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<p class="MsoNormal">Hi Yohei,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">ECCOv4 reads profile data from NetCDF files but does not generate output in NetCDF format; instead, all outputs are in binary or ASCII format. Besides using the xmitgcm package as Takaya mentioned, you can also use ECCOv4-py to read the
model's binary output, as detailed in its tutorial at <a href="https://ecco-v4-python-tutorial.readthedocs.io/" target="_new">
https://ecco-v4-python-tutorial.readthedocs.io/</a>.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best,<o:p></o:p></p>
<p class="MsoNormal">Ou Wang<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From:
</span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Yohei Takano - BAS <yokano@bas.ac.uk><br>
<b>Date: </b>Wednesday, April 10, 2024 at 8:08</span><span style="font-size:12.0pt;font-family:"Arial",sans-serif;color:black"> </span><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">AM<br>
<b>To: </b>mitgcm-support@mitgcm.org <mitgcm-support@mitgcm.org><br>
<b>Subject: </b>[EXTERNAL] Re: [MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Hi Martin, all.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">I tried with debug mode but couldn't find a meaningful information (such as lines) so after talking to<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">my colleague, I decided to leave this for now since binary output will be good for now for the ECCOv4<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">runs I am working on. Looking STDOUT, it might stop at the place related to profiles but turning this<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">package off did not solve the problem...<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">I am wondering whether the community working on ECCOv4 use NetCDF package (or just convert binary<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">output to NetCDF, post-processing). <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Thank you again for your support, I might come back to this later.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">I appreciate your input, Martin.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Yohei<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Yohei Takano - BAS <yokano@bas.ac.uk><br>
<b>Sent:</b> 08 April 2024 12:11<br>
<b>To:</b> MITgcm Support <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled</span>
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<p class="MsoNormal"> </p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Hi Matin,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Thank you again, I will check with the sys-admin on the debugging. I will update once I manage to backtrace.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Yohei<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From:</span></b><span style="color:black"> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Martin Losch <Martin.Losch@awi.de><br>
<b>Sent:</b> 08 April 2024 10:53<br>
<b>To:</b> MITgcm Support <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled</span>
<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Yohei, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">this depends very much on your specific computer and compiler. I suggest that you ask your sys-admins or colleages in your lab, how you can get a backtrace for your setup.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The tail of the STDOUT.0000 may tell you how far you have gotten in your run (again, depends on how often your maschine flushes the std output etc)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Martin<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
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<p class="MsoNormal">On 8. Apr 2024, at 11:32, Yohei Takano - BAS <yokano@bas.ac.uk> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Hi Martin,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Thank you for the suggestion. I turned on the debugger by setting -devel when executing genmake2<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">and ran the model but did not show any additional information... Do I need to also turn on some options<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">in the namelist before running the model (sorry I am not used to using much of debug tools which I should)?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Thank you,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Yohei<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b>From:</b> MITgcm-support <mitgcm-support-bounces@mitgcm.org> on behalf of Martin Losch <Martin.Losch@awi.de><br>
<b>Sent:</b> 08 April 2024 08:10<br>
<b>To:</b> MITgcm Support <mitgcm-support@mitgcm.org><br>
<b>Subject:</b> Re: [MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled<span style="font-size:9.0pt;font-family:Helvetica">
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Hi Yohai,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">the error is difficult to debug, if you don’t know where it happens.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Please recompile with debugger options or similar turned on (e.g. by setting -devel at the genmake2 step) and then you should get more information in which routine and which line this
happens (i.e. a backtrace).<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Maybe a file name that you specified was too long?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">Martin<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">On 5. Apr 2024, at 18:22, Yohei Takano - BAS <yokano@bas.ac.uk> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"> I am trying to turn on NetCDF in ECCOv4 (I am using ECCOv4-r2) configuration, what I did is<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">simply turning on "mnc" in the package.conf before compiling and then prepared data.mnc,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">turned on "mnc" in data.pkg. My aim is to obtain monitoring and diagnostics output in NetCDF files.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"> However, the model immediately crashes with below error, and I am not sure what is causing this error<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">(my colleague said it could be a memory reason). The same mnc setting worked with another configuration<br>
(coarse resolution global model) so I think the setup is fine (but I could have missed something specific for<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">ECCOv4 setups).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">-----<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">lib-4211 : UNRECOVERABLE library error<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"> A WRITE operation tried to write a record that was too long.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Encountered during a sequential formatted WRITE to an internal file (character variable)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">-----<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"> Has anyone encountered similar error? The same <span style="color:black;background:white">ECCOv4-r2</span> configuration runs fine without NetCDF.</span><span style="font-size:9.0pt;font-family:"Aptos",sans-serif"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Thank you in advance.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif">Yohei<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica"><br>
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