Zoom example in Nemo 4.2.2

1

Dear All,

I’m trying to extract hourly SSH in a single location in a Nemo 4.2.2 based run. And it does not work, the model just holds, and does nothing when it’s time to print. Although I have done that fine when using previous versions of Nemo.
Has anyone an example on how to code a zoom properly in the xml files, domain, grid, field and file ?

Thanks for your help,

Robinson

2

Hi Robinson,

The “1point” zoom domain is given as an example in the domain_def_nemo.xml and grid_def_nemo.xml files.

It would be used to extract a scalar timeseries from SSH data by including grid_ref="grid_1point" in the file_def.xml type files, e.g.

<field field_ref="ssh" grid_ref="grid_1point" />

Is this consistent with your zoom syntax? Do you also have this issue when using other diagnostic frequencies?

Daley

3

Hei Daley,

Thanks for your reply, but unless I am wrong I have followed exactly this procedure.
And it always worked in previous versions of Nemo. Will check again,

Thanks again,

Robinson

4

Hei again,

Just to be sure, is there a specific XIOS version one should compile Nemo 4.2.2 with ?

Thanks for your help,

Robinson

5

Hi Robinson,

You should use at least r2131 of XIOS 2, since this contains changes required for the tiling.

I’m not sure if this is related to your error, however, so I would recommend using the latest version of XIOS 2 if you can.

Daley

6

Hei Daley,

Thank you, i will try.

/robinson

7

Hei Daley,

I have tried everything, even changing the Netcdf and/or HDF5 versions, same results. Normal outputs that contain the entire domain work, but zooms do not.

Any idea is welcome,

Thanks for your help,

Robinson

8

Hi Robinson,

Could you attach the XIOS .xml files you are using? I will try to replicate the issue.

Daley

9

Hei Daley,

Thanks a lot for your help, I really appreciate because I’m really blocked now.
I have put the xml files here:

https://ns5001k.web.sigma2.no/ROBINSON_DIRECTORIES/DALEY/

I’m trying to output a simple ssh time series at a point, which you can easily identify using the grep command, it contains the word “andenes”.

Thanks again,

Robinson

10

Hi Robinson,

In your field_def.xml you have:

<field_group id="tide_gauges" grid_ref="grid_T">
   <field id="ssh_andenes" field_ref="ssh" grid_ref="grid_1point"/>
</field_group>

and in your file_def.xml you have:

<file id="file172" name_suffix="_ssh" description="ocean T grid variables">
   <field field_ref="ssh_andenes" name="ssh_andenes"/>
</file>

Have you tried using the grid_ref="grid_1point" in the file_def.xml and not in the field_def.xml? I.e.

<file id="file172" name_suffix="_ssh" description="ocean T grid variables">
   <field field_ref="ssh_andenes" name="ssh_andenes" grid_ref="grid_1point"/>
</file>

To my understanding, grid_ref has different meanings depending on whether it appears in a field or file definition:

  • In a field definition, it determines the grid the data will be received on from NEMO
  • In a file definition, it determines the grid the data will be output on in netCDF files

I think your run may be hanging because in your current definition, XIOS is expecting to receive data for a single point. I may be wrong about this, so please give my suggestion a try and let me know what happens.

11

Hei Daley,

Thanks a lot for the help, I will try this right now. I think i had tried what you suggest, but I will try again just to be sure.

Thanks again,

13

I remove the definition in field_def, and wrote in file_def:

<file id="file172" name_suffix="_ssh" description="ocean T grid variables" >
 <field field_ref="ssh"         name="ssh_andenes"  grid_ref="grid_1point"  />
 </file>

Same result… the model freezes when it is time to print the ssh at a single point.

14

I’ve just tried using your XIOS files in an ORCA2 ocean-only run (using different zoom points and using XIOS in server mode), and it ran ok.

However, when I ran this using XIOS in attached mode (as your iodef.xml seems to suggest you are doing), I got a floating point error in XIOS. Removing the ssh_andenes variable resolved this. So, there seems to be an issue with the zoom when using XIOS in attached mode.

I wonder if you also have this issue, but XIOS is hanging instead of crashing. Could you try running XIOS in detached/server mode?

15

This is a great idea, thanks a lot, I will try tomorrow. By attached mode, you mean i run only nemo.exe, right ? Indeed this is what I do, but it was never a problem with the zoom.

Thanks again, I would have never thought about it,

16

It works !!! Daley, if we ever meet do remind me to offer you a beer, you saved my life. I would have never thought of this server idea.

17

Hooray! Glad to hear it Robinson :smiley:

18

Hello everyone, I try to use the same to extract different points in my grid, my domain_def.xml are:

< domain id=“1point” domain_ref=“grid_T” >
<zoom_domain ibegin=“1127” jbegin=“722” ni=“1” nj=“1”/>
<zoom_domain ibegin=“1133” jbegin=“694” ni=“1” nj=“1”/>
<zoom_domain ibegin=“1114” jbegin=“763” ni=“1” nj=“1”/>
< /domain>

but it only extracts the last point. Does anyone have any ideas to fix it? thank you so much

19

Hei Elsy,

Each subdomain that you call “1point”, is a box of consecutive points, consecutive meaning here it can also be a single point. In your case you try to define 3 unrelated points so it cannot work.
You need to define 3 boxes, named for example point_1, point_2, point_3, which are independent.
And then it should work.

/robinson

1 Like
20

It works, you also need to define grid_def.xml, many thanks.