jklymak

import smtplib
import yaml

from email.message import EmailMessage
from email.utils import make_msgid
from email.mime.base import MIMEBase
from email import encoders
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
from email.mime.application import MIMEApplication

jklymak

import numpy as np
import matplotlib.pyplot as plt
import seawater
%matplotlib widget
import pooch
import xarray as xr
import pandas

"""
eg 

jklymak

import xarray as xr
# https://oceandata.sci.gsfc.nasa.gov/ob/getfile/AQUA_MODIS.20230606T215500.L2.SST.NRT.nc

with xr.open_dataset('/Users/jklymak/Downloads/AQUA_MODIS.20230606T215500.L2.OC.NRT.nc',group='geophysical_data') as ds, xr.open_dataset('/Users/jklymak/Downloads/AQUA_MODIS.20230606T215500.L2.OC.NRT.nc',group='navigation_data') as nav:
    print(nav)
    ds['lon'] = (('number_of_lines', 'pixels_per_line'), nav['longitude'].values)
    ds['lat'] = (('number_of_lines', 'pixels_per_line'), nav['latitude'].values)
    for j in range(0, 2030):
        if np.any(~np.isfinite(ds.lat[j, :])):
            print(j)

jklymak

# output from the MITgcm using xmitgcm

import xarray as xr
import numpy as np
import xgcm

with xr.open_dataset(fname, decode_times=False) as ds:
    grid = xgcm.Grid(ds, coords={'Z':{'center':'Z', 'outer':'Zp1'}}, periodic=False)
    ds = preprocess(ds)

jklymak

#!/bin/bash
#SBATCH --account=def-jklymak
#SBATCH [email protected]
#SBATCH --mail-type=ALL
#SBATCH --ntasks-per-node=1
#SBATCH --time=0-00:15
#SBATCH --mem=64G

cd ${SLURM_SUBMIT_DIR}

jklymak

#!/bin/bash -l
for todo in OneHill100lowU10N10Amp305f141B059Rough
do
    day=86400
    jobid=$(sbatch -J $todo --export=start=0,stop=$((day*6 + 180)),dt=90 runModel.sh)
    #echo $jobid
    jobid1=$(sbatch  -J $todo  --dependency=afterok:${jobid##* } --export=start=$((day*6)),stop=$((day*12 + 180)),dt=90 runModel.sh)
    jobid2=$(sbatch  -J $todo --dependency=afterok:${jobid1##* } --export=start=$((day*12)),stop=$((day*18 + 180)),dt=90 runModel.sh)
    jobid3=$(sbatch  -J $todo --dependency=afterok:${jobid2##* } --export=start=$((day*18)),stop=$((day*24 + 180)),dt=90 runModel.sh)

jklymak

#MITgcm checkin runs

Sometimes we want to store versions of config files for a model run. This uses runname to make a new branch, and to make a commit on the main branch. You need to set the model config up to be tracked, of course.

_log.info('doing this via git!!')

jklymak

import sys
import os
import subprocess

os.system('sq')
out=subprocess.check_output('squeue -h -t RUNNING -u jklymak --Format="Name:50"', 
                            shell=True, text=True)
out = out.splitlines()
# print(out)
for dd in out:

jklymak

Chaining multiple MITgcm jobs

These were done for AbHillInter, on the machine koehr.

runAll.sh

#!/bin/sh -l
todo=Iso1kmlowU10Amp305f141B059Wall

one=$(qsub -N $todo -v "start=0, stop=259300, dt=50" runModelRestarts.sh)
two=$(qsub -N $todo -v "start=259200, stop=518500, dt=50"  -W depend=afterok:$one runModelRestarts.sh)

jklymak

"""
Use https://github.com/jklymak/waypoint_distance instead!
"""

def get_xy(ds, lat0, lon0):
    x = (ds.longitude - lon0) * np.cos(np.deg2rad(lat0)) * 60 * 1.852
    y = (ds.latitude - lat0) * 60 * 1.852
    ds['x'] = x
    ds.x.attrs['units'] = f'km east of {lon0}'
    ds['y'] = y