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JMMP-Group / SEVERN-SWOT

Severn estuary 500m ocean model
MIT License
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Generate tidal boundaries #7

Open jpolton opened 3 years ago

jpolton commented 3 years ago

Generate tidal boundary forcing as harmonic files using FES2014 data and the PyNEMO tool.

  1. Compile PyNEMO (ideally on Archer2, otherwise livljobs)
  2. Set up namelists
  3. get necessary input files together
  4. run and generate netcdf files of boundary harmonics

Acceptance criteria:

jpolton commented 3 years ago

The wiki for installing PyNEMO and generating tidal boundaries is complete and tested.

Over to @mpayopayo for testing/bug-squashing/improving.

There are no scripts for this. It is all in the wiki at present as it was my first iteration of the new PyNEMO.

mpayopayo commented 3 years ago

@jpolton I'm struggling to install PyNEMO. 

# clone the configuration repository
cd /work/$USER # or wherever you want to do this
git clone https://github.com/JMMP-Group/SEVERN-SWOT.git

# clone the PyNEMO repository
git clone https://github.com/NOC-MSM/PyNEMO.git
cd PyNEMO
git checkout IMMERSE
module load anaconda/3-5.1.0
conda env create -f pynemo_37.yml
conda activate pynemo3

and I get: image so I follow that and go with 

echo ". /packages/lmodmodules/apps/anaconda/3-5.1.0/etc/profile.d/conda.sh" >> ~/.bashrc
echo "conda activate" >> ~/.bashrc

Now at the bottom of my ~/.bashr reads: image try to activate again but still not happy and I'm getting the same error:

conda activate pynemo3

image

any suggestion?

SORTED: it's source activate pynemo3 and not conda activate pynemo3. Changing that in the wiki

mpayopayo commented 3 years ago

@jpolton I don't have permission for /projectsa/accord/SANH_jenjar/CMEMS_SANH/CMEMS_subdomain_coordinates.nc or any /projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3/ Could you please change that?

jpolton commented 3 years ago

@jpolton I don't have permission for /projectsa/accord/SANH_jenjar/CMEMS_SANH/CMEMS_subdomain_coordinates.nc or any /projectsa/accord/SANH_jenjar/CMEMS_SANH/TEST_pynemo3/ Could you please change that?

I've sent an email to NOC IT to address this.

jpolton commented 3 years ago

@jpolton I'm struggling to install PyNEMO.

# clone the configuration repository
cd /work/$USER # or wherever you want to do this
git clone https://github.com/JMMP-Group/SEVERN-SWOT.git

# clone the PyNEMO repository
git clone https://github.com/NOC-MSM/PyNEMO.git
cd PyNEMO
git checkout IMMERSE
module load anaconda/3-5.1.0
conda env create -f pynemo_37.yml
conda activate pynemo3

and I get: image so I follow that and go with

echo ". /packages/lmodmodules/apps/anaconda/3-5.1.0/etc/profile.d/conda.sh" >> ~/.bashrc
echo "conda activate" >> ~/.bashrc

Now at the bottom of my ~/.bashr reads: image try to activate again but still not happy and I'm getting the same error:

conda activate pynemo3

image

any suggestion?

SORTED: it's source activate pynemo3 and not conda activate pynemo3. Changing that in the wiki

My suspicion that if you remove activate conda from .bashrc then conda activate pynemo3 would work. Maybe...

mpayopayo commented 3 years ago

It does work when I do source activate pynemo3 instead of conda activate pynemo3 so I changed the wiki accordingly. There was no activate conda in .bashrc anyway ...