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DEHewitt / portunid_particle_tracking

Code for simulation and analysis of particle tracking experiments for Giant Mud Crab (Scylla serrata) and Blue Swimmer Crab (Portunus armatus)
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Parcels on Katana - Help #26

Open jaseeverett opened 4 years ago

jaseeverett commented 4 years ago

@HaydenSchilling @DEHewitt I have just setup a new venv on Katana and installed a fresh Parcels version from Git. Please note that random has been updated to ParcelsRandon which will need to be updated in the import line and the random.seed line when you both next update parcels.

See this pull history for details https://github.com/OceanParcels/parcels/pull/912

HaydenSchilling commented 4 years ago

Thanks @jaseeverett , compared to the version Dan is running (v2.1.4, I have v2.2.0) the diffusion kernel was also updated from BrownianMotion2D to DiffusionUniformKh. Only change is the import line, functionality is the same.

jaseeverett commented 4 years ago

When I get up and running, I will confirm that the latest version from GitHub is running ok, and then we should update so the code is consistent.

jaseeverett commented 4 years ago

Just checking - did you guys install the GitHub version of Parcels or the pip version? I'm reinstalling (again) after more problems. Checking if wiping the venv and starting again will help.

HaydenSchilling commented 4 years ago

We installed from Github using the instructions for a non-released version on the Oceanparcels homepage except we specified the release (rather than the master):

pip install git+https://github.com/OceanParcels/parcels.git@v2.2.0

We did have some issues where we needed to install a number of additional packages into the virtual environment with the pip command in an interactive session. We are also using python 3.6 as 3.8 didn't work when we attempted it.

Duncan gave us these instructions to install the virtual environment:

? If not the basic information is:

To create it

mkdir p365
module add python/3.6.5
python3 -m venv --system-site-packages p365

Then each time that you want to use it run

module add python/3.6.5
source p365/bin/activate

and when you are finished

deactivate

Once you have it activated you can download the code, make the change and install it for yourself. If it does what you want you can then provide feedback to the developer in the hope that it will be able to be changed by a variable and let me know so that I can make the change in the next Python version I installed.

jaseeverett commented 4 years ago

Thanks @HaydenSchilling Thats helpful. I had most of the venv info from the Katana help pages (https://unsw-restech.github.io/software/python-virtualenvs.html) but I wasn't aware of the python 3.8 issue. Perhaps that is why I had trouble.

We should turn this thread into a help document for us and future users who need to install Parcels on Katana