[MITgcm-support] Barotropic ocean gyre tutorial

Jeremy Miller jeremysharonmiller at gmail.com
Sun Apr 4 10:48:14 EDT 2021


Great, thanks very much.

On Sun, 4 Apr 2021 at 17:46, Oliver Jahn <jahn at mit.edu> wrote:

> dtype='>f4'
>
> On 2021-04-04 10:21, Jeremy Miller wrote:
> > Dear Oliver,
> >
> > Thanks. That appears to have worked. The plots I got look similar to the
> > ones in the tutorial.
> > I ran Jeff Scott's code in the exact same form (but
> > with h.astype('>f4').tofile('bathy.bin')
> > and tau.astype('>f4').tofile('windx_cosy.bin') commented).
> > I still get a mismatch between the outputs from snippet tauMax*sin(Y*pi)
> > and np.fromfile('windx_siny.bin',dtype='f4').
> > Why is that?
> >
> > Best
> >
> > Jeremy
> >
> > On Sun, 4 Apr 2021 at 16:41, Oliver Jahn <jahn at mit.edu
> > <mailto:jahn at mit.edu>> wrote:
> >
> >     This
> >
> >     [X,Y]=np.meshgrid(x,y,indexing='ij')
> >
> >     should be
> >
> >     [Y,X]=np.meshgrid(y,x,indexing='ij')
> >
> >     (with indexing 'ij' it is y,x, with indexing 'xy' it is x,y)
> >
> >     I am attaching the script from Jeff's pull request where this is all
> >     done correctly.
> >
> >     Oliver
> >
> >
> >     On 2021-04-04 09:00, Jeremy Miller wrote:
> >     > Dear Oliver,
> >     >
> >     > Thanks for coming back to me. I did just that. I now get a plot for
> >     > "eta" that appears to be two sets of constant values, on the left
> and
> >     > right of the line x=0.6*1e6 m (see the attached plot in
> >     > fig_bar_gyre_windx_siny.png). I also notice that the output bin
> file
> >     > (tau_2_1) still shows different values to the original numpy array
> >     > (tau_2). I have attached the latest version of the python script
> >     used to
> >     > generate the data (gendata_tut4.1.py <http://gendata_tut4.1.py>
> >     <http://gendata_tut4.1.py>) and the
> >     > script used to generate the plots (tut_4.1_plots.py
> >     <http://tut_4.1_plots.py>
> >     > <http://tut_4.1_plots.py>).
> >     >
> >     > Best
> >     > Jeremy
> >     >
> >     > On Sun, 4 Apr 2021 at 13:48, Oliver Jahn <jahn at mit.edu
> >     <mailto:jahn at mit.edu>
> >     > <mailto:jahn at mit.edu <mailto:jahn at mit.edu>>> wrote:
> >     >
> >     >     Hi Jeremy,
> >     >
> >     >     this will not work:
> >     >
> >     >     > if sys.byteorder == 'little': tau_2.byteswap(True)
> >     >     > fid = open('windx_siny.bin', 'wb')
> >     >     > tau_2.astype('float32').tofile(fid)
> >     >
> >     >     Can you instead try Jeff's suggestion:
> >     >
> >     >     tau_2.astype('>f4').tofile('windx_siny.bin')
> >     >
> >     >     and NOT use the byteswap command?  Mixing byteswap and astype
> >     is a bad
> >     >     idea as byteswap will create a mismatch between the data in
> >     memory and
> >     >     numpy's assumption of the data type.
> >     >
> >     >     Best,
> >     >     Oliver
> >     >
> >     >
> >     >     > as you suggested, the plot still came out blank.
> >     >     > Regarding Jeffrey Scott's comment that the reason I
> >     could not read
> >     >     back
> >     >     > the bin file was due to a mismatch between float32 and
> >     float64, I
> >     >     > followed his advice and read in the
> >     >     > bin file using the snippet
> >     >     >
> >     >     > tau_2_1 = np.fromfile('windx_siny.bin',dtype='float32')
> >     >     >
> >     >     > and I got back an array with every entry being 'inf'
> except the
> >     >     > penultimate column, being all '0'.
> >     >     >
> >     >     > Is it possible that the snippet
> >     >     >
> >     >     > # X=X.astype('float128')
> >     >     > # Y=Y.astype('float128')
> >     >     >
> >     >     > (which is commented) needs to be included but with
> >     'float128' replaced
> >     >     > with 'float32'?
> >     >     >
> >     >     > Best
> >     >     > Jeremy
> >     >     >
> >     >     >
> >     >     >
> >     >     >
> >     >     >
> >     >     > On Thu, 1 Apr 2021 at 16:47, Jan Klaus Rieck
> >     >     <jan.rieck at mail.mcgill.ca <mailto:jan.rieck at mail.mcgill.ca>
> >     <mailto:jan.rieck at mail.mcgill.ca <mailto:jan.rieck at mail.mcgill.ca>>
> >     >     > <mailto:jan.rieck at mail.mcgill.ca
> >     <mailto:jan.rieck at mail.mcgill.ca>
> >     >     <mailto:jan.rieck at mail.mcgill.ca
> >     <mailto:jan.rieck at mail.mcgill.ca>>>> wrote:
> >     >     >
> >     >     >     Hello Jeremy Miller,
> >     >     >
> >     >     >     I also use python to to generate input data for the
> >     MITgcm. I
> >     >     found
> >     >     >     that, to generate files that can be read by the MITgcm
> >     >     consistently,
> >     >     >     I needed to specify the type explicitly.
> >     >     >     My way of saving the files would look like this in your
> >     case:
> >     >     >
> >     >     >     if sys.byteorder == 'little': tau_2.byteswap(True)
> >     >     >     fid = open(''windx_siny.bin', 'wb')
> >     >     >     tau_2.astype('float32').tofile(fid)
> >     >     >
> >     >     >     Of course, 'float32' could be replaced by 'float64' if
> >     you require
> >     >     >     double precision.
> >     >     >
> >     >     >     I hope this helps,
> >     >     >     Jan Rieck
> >     >     >
> >     >     >     On Thu, 2021-04-01 at 10:22 +0300, Jeremy Miller wrote:
> >     >     >>     Dear MITGCM forum,
> >     >     >>
> >     >     >>     I am Jeremy Miller, I am new to MITgcm and I've been
> going
> >     >     through
> >     >     >>     the tutorials. I have a question about the "Barotropic
> >     Ocean
> >     >     Gyre"
> >     >     >>     tutorial (section 4.1).
> >     >     >>
> >     >     >>     I managed to compile and run the code, and re-produce
> >     the first
> >     >     >>     two plots shown in section 4.1.5 for  wind stress of τ
> >     = τ0 cos(
> >     >     >>     πy/Ly), for both the advection and non-advection cases
> >     (with the
> >     >     >>     provided input binary files).
> >     >     >>     I ran into problems when trying to produce the third
> plot,
> >     >     for the
> >     >     >>     case where τ = τ0 sin( πy/Ly). I am a python user, so I
> >     >     translated
> >     >     >>     gendata.m into python to write the input binary
> >     >     >>     files 'windx_cosy.bin' 'windx_siny.bin' (see the file
> >     >     >>     gendata_tut4.1py attached).  As explained in section
> >     3.9 I've
> >     >     >>     included the snippet
> >     >     >>
> >     >     >>     if sys.byteorder == 'little': tau_2.byteswap(True)
> >     >     >>
> >     >     >>     where "tau2" is the array to be output. There was no
> >     issue in the
> >     >     >>     cosine wind stress, and I managed to reproduce the
> >     results that I
> >     >     >>     got with the original 'windx_cosy.bin' provided in the
> >     tutorial.
> >     >     >>     However, with the sine wind stress case, the output in
> >     >     >>     'Eta.0000077760.001.001' is all zeros.
> >     >     >>
> >     >     >>     When I attempt to read  'windx_siny.bin' with python
> >     into a new
> >     >     >>     array called tau2_1. I get absurdly big numbers back,
> which
> >     >     do not
> >     >     >>     match the original array tau2 that I created. If I
> >     Remove the
> >     >     >>     snippet " if sys.byteorder == 'little':
> >     tau_2.byteswap(True)
> >     >     ", in
> >     >     >>     the python gendata code, tau2_1 and tau2 match. But,
> >     then when I
> >     >     >>     run the code again, the file output.txt contains a long
> >     list
> >     >     of NaNs.
> >     >     >>
> >     >     >>     I have also included the python code used to generate
> the
> >     >     plots in
> >     >     >>     the file tut_4.1_plots.py <http://tut_4.1_plots.py>
> >     <http://tut_4.1_plots.py>
> >     >     <http://tut_4.1_plots.py/>
> >     >     >>
> >     >     >>     Look forward to hearing from you.
> >     >     >>     Yours sincerely
> >     >     >>     Jeremy Miller
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