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GLIMMER Ice Shelf Modeling (OS X HowTo)

May 14th, 2010 | 3 Comments | By Ken Mankoff

A new beta version of the Community Ice Sheet Model, Glimmer-CISM, has been released. Below are instructions to compile and run it on OS X.

# build NetCDF
export CFLAGS=-m32
export FFLAGS=-m32
./configure --prefix=/Users/mankoff/local/netcdf-4.1.1 \
          --disable-cxx --disable-curl  --disable-dap
make && make install
say netCDF done

# build GLIMMER
cd ~/local/src/
wget http://download.berlios.de/glimmer-cism/glimmer-1.7.0.tar.gz
tar zxvf glimmer-1.7.0.tar.gz
cd glimmer-1.7.0/

# OS X has issues with 32 and 64 bit libraries.
# The -m32 flag forces 32 bit compilation.
# The following should be one long line:
./configure --prefix=/Users/mankoff/local/glimmer-1.7.0 \
     --with-netcdf=/Users/mankoff/local/netcdf-4.0.1 \
     FC=gfortran F77=gfortran CFLAGS=-m32

make
make install
say GLIMMER done

There are a few ways to test the installation. The source folder provides a test folder:

export PATH=/Users/mankoff/local/glimmer-1.7.0/bin:$PATH
cd ~/local/src/glimmer-1.7.0/tests/shelf
python circular-shelf.py circular-shelf.PP.config
python confined-shelf.py confined-shelf.PP.config
say GLIMMER Test Done # Takes a while. Turn up your volume

Running the above command will result in NetCDF files being created in the output/ subdirectory. You can view the contents of example.nc with most any generic NetCDF viewer. While theses tests run over a given period of time, the output only has one time stored. If you want to see an evolution of the ice shelf, older test suites available from the previous code repository site should be used:

cd ~/tmp/
wget http://forge.nesc.ac.uk/download.php/200/glimmer-example-0.6.tar.gz
tar zxvf glimmer-example-0.6.tar.gz
cd glimmer-example-0.6/
~/local/glimmer-1.7.0/bin/glide_launch.py ./example.config
say done

Examine the output file example.nc to see ice sheet evolution over time. Basal melt is shown below:


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@article{Rutt:2009,
  Author = {Ian C. Rutt and Nicholas R. J. Hulton and Antony J. Payne},
  Title = {{The Glimmer community ice sheet model}},
  Year = {2009}}
  Journal = {J. Geophys. Res.},
  Volume = {114},
  Number = {F2},
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Pine Island Glacier Publication TimeMap

March 19th, 2010 | No Comments | By Ken Mankoff

In which I present a rough geo-spatial-temporal map of Pine Island Glacier (PIG) publications.

Geo-spatial-temporal time-map of Pine Island Glacier (PIG) publications

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Building a Software/Hardware Environment for Research

March 15th, 2010 | 5 Comments | By Ken Mankoff

Sometimes I get asked what software/hardware systems I recommend for research. Below is my standard advice. I am a scientific programmer and student and my day-to-day tasks involve research, data analysis,  scientific programming, and writing. Data sets might include satellite images, model output, GPS, seismic, and a variety of other data. Data domains are ocean, atmosphere, and/or ice. I travel a lot, either from home to the office or to the field (which might mean months on a boat with no internet connection). Therefore I try to have a setup that supports high performance computing (HPC) on a laptop.

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Giant Diatoms

August 7th, 2009 | No Comments | By Ken Mankoff

I’m in Portland, OR, half-way through a two week Ice Sheet Summer Modeling School. It is educational and intense. Portland, OR is a very nice city. At least the section around Portland State University is. It is slow and green and calm and quiet. Which does not mean that the un-{slow,green,calm,quiet} New York City is not also very nice.

But where else can you walk down the street and see giant diatoms larger than truck tires?

Giant Diatoms lining the streets of Portland, Oregon

Giant Diatoms lining the streets of Portland, Oregon

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KML Interactive Sampler

July 16th, 2009 | No Comments | By Ken Mankoff

If you create Google Earth or KML layers, you’ll want to find a 2nd monitor and keep the KML Interactive Sampler open full screen. An invaluable resource for hand-building a KML or when writing code.

KML Interactive Sampler

KML Interactive Sampler

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My Twitter Experiment

June 14th, 2009 | 1 Comment | By Ken Mankoff

Everybody else seems to be discussing and commenting on Twitter so I figured I would too. I don’t know what it is, nor why it is popular, but I do use it from time to time, and will begin a Twitter experiment starting tomorrow morning.

My Twitter usage is limited to following some friends who have chosen to broadcast their activities there rather than on a blog. Most of these people have blogs too, and I follow those also. In addition to following others, I have posted some thoughts there myself, and I’ve set up my parents solar thermal system to tweet when it starts to overheat. I chose this simply because it was the easiest way for them and the technicians to get an SMS on their phone, although there exists an infinite number of non-twitter implementations.

My Twitter Experiment will begin tomorrow, Monday June 14 and continue to Friday, June 19. I am beginning a new project for work, and will tweet my thoughts, progress, trials and tribulations as I go along. The project is officially one week long, although it will continue in other forms for the next few years until I finish my PhD.

The work this coming week will be to write some software to access, visualize, and analyze oceanographic data from the Amundsen and Bellingshausen seas in Antarctica.

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Free Online Climate Textbook

December 11th, 2008 | No Comments | By Ken Mankoff

The first version of the online textbook, “Introduction to Climate Dynamics and Climate Modelling,” by H. Goosse, P.Y. Barriat, W. Lefebvre, M.F. Loutre, and V. Zunz, and published by the Universite Catholique de Louvain is now available.

http://www.climate.be/textbook

The reader should be able to understand the dominant causes of past climate change and to critically evaluate the projections of climate change over the next centuries or millennia. The book is also intended to give the student the bases to understand how climate models are built and how they could be used to make quantitative estimates of climate variability and climate change, as well as to illustrate how models could be used to understand the most important concepts of climate science.

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Managing Papers and Sources

October 8th, 2008 | 1 Comment | By Ken Mankoff

If you author scientific publications using LaTeX and OS X, there is a useful tool chain you should know about. Even if you write non-scientific papers in MS Word on Windows you might find something useful in this post. If you don’t write, or you already use Zotero, BibDesk, zot2bib, and LaTeXiT or EquationEditor, then you should probably skip this post.

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Sci Viz

July 2nd, 2007 | No Comments | By Ken Mankoff

I'm finally home from a wonderful week-long trip to Minneapolis and Madison. A group of ANDRILL and ARISE people met in Minneapolis to discuss scientific education. This involved spending time playing with a Geowall, mini golf in the science museum of Minnesota Big Back Yard, and learning about PSICAT and Corelyzer. We also watched a video of a Rain Table but did not get to play with it.

All this was in the context of ANDRILL and ARISE and meeting the team members and brainstorming about what interesting science education topics we will do on the ice. It is a great group and I'm excited to spend a few months with them in Antarctica.

The highlight of the trip was a morning in the Saint Anthony Falls Laboratory, a hydrology and fluid mechanics research center with the mission to, “conduct research for developing innovative and sustainable engineering solutions to major environmental, water-resources, and energy-related problems”. I wish I had brought my camera so I could show some picture of all the streams and the Jurassic Tank they have inside the building…

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