<div dir="ltr">Dear Oliver,<div><br></div><div>Thanks. That appears to have worked. The plots I got look similar to the ones in the tutorial.</div><div>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).</div><div>I still get a mismatch between the outputs from snippet tauMax*sin(Y*pi) and np.fromfile('windx_siny.bin',dtype='f4').</div><div>Why is that?</div><div><br></div><div>Best</div><div><br></div><div>Jeremy <br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, 4 Apr 2021 at 16:41, Oliver Jahn <<a href="mailto:jahn@mit.edu">jahn@mit.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">This<br>
<br>
[X,Y]=np.meshgrid(x,y,indexing='ij')<br>
<br>
should be<br>
<br>
[Y,X]=np.meshgrid(y,x,indexing='ij')<br>
<br>
(with indexing 'ij' it is y,x, with indexing 'xy' it is x,y)<br>
<br>
I am attaching the script from Jeff's pull request where this is all<br>
done correctly.<br>
<br>
Oliver<br>
<br>
<br>
On 2021-04-04 09:00, Jeremy Miller wrote:<br>
> Dear Oliver,<br>
> <br>
> Thanks for coming back to me. I did just that. I now get a plot for<br>
> "eta" that appears to be two sets of constant values, on the left and<br>
> right of the line x=0.6*1e6 m (see the attached plot in<br>
> fig_bar_gyre_windx_siny.png). I also notice that the output bin file<br>
> (tau_2_1) still shows different values to the original numpy array<br>
> (tau_2). I have attached the latest version of the python script used to<br>
> generate the data (<a href="http://gendata_tut4.1.py" rel="noreferrer" target="_blank">gendata_tut4.1.py</a> <<a href="http://gendata_tut4.1.py" rel="noreferrer" target="_blank">http://gendata_tut4.1.py</a>>) and the<br>
> script used to generate the plots (<a href="http://tut_4.1_plots.py" rel="noreferrer" target="_blank">tut_4.1_plots.py</a><br>
> <<a href="http://tut_4.1_plots.py" rel="noreferrer" target="_blank">http://tut_4.1_plots.py</a>>).<br>
> <br>
> Best<br>
> Jeremy<br>
> <br>
> On Sun, 4 Apr 2021 at 13:48, Oliver Jahn <<a href="mailto:jahn@mit.edu" target="_blank">jahn@mit.edu</a><br>
> <mailto:<a href="mailto:jahn@mit.edu" target="_blank">jahn@mit.edu</a>>> wrote:<br>
> <br>
> Hi Jeremy,<br>
> <br>
> this will not work:<br>
> <br>
> > if sys.byteorder == 'little': tau_2.byteswap(True)<br>
> > fid = open('windx_siny.bin', 'wb')<br>
> > tau_2.astype('float32').tofile(fid)<br>
> <br>
> Can you instead try Jeff's suggestion:<br>
> <br>
> tau_2.astype('>f4').tofile('windx_siny.bin')<br>
> <br>
> and NOT use the byteswap command? Mixing byteswap and astype is a bad<br>
> idea as byteswap will create a mismatch between the data in memory and<br>
> numpy's assumption of the data type.<br>
> <br>
> Best,<br>
> Oliver<br>
> <br>
> <br>
> > as you suggested, the plot still came out blank.<br>
> > Regarding Jeffrey Scott's comment that the reason I could not read<br>
> back<br>
> > the bin file was due to a mismatch between float32 and float64, I<br>
> > followed his advice and read in the<br>
> > bin file using the snippet <br>
> ><br>
> > tau_2_1 = np.fromfile('windx_siny.bin',dtype='float32')<br>
> ><br>
> > and I got back an array with every entry being 'inf' except the<br>
> > penultimate column, being all '0'.<br>
> ><br>
> > Is it possible that the snippet <br>
> ><br>
> > # X=X.astype('float128')<br>
> > # Y=Y.astype('float128')<br>
> ><br>
> > (which is commented) needs to be included but with 'float128' replaced<br>
> > with 'float32'?<br>
> ><br>
> > Best<br>
> > Jeremy<br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > On Thu, 1 Apr 2021 at 16:47, Jan Klaus Rieck<br>
> <<a href="mailto:jan.rieck@mail.mcgill.ca" target="_blank">jan.rieck@mail.mcgill.ca</a> <mailto:<a href="mailto:jan.rieck@mail.mcgill.ca" target="_blank">jan.rieck@mail.mcgill.ca</a>><br>
> > <mailto:<a href="mailto:jan.rieck@mail.mcgill.ca" target="_blank">jan.rieck@mail.mcgill.ca</a><br>
> <mailto:<a href="mailto:jan.rieck@mail.mcgill.ca" target="_blank">jan.rieck@mail.mcgill.ca</a>>>> wrote:<br>
> ><br>
> > Hello Jeremy Miller,<br>
> ><br>
> > I also use python to to generate input data for the MITgcm. I<br>
> found<br>
> > that, to generate files that can be read by the MITgcm<br>
> consistently,<br>
> > I needed to specify the type explicitly. <br>
> > My way of saving the files would look like this in your case: <br>
> ><br>
> > if sys.byteorder == 'little': tau_2.byteswap(True)<br>
> > fid = open(''windx_siny.bin', 'wb')<br>
> > tau_2.astype('float32').tofile(fid)<br>
> ><br>
> > Of course, 'float32' could be replaced by 'float64' if you require<br>
> > double precision.<br>
> ><br>
> > I hope this helps,<br>
> > Jan Rieck<br>
> > <br>
> > On Thu, 2021-04-01 at 10:22 +0300, Jeremy Miller wrote:<br>
> >> Dear MITGCM forum,<br>
> >><br>
> >> I am Jeremy Miller, I am new to MITgcm and I've been going<br>
> through<br>
> >> the tutorials. I have a question about the "Barotropic Ocean<br>
> Gyre"<br>
> >> tutorial (section 4.1).<br>
> >><br>
> >> I managed to compile and run the code, and re-produce the first<br>
> >> two plots shown in section 4.1.5 for wind stress of τ = τ0 cos(<br>
> >> πy/Ly), for both the advection and non-advection cases (with the<br>
> >> provided input binary files). <br>
> >> I ran into problems when trying to produce the third plot,<br>
> for the<br>
> >> case where τ = τ0 sin( πy/Ly). I am a python user, so I<br>
> translated<br>
> >> gendata.m into python to write the input binary<br>
> >> files 'windx_cosy.bin' 'windx_siny.bin' (see the file<br>
> >> gendata_tut4.1py attached). As explained in section 3.9 I've<br>
> >> included the snippet <br>
> >><br>
> >> if sys.byteorder == 'little': tau_2.byteswap(True)<br>
> >><br>
> >> where "tau2" is the array to be output. There was no issue in the<br>
> >> cosine wind stress, and I managed to reproduce the results that I<br>
> >> got with the original 'windx_cosy.bin' provided in the tutorial.<br>
> >> However, with the sine wind stress case, the output in<br>
> >> 'Eta.0000077760.001.001' is all zeros. <br>
> >><br>
> >> When I attempt to read 'windx_siny.bin' with python into a new<br>
> >> array called tau2_1. I get absurdly big numbers back, which<br>
> do not<br>
> >> match the original array tau2 that I created. If I Remove the<br>
> >> snippet " if sys.byteorder == 'little': tau_2.byteswap(True)<br>
> ", in<br>
> >> the python gendata code, tau2_1 and tau2 match. But, then when I<br>
> >> run the code again, the file output.txt contains a long list<br>
> of NaNs.<br>
> >><br>
> >> I have also included the python code used to generate the<br>
> plots in<br>
> >> the file <a href="http://tut_4.1_plots.py" rel="noreferrer" target="_blank">tut_4.1_plots.py</a> <<a href="http://tut_4.1_plots.py" rel="noreferrer" target="_blank">http://tut_4.1_plots.py</a>><br>
> <<a href="http://tut_4.1_plots.py/" rel="noreferrer" target="_blank">http://tut_4.1_plots.py/</a>><br>
> >><br>
> >> Look forward to hearing from you.<br>
> >> Yours sincerely<br>
> >> Jeremy Miller<br>
> >> _______________________________________________<br>
> >> MITgcm-support mailing list<br>
> >> <a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a> <mailto:<a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a>><br>
> >> <mailto:<a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a><br>
> <mailto:<a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a>>><br>
> >><br>
> >> <a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support" rel="noreferrer" target="_blank">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a><br>
> >><br>
> > _______________________________________________<br>
> > MITgcm-support mailing list<br>
> > <a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a> <mailto:<a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a>><br>
> <mailto:<a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a> <mailto:<a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a>>><br>
> > <a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support" rel="noreferrer" target="_blank">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > MITgcm-support mailing list<br>
> > <a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a> <mailto:<a href="mailto:MITgcm-support@mitgcm.org" target="_blank">MITgcm-support@mitgcm.org</a>><br>
> > <a href="http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support" rel="noreferrer" target="_blank">http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support</a><br>
> ><br>
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</blockquote></div>