[MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled

Wed Apr 10 11:11:22 EDT 2024

Hi Yohei,

If you’re using Python, the xmitgcm package (https://xmitgcm.readthedocs.io/en/latest/) is very useful in reading the binary files directly without having to resort to NetCDF formats.

Best,
Takaya
———————
Assistant Research Scientist
Center for Ocean-Atmospheric Prediction Studies
Florida State University, USA
https://roxyboy.github.io/

On Apr 10, 2024, at 11:07 AM, Yohei Takano - BAS <yokano at bas.ac.uk> wrote:

Hi Martin, all.

I tried with debug mode but couldn't find a meaningful information (such as lines) so after talking to
my colleague, I decided to leave this for now since binary output will be good for now for the ECCOv4
runs I am working on. Looking STDOUT, it might stop at the place related to profiles but turning this
package off did not solve the problem...

I am wondering whether the community working on ECCOv4 use NetCDF package (or just convert binary
output to NetCDF, post-processing).

Thank you again for your support, I might come back to this later.
I appreciate your input, Martin.

Regards,

Yohei
________________________________
From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of Yohei Takano - BAS <yokano at bas.ac.uk>
Sent: 08 April 2024 12:11
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled

Hi Matin,

Thank you again, I will check with the sys-admin on the debugging. I will update once I manage to backtrace.

Regards,

Yohei
________________________________
From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of Martin Losch <Martin.Losch at awi.de>
Sent: 08 April 2024 10:53
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled

Hi Yohei,

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.

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)

Martin

On 8. Apr 2024, at 11:32, Yohei Takano - BAS <yokano at bas.ac.uk> wrote:

Hi Martin,

Thank you for the suggestion. I turned on the debugger by setting -devel when executing genmake2
and ran the model but did not show any additional information... Do I need to also turn on some options
in the namelist before running the model (sorry I am not used to using much of debug tools which I should)?

Thank you,

Yohei

________________________________

From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of Martin Losch <Martin.Losch at awi.de>
Sent: 08 April 2024 08:10
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Error from the ECCOv4 Setup with NetCDF Enabled

Hi Yohai,

the error is difficult to debug, if you don’t know where it happens.
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).
Maybe a file name that you specified was too long?

Martin

On 5. Apr 2024, at 18:22, Yohei Takano - BAS <yokano at bas.ac.uk> wrote:

Dear all,

   I am trying to turn on NetCDF in ECCOv4 (I am using ECCOv4-r2) configuration, what I did is
simply turning on "mnc" in the package.conf before compiling and then prepared data.mnc,
turned on "mnc" in data.pkg. My aim is to obtain monitoring and diagnostics output in NetCDF files.

   However, the model immediately crashes with below error, and I am not sure what is causing this error
(my colleague said it could be a memory reason). The same mnc setting worked with another configuration
(coarse resolution global model) so I think the setup is fine (but I could have missed something specific for
ECCOv4 setups).

-----
lib-4211 : UNRECOVERABLE library error
  A WRITE operation tried to write a record that was too long.

Encountered during a sequential formatted WRITE to an internal file (character variable)
-----

    Has anyone encountered similar error? The same ECCOv4-r2 configuration runs fine without NetCDF.
Thank you in advance.

Best regards,

Yohei

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