1/20/2024 0 Comments Iceberg with penguinsThe study, published in Biology Letters, shows how penguin populations can be deeply affected by small changes in their icy environment, which will grow more unpredictable as the region warms due to climate change. They found that a single iceberg, which collided with a glacier near the colony in 2010, led to a build-up of ice that indirectly caused many chicks to starve. Using multiple 39-year datasets, an international research team recently stitched together the most comprehensive study to date of the relationship between Emperor Penguin breeding and land-fast ice. More than 7,000 seabirds congregate along this desolate archipelago to breed on a particular type of platform: land-fast ice, a kind of sea ice that stays connected to a coastline or glacier instead of floating free. From April to November, it is home to one of the world’s best-documented Emperor Penguin colonies. data/MY_IMG_TILE.Point Géologie, off the coast of Adélie Land, Antarctica, is an ice-locked island chain that ranks among the most inhospitable places on Earth-unless you’re an Emperor Penguin. Iceberg_tect -gpu-ids 0 -name MY_MODEL -epoch 300 -checkpoints_dir './model_path/' -output test -input_im. Then, follow the environment setup commands under 'To test' above.įinally, the script to run the prediction for a single PNG image tile is: Please put the model file here: /MY_MODEL/ The one provided here is at the epoch 300 of the model we will call "MY_MODEL". You can download to your local machine and use scp, ftp, rsync, or Globus to transfer to bridges. $ iceberg_tect -help # this will display a help screen of available usage and parameters. $ source penguins_env/bin/activate # activate your environment, no need to create a new environment because the Penguins tools are installed and isolated here. $ module load python3 # load correct python version, as before. $ module load cuda # load parallel computing architecture, as before. $ cd $SCRATCH/Penguins # make sure you are in the same directory where everything was set up before. (this may take a minute or two or more to receive an allocation). This package has been tested on P100 GPUs on bridges, but that does not exclude any other resource that offers the same GPUs. $ interact -p GPU-small # request a compute node. To test $ deactivate # exit your virtual environment. $ export PYTHONPATH =/penguins_env/lib/python3.5/site-packages Method #2 (Installing from source recommended for developers only): $ git clone $ pip install iceberg_arch # pip is a python tool to extract the requested software (iceberg_arch in this case) from a repository. (Replace with the results of pwd command above. $ export PYTHONPATH =/penguins_env/lib/python3.5/site-packages # set a system variable to point python to your specific code. Notice the command line prompt changes to show your environment on the next line. $ source penguins_env/bin/activate # activate your environment. $ virtualenv penguins_env # create a virtual environment to isolate your work from the default system. $ module load python3 # load correct python version. $ module load cuda # load parallel computing architecture. $ cd Penguins # move into your working directory. $ mkdir Penguins # create a directory to work in. $ cd $SCRATCH # switch to your working space. Lines that do not start with '$' or ' $' are output you should expect to see. The lines below following a '$' are commands to enter (or cut and paste) into your terminal (note that all commands are case-sensitive, meaning capital and lowercase letters are differentiated.) Everything following '#' are comments to explain the reason for the command and should not be included in what you enter. Once you have logged into Bridges, you can follow one of two methods for installing iceberg-penguins. Please see Ubuntu, MobaXterm or PuTTY PSC Bridges Many tools are available for ssh access to bridges. Login is available to bridges directly or through the XSEDE portal. Login to bridges via ssh using a Unix or Mac command line terminal. These instructions are specific to XSEDE Bridges but other resources can be used if cuda, python3, and a NVIDIA P100 GPU are present, in which case 'module load' instructions can be skipped, which are specific to Bridges. Software Dependencies - these will be installed automatically with the installation below. Prerequisites - all available on bridges via the commands below
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