Home > climate models, models > UVic_ESCM 2.8 Build Notes

UVic_ESCM 2.8 Build Notes

2011 November 27


A new earth system climate model of intermediate complexity has been developed and its climatology compared to observations. The UVic Earth System Climate Model consists of a three-dimensional ocean general circulation model coupled to a thermodynamic/dynamic sea-ice model, an energy-moisture balance atmospheric model with dynamical feedbacks, and a thermomechanical land-ice model. In order to keep the model computationally efficient a reduced complexity atmosphere model is used. Atmospheric heat and freshwater transports are parametrized through Fickian diffusion, and precipitation is assumed to occur when the relative humidity is greater than 85%. Moisture transport can also be accomplished through advection if desired. Precipitation over land is assumed to return instantaneously to the ocean via one of 33 observed river drainage basins. Ice and snow albedo feedbacks are included in the coupled model by locally increasing the prescribed latitudinal profile of the planetary albedo. The atmospheric model includes a parametrization of water vapour/planetary longwave feedbacks, although the radiative forcing associated with changes in atmospheric CO2 is prescribed as a modification of the planetary longwave radiative flux. A specified lapse rate is used to reduce the surface temperature over land where there is topography. The model uses prescribed present-day winds in its climatology, although a dynamical wind feedback is included which exploits a latitudinally-varying empirical relationship between atmospheric surface temperature and density. The ocean component of the coupled model is based on the Geophysical Fluid Dynamics Laboratory (GFDL) Modular Ocean Model 2.2, with a global resolution of 3.6° (zonal) by 1.8° (meridional) and 19 vertical levels, and includes an option for brine-rejection parametrization. The sea-ice component incorporates an elastic-viscous-plastic rheology to represent sea-ice dynamics and various options for the representation of sea-ice thermodynamics and thickness distribution. The systematic comparison of the coupled model with observations reveals good agreement, especially when moisture transport is accomplished through advection.

The UVic Earth System Climate Model: Model Description, Climatology, and Applications to Past, Present and Future Climates
Andrew J. Weaver, Michael Eby, Edward C. Wiebe, Cecilia M. Bitz, Phil B. Duffy,
Tracy L. Ewen, Augustus F. Fanning, Marika M. Holland, Amy MacFadyen, H. Damon Matthews,
Katrin J. Meissner, Oleg Saenko, Andreas Schmittner, Huaxiao Wang and Masakazu Yoshimori (2001)
http://mgg.coas.oregonstate.edu/~andreas/pdf/W/weaver01ao.pdf

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Prerequisites
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Download Ubuntu 11.10 32 bit

Download Oracle VM VirtualBox 4.1.6
Install Oracle VM VirtualBox 4.1.6

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Create VM
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Oracle VM VirtualBox Manager, select [New]
In “Create New Virtual Machine”, select [Next]

In “VM Name and OS Type” dialog,
In the “Name” field, enter: ub1110x32
For the “Operating System”, select “Linux”
For “Version”, select “Ubuntu”
Select [Next]

In “Memory” dialog,
Select “2048” MB
Select [Next]

In the “Virtual Hard Disk” dialog,
select “Start-up Disk”,
select “Create new hard disk”
select [Next]

In the “Welcome to the virtual disk creation wizard” dialog,
select “VDI”
select [Next]

In the “Virtual disk storage details” dialog,
select “Fixed Size”
select [Next]

In the “Virtual disk file location and size” dialog,
select “16.00 GB”
select [Next]

In the “Summary” dialog,
select [Create]
select [Create]

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Install Ubuntu
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Oracle VM VirtualBox Manager, select [New]
Select “ub1110x32”
Select “start”

In the “Welcome to the First Run Wizard”,
select [Next]

In the “Select the Installation Media”
Select “ubuntu-11.10-desktop-i386.iso”
Select [Next]

In the “Summary”,
select [Start]

In the Ubuntu Install “Welcome” dialog,
select [Install Ubuntu]

In the “Installation type” dialog,
select “Erase disk and install Ubuntu”
select [Continue]

In the “Erase disk and install Ubuntu” dialog,
select [Install Now]

In the “Where are you” dialog,
select an appropriate time zone,
select [Continue]

In the “Keyboard layout” dialog,
select “English (US)”
Select [Continue]

In the “Who are you” dialog,
Enter ‘Your Name’: madmin
Enter ‘Your computers name’: ub1110x32
“Pick a username”: madmin
“Choose a password”: [some password]
“Confirm your password”: [same password]
Select “Require my password to log in”
Select [Continue]

In the “Installation Complete” dialog,
select [Restart Now]

In the reboot command line,
‘click’ and ‘enter’

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Update Software
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In the Ubuntu login screeen
In the password field, enter: madmin

In the right hand corner,
select the “Tools” icon,
select “Update Software”

In the “Update Manager” window,
Select [Install Updates]

In the “Authenticate” window,
enter the password
Select [Authenticate]

In the “Update Manager” window,
Select [Install Updates]

This will take several minutes.
There is a progress bar in the toolbar to the left.

After installing updates,
select [Reboot Now]

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Shutdown and Take a Snapshot
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In the right hand corner,
select the “Tools” icon,
select “Update Software”

In the confirmation dialog,
select “Shutdown”

In the “Oracle VM VirturalBox Manager”,
highlight the VM by name: ub1110x32

In the right hand corner,
select the “Snapshots” icon

In the upper left of the right hand panel,
select the “Snapshot” icon

In the “Snapshot Name”, enter: Fresh Install with Updates
Select the [OK] button

In the “Oracle VM VirturalBox Manager”,
highlight the VM by name: ub1110x32
Select the [Start] button

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Install the Intel Fortran Composer XE compiler
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On the top of the left hand toolbar,
click the “Dash” icon

In the search bar, enter: terminal
Drag “Terminal (gnome-terminal)” to the toolbar

In the left hand toolbar,
click on the “Terminal” icon

In the left hand tool bar,
click on the “FireFox” icon

Navigate to: http://software.intel.com/en-us/articles/intel-composer-xe
Select “Tools & Downloads” -> Free Non-Commercial
Accept the license
Select “Intel Fortran Composer XE 2011 for Linux”
Enter your registration information
Select the 32 bit compiler
Download file

In the “Terminal” window,
enter: cd ~/projects/pkgs
enter: tar xvzf ../../Downloads/l_fcompxe_ia32_2011.7.256.tgz
enter: cd l_fcompxe_ia32_2011.7.256
enter: sudo apt-get install build-essentials
enter: sudo apt-get install gcc-multilib
enter: sudo apt-get install rpm
enter: sudo apt-get install openjdk-6-jre-headless
enter: sudo ./install.sh

1: to skip welcome screen, enter: [enter]
to skip prerequisites screen, enter: [enter]
2: scroll through license, enter: accept
3: to use a serial number, enter: [enter]
enter the serial number: XXXX-XXXXXXXX
(the serial number will be sent to the registration email address)
4: to start install, enter: [enter]
5: when complete, enter: [enter]
6: to exit install, enter: [enter]

enter: echo “source /opt/intel/composer_xe_2011_sp1.7.256/bin/compilervars.sh ia32” >>

~/.bashrc

To test the install
enter: . ~/.bashrc
enter: ifort -help

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Install HD5
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In the left hand tool bar,
click on the “FireFox” icon

Navigate to: http://www.hdfgroup.org/ftp/HDF5/current/src/
Download: hdf5-1.8.8.tar.gz

In the “Terminal” window,
enter: mkdir -p projects/pkgs
enter: cd projects/pkgs
enter: tar xvzf ../../Downloads/hdf5-1.8.8.tar.gz
enter: cd hdf5-1.8.8
enter: ./configure –prefix=/usr/local
enter: make
enter: sudo make install

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Install NetCDF
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In the left hand tool bar,
click on the “FireFox” icon

Navigate to: ftp://ftp.unidata.ucar.edu/pub/netcdf/
Download: netcdf.tar.gz

In the “Terminal” window,
enter: cd ~/projects/pkgs
enter: tar xvzf ../../Downloads/netcdf.tar.gz
enter: cd netcdf-4.1.3
enter: sudo apt-get install libz-dev
enter: ./configure –prefix=/usr/local
enter: gedit libtool &
edit the two lines reading: CC=”ifort”
to read: CC= “/opt/intel/composer_xe_2011_sp1.7.256/bin/ia32/ifort”
enter: make
enter: sudo make install

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Install ncview
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# todo: lib udunits

In the left hand tool bar,
click on the “FireFox” icon

Navigate to: ftp://cirrus.ucsd.edu/pub/ncview
Download: ncview-2.1.1.tar.gz

In the “Terminal” window,
enter: cd ~/projects/pkgs
enter: tar xvzf ../../Downloads/ncview-2.1.1.tar.gz
enter: cd ncview-2.1.1.tar.gz
enter: sudo apt-get install xorg-dev
enter: sudo apt-get install libpng-dev
enter: ./configure –prefix=/usr/local
enter: make
enter: sudo make install

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Download UVIC ESCM
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To begin this procedure,
you will need to send email to
Michael Eby (eby@uvic.ca)
to request a username and password.

See also …
http://climate.uvic.ca/model/2.8/notes.html#Getting_Started

In the left hand tool bar,
click on the “FireFox” icon

Navigate to: http://climate.uvic.ca/model/2.8/
When prompted, provide the username and password
Download:
1: UVic_ESCM.2.8.tar.gz
2: UVic_ESCM.mk.tar.gz
3: UVic_ESCM.2.8.example.tar.gz

In the “Terminal” window,
enter: cd ~/projects
enter: mkdir models
enter: cd models
enter: tar xvzf ../../Downloads/UVic_ESCM.2.8.tar.gz
enter: tar xvzf ../../Downloads/UVic_ESCM.2.8.example.tar.gz
enter: tar xvzf ../../Downloads/UVic_ESCM.mk.tar.gz

— Configure ESCM to use the system libs
enter: cd ~/projects/models/UVic_ESCM/2.8/lib
enter: mv lib_linux lib_linux-orig
enter: ln -s /usr/local/lib lib_linux

— Configure the lib links
enter: cd ~/projects/models/UVic_ESCM/2.8/run
enter: cp mk.ver mk.ver-orig
enter: gedit mk.ver &
edit the Libraries_Default line to read: Libraries_Default = -lnetcdf -lnetcdff
save and exit

— Fix a file open/close issue in topog.F
enter: cd ~/projects/models/UVic_ESCM/2.8/source/common
enter: cp topog.F topog.F-orig
enter: gedit topog.F &
scroll to line 206 which reads: call relunit (iou)
comment out the line by placing a hash mark (#) in the first column
save and exit

— Configure UVic_ESCM.cmd
enter: cd ~/projects/models/UVic_ESCM/2.8/example
enter: gedit UVic_ESCM.cmd &
edit the line to reflect the true path
/home/madmin/projects/models/UVic_ESCM/2.8/example/UVic_ESCM.run &

— Add UVic_ESCM directory to the path
enter: echo “PATH=\$PATH:/home/madmin/projects/models/UVic_ESCM:.” >> ~/.bashrc

==================================================
Shutdown and Take a Snapshot
==================================================

In the right hand corner,
select the “Tools” icon,
select “Update Software”

In the confirmation dialog,
select “Shutdown”

In the “Oracle VM VirturalBox Manager”,
highlight the VM by name: ub1110x32

In the right hand corner,
select the “Snapshots” icon

In the upper left of the right hand panel,
select the “Snapshot” icon

In the “Snapshot Name”, enter: UVic_ESCM
In the “Snatpshot Description”, enter: Intel ifort, HDF5, NetCDF, NCView
Select the [OK] button

In the “Oracle VM VirturalBox Manager”,
highlight the VM by name: ub1110x32
Select the [Start] button

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Run UVIC ESCM
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In the left hand tool bar,
click on the “Terminal” icon

In the Terminal window,
enter: cd projects/models
enter: mkdir -p uvic_escm/test01
enter: cp -rp UVic_ESCM/2.8/example/* uvic_escm/test01
enter: cd uvic_escm/test01
enter: gedit UVic_ESCM.cmd &
edit the line to reflect the true path
/home/madmin/projects/models/uvic_escm/test01/UVic_ESCM.run &
enter: cp mk.in mk.in.orig
enter: gedit mk.in &
edit the first line to read:
Version_Directory = /home/madmin/projects/models/UVic_ESCM/2.8
save and exit
enter: mk c
enter: mk r
after 2 minutes, in another terminal enter: tail -f pr
you should see data scrolling
when complete (about 12 minutes on my box), you can use ‘ncview’
to examine the three .nc files in the directory.