-I/usr/local/netcdf/include ./configure --enable-shared --prefix=/usr/local/netcdf
   
5. make
   
6. make check
   
7. sudo make install
   
8. cd ..

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netcdf-fortran

1. wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-fortran-4.4.2.tar.gz
   
2. tar xf netcdf-fortran-4.4.2.tar.gz
   
3. cd netcdf-fortran-4.4.2
   
4. LDFLAGS=-L/usr/local/netcdf/lib CPPFLAGS=-I/usr/local/netcdf/include ./configure --enable-shared --prefix=/usr/local/netcdf
   
5. make
   
6. make check
   
7. sudo make install
   
8. cd ..

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mpich #if you need run CMAQ with multi-cores

1. wget http://www.mpich.org/static/downloads/3.1.4/mpich-3.1.4.tar.gz
   
2. tar xf mpich-3.1.4.tar.gz
   
3. cd mpich-3.1.4
   
4. ./configure --prefix=/usr/local/mpich
   
5. make -j 4
   
6. make -j 4 check
   
7. sudo make  -j 4 install
   
8. cd ..

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If -j 4 does not work well, please delete it.

Set environment variables
gedit ~/.bashrc
Add

1. #for netcdf
   
2. export NETCDF=/usr/local/netcdf
   
3. export PATH=$NETCDF/bin:$PATH
   
4. export LD_LIBRARY_PATH=$NETCDF/lib:$LD_LIBRARY_PATH
   
5. #for mpich
   
6. export PATH=/usr/local/mpich/bin:${PATH}
   
7. export LD_LIBRARY_PATH=/usr/local/mpich/lib:${LD_LIBRARY_PATH}
   
8. export MANPATH=/usr/local/mpich/share/man:${MANPATH}

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Save and exit
source ~/.bashrc
Check installation

1. which ncdump
   
2. which mpirun

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If return installation path, OK!

ioapi
Please see
https://gcc.gnu.org/wiki/GfortranBuild#ioapi
Notice: modify downloading site and installation directory

• install CMAQ v5.0.2
  

Download source code and benchmark data from:
https://www.cmascenter.org/download/forms/step_1.cfm?CFID=2515215&CFTOKEN=5369c1c2829a158c-8C7B562E-F233-2A36-FF743386F3773A43


unzip them in to same directory then you will see [size=12.8000001907349px]following subdirectories:[size=12.8000001907349px]

1. data/
   
2.       bcon/   <<<<<<< empty, to befilled by the user
   
3.       cctm/   <<<<<<< empty, to befilled by the user
   
4.       crop/
   
5.       dust/
   
6.       emis/
   
7.       icon/   <<<<<<< empty, to befilled by the user
   
8.       jproc/  <<<<<<< empty
   
9.       lightning/
   
10.       mcip/
    
11.       ocean/
    
12.       procan/
    
13.       raw/
    
14.          phot/
    

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[size=12.8000001907349px]
Enter c-shell before installing CMAQ

1. csh

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1. cd /home/leo/CMAQv5.0.2/scripts
   
2. gedit config.cmaq

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Modfiy CMAQ home directory and compiler options in config.cmaq


#> config.cmaq
#> sourced from bldit.<model>

#> model repository location
setenv M3HOME /home/leo/CMAQv5.0.2
setenv M3MODEL${M3HOME}/models
setenv M3DATA  ${M3HOME}/data

#===============================================================================

#> architecture & compiler specific settings
#-------------------------------------------------------------------------------

#> set the COMPILER
# setenv COMPILER intel
# setenv COMPILER pgi
setenv COMPILER gcc



Save and exit

1. source config.cmaq

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Copy or link libraries

1. cd $M3LIB
   
2. cp –rf /usr/local/netcdf/ ./
   
3. cp –rf /usr/local/mpich/ ./
   
4. cp –rf /usr/local/ioapi_3.1/ ./

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Notice:1 you can also use command "ln -s"
Notice:2 if your install directory is not named by netcdf, mpich, ioapi_3.1 please rename it into netcdf, mpich, ioapi_3.1 after copy.


Start building

1. cd $M3HOME/scripts/stenex
   
2. ./bldit.se
   
3. ./bldit.se_noop

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1. cd $M3HOME/scripts/pario
   
2. ./bldit.pario

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1. cd $M3HOME/scripts/jproc
   
2. gedit bldit.jproc

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Modify corresponding lines in bldit.jproc

set LIB1 = "-L${IOAPI}"
set LIB2 = "-L${NETCDF}"
set LIBS = "$LIB1 $LIB2 -lgomp -lnetcdff"

Save and exit

1. ./bldit.jproc

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Notice:1 you may need install "gomp" and "git"
Notice:2 if report: fatal:Nota git repository (or any of the parent&.... do following:

1. cd $M3HOME/models
   
2. git init
   
3. cd $M3HOME/scripts/jproc
   
4. ./bldit.jproc

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1. cd $M3HOME/scripts/build
   
2. ./bldit.bldmake
   
3. cd $M3HOME/scripts/mcip/src
   
4. gedit Makefile

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Modify corresponding lines in Makefile
select gfortran compiler
NETCDF = $M3LIB/netcdf
IOAPI_ROOT = $M3LIB/ioapi_3.1
FC = gfortran
FFLAGS = -O3 -I$(NETCDF)/include -I$(IOAPI_ROOT)/Linux2_x86_64gfort
LIBS = -L$(IOAPI_ROOT)/Linux2_x86_64gfort -lioapi \
-L$(NETCDF)/lib -lnetcdf -lnetcdff \
-lgomp

If you did not install pvm3, please delete any line about pvm3!
Save and exit

1. make

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1. cd $M3HOME/scripts/icon
   
2. gedit bldit.icon

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Modify corresponding lines in bldit.icon

set LIB1 = "-lgomp -lnetcdff"

set NETCDF = "${M3LIB}/netcdf/lib -lnetcdf-lnetcdff"

Save and exit

1. ./bldit.icon
   
2. gedit bldit.bcon

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Modify corresponding lines in  bldit.bcon

set LIBS = "$LIB1 $LIB2 -lgomp -lnetcdff"

Save and exit

1. ./bldit.bcon

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1. cd $M3HOME/scripts/cctm
   
2. gedit bldit.cctm

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Modify corresponding lines in  bldit.cctm

set MPI_INC = ${M3LIB}/mpich/include

set NETCDF = "${M3LIB}/netcdf/lib -lnetcdf-lnetcdff"

Save and exit

1. ./bldit.cctm

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• Start to run
  

1. cd $M3HOME/scripts/icon
   
2. ./run.icon
   
3. cd $M3HOME/scripts/bcon
   
4. ./run.bcon
   
5. cd $M3HOME/scripts/cctm
   
6. ./run.cctm

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Notice: If you need use multi-cores

Before ./run.cctm

1. gdit run.cctm

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Modify corresponding lines in run.cctm

set PROC     = mpi

setenv NPCOL_NPROW "2 2"; set NPROCS   = 4

Make sure 2*2 = 4 if you want to use more cores

then ./run.cctm


That's all. May you succeed!

宁小才

谢谢楼主的分享，学习学习

mlhan

谢谢楼主分享！

heiheiheiheihei

我想问下，跑出来的数据是放到哪儿的

mlhan

谢谢楼主分享！

mlhan

楼主辛苦了！