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TryCOSINE.md

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My notes for setting up cosine-box are here: compiling, setting up nml files, changing the python for initial conditions, and how I chose values for initial conditions.

I tarred up everything so you can try COSINE on the box model. I just transferred files locally and used VisIt to look at them.

All steps are recorded in this YouTube video.

These text instructions follow what is shown in the video:

  • go to the scratch directory
  • copy my tarball, untar, cd into directory
  • look at input files
  • change something write_initial_conditions.py
  • check out the batch script
  • run via batch script, not on command line (because of environment stuff)
  • look at ICs again, see it changed
  • look at run batch script
  • use shared queue because not many processors
  • procs needed depend out outputs
  • I'm outputting each cosine variable, outputs are every 6 hours
  • nothing in outputs, but the directory needs to exist
  • submit the job
  • check on it
  • look at stderr file
  • took 1 minute
  • there are a bunch of small files...not good for transfers. remove them with a script.
  • just nc files
  • use Globus to transfer locally...Expanse endpoint starts at '/scratch'
  • open visit
  • open a file - remember to choose SCHISM as type
  • Transform to make it more box
  • look at it
  • Open another one in the same window...this is because it creates a time correlation
  • Set view and time to 'locked'
  • Clone the window (we want a time correlation and locked view/time before cloning, or you have to do that for each window)
  • Delete 'extra' plots (if you want)
  • Now they dance together in space and time
  • To see what is going on, fix the colormap...try to find good limits
  • Change the colormap. Try to use continuous ones, or it looks like weird stratification

These are the commands used.

cd /expanse/lustre/scratch/$USER/temp_project
cp /home/llowe/cosine-box.tar .
tar -xvf cosine-box.tar
cd cosine-box
head 3 COS*ic
vi write_initial_conditions.py
sbatch submit.python.sh
squeue -u $USER
rm *.bak
head 3 COS*ic
vi submit.sh
vi param.nml
ls outputs
sbatch submit.sh
squeue -u $USER
ls -lrth
more cosine-box[...numbers...].err
source rm.sh
ls -lhrt outputs