<div dir="ltr"><div>My recollection is that singleCpuIO only works with binary (MDS) files, but not with netCDF,</div><div>which is very unfortunate.</div><div>Here we've been using singleCpuIO, along with the diagnostics package, to output "global" binary</div><div>files, then a bunch of scripts (we like NCL) to convert to netCDF<br></div><div>Some conversion scripts (binary to netCDF), mostly Matlab and Python, are available along with the MITgcm code, <br></div><div>sometimes in the verification experiments, sometimes in the tools (?) directory, but they may need to be</div><div>tweaked with for the specific experiment (and grid!) that you're using.</div><div><br></div><div><br><div class="gmail_quote"><div dir="ltr">On Wed, Nov 14, 2018 at 5:10 PM Ali Ramadhan <<a href="mailto:alir@mit.edu">alir@mit.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div style="direction:ltr;font-family:Tahoma;color:#000000;font-size:10pt">
<div>Hi Sanjiv,</div>
<div><br>
</div>
<div>I'm not familiar with the netCDF MATLAB module so I probably can't help there but it might be helpful if you posted the new errors you're getting.</div>
<div><br>
</div>
<div>To answer (iii) you can set <code class="m_-8847765874820918857m_-1188343061455876705gmail-docutils m_-8847765874820918857m_-1188343061455876705gmail-literal m_-8847765874820918857m_-1188343061455876705gmail-notranslate">
<span class="m_-8847765874820918857m_-1188343061455876705gmail-pre"><span class="m_-8847765874820918857m_-1188343061455876705gmail-highlighted">useSingleCpuIO</span></span>
<span class="m_-8847765874820918857m_-1188343061455876705gmail-pre">=</span> <span class="m_-8847765874820918857m_-1188343061455876705gmail-pre">
.TRUE.</span></code> in the <code class="m_-8847765874820918857m_-1188343061455876705gmail-docutils m_-8847765874820918857m_-1188343061455876705gmail-literal m_-8847765874820918857m_-1188343061455876705gmail-notranslate">
<span class="m_-8847765874820918857m_-1188343061455876705gmail-pre">PARM01</span></code> namelist within the main
<code class="m_-8847765874820918857m_-1188343061455876705gmail-docutils m_-8847765874820918857m_-1188343061455876705gmail-literal m_-8847765874820918857m_-1188343061455876705gmail-notranslate">
<span class="m_-8847765874820918857m_-1188343061455876705gmail-pre">data</span></code> file (<a href="https://mitgcm.readthedocs.io/en/latest/outp_pkgs/outp_pkgs.html?highlight=useSingleCpuIO" target="_blank">Section
9.2.1.3</a>) so that all tiles are sent to a single CPU which combines them and writes out a single file for the entire grid. I imagine you'll lose some performance but unless you have many tiles or very large tiles it shouldn't be too noticeable. Also took
me a while to find this setting when I first started!<br>
</div>
<div><br>
</div>
<div>Cheers,</div>
Ali
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<hr>
<div id="m_-8847765874820918857divRpF46453" style="direction:ltr"><font size="2" face="Tahoma" color="#000000"><b>From:</b> MITgcm-support [<a href="mailto:mitgcm-support-bounces@mitgcm.org" target="_blank">mitgcm-support-bounces@mitgcm.org</a>] on behalf of Sanjiv Ramachandran [<a href="mailto:sramachandran@umassd.edu" target="_blank">sramachandran@umassd.edu</a>]<br>
<b>Sent:</b> Wednesday, November 14, 2018 4:57 PM<br>
<b>To:</b> <a href="mailto:mitgcm-support@mitgcm.org" target="_blank">mitgcm-support@mitgcm.org</a><br>
<b>Subject:</b> [MITgcm-support] Matlab scripts for viewing netcdf files<br>
</font><br>
</div>
<div></div>
<div>
<div id="m_-8847765874820918857divtagdefaultwrapper" dir="ltr" style="font-size:12pt;color:#000000;font-family:Calibri,Helvetica,sans-serif">
<p style="margin-top:0;margin-bottom:0">Hi,</p>
<p style="margin-top:0;margin-bottom:0"> I am trying to set up the 'MLadjust' test case, which is one of the cases in the 'verification' folder. My output gets written into multiple files, one for each tile, as I am using MPI. I am using the latest version
of MITgcm.<br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I have some questions regarding the 'mnc_assembly.m' file in the utils/matlab/ folder:</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">(i) The file has commands of the form: <span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span><br>
</span></p>
<p style="margin-top:0;margin-bottom:0"><span>fnc = netcdf(fnm, 'nowrite');</span><br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">I replaced 'netcdf' with 'netcdf.open' as otherwise the command would not execute. But after the replacement, I am getting other errors. </p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">(ii) How do you assemble files across multiple folders? The file mnc_assembly.m only assembles all the tiles within a folder.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">(iii) Is there any way to get MITgcm to just return the fields for the entire grid in one big file (eg. <a href="http://state.0000100000.nc" target="_blank">state.0000100000.nc</a>)? For my purposes, there are no benefits to having the output written separately for each tile.</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p style="margin-top:0;margin-bottom:0">Thanks,</p>
<p style="margin-top:0;margin-bottom:0">Sanjiv <br>
</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
</div>
</div>
</div>
</div>
</div>
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