[MITgcm-support] Zeros in inactive tiles in the regional model

WU Yue vywu at ust.hk
Thu Mar 20 02:51:49 EDT 2025 

Hi Matt and Martin,

Thank you very much for your replies. Yes Martin, you understand correctly, I’ve used ‘blanklist’ in data.exch2 to not let some of the tiles go into the comutation. Thank you for your suggestion. I tried by redefining the grid (starting at j=900) and it works with outputs nearly half zise than they were.

Yue


From: MITgcm-support <mitgcm-support-bounces at mitgcm.org> on behalf of mitgcm-support-request at mitgcm.org <mitgcm-support-request at mitgcm.org>
Date: Wednesday, March 19, 2025 at 22:23
To: mitgcm-support at mitgcm.org <mitgcm-support at mitgcm.org>
Subject: MITgcm-support Digest, Vol 261, Issue 7
Send MITgcm-support mailing list submissions to
        mitgcm-support at mitgcm.org

To subscribe or unsubscribe via the World Wide Web, visit
        https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.mitgcm.org%2Fmailman%2Flistinfo%2Fmitgcm-support&data=05%7C02%7Cvywu%40ust.hk%7C6f826ca220de49d6ce8b08dd66f1a77f%7Cc917f3e2932249269bb3daca730413ca%7C1%7C0%7C638779910271343563%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=G%2F5SACp6IWFkRsCkXD6YlPCZh8iDhi8vQAMGC4YPIZE%3D&reserved=0<http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support>
or, via email, send a message with subject or body 'help' to
        mitgcm-support-request at mitgcm.org

You can reach the person managing the list at
        mitgcm-support-owner at mitgcm.org

When replying, please edit your Subject line so it is more specific
than "Re: Contents of MITgcm-support digest..."


Today's Topics:

   1. Re: Zeros in inactive tiles in the regional model
      (Matthew Mazloff)
   2. Re: Zeros in inactive tiles in the regional model (Martin Losch)


----------------------------------------------------------------------

Message: 1
Date: Wed, 19 Mar 2025 06:52:24 -0700
From: Matthew Mazloff <mmazloff at ucsd.edu>
To: mitgcm-support at mitgcm.org
Subject: Re: [MITgcm-support] Zeros in inactive tiles in the regional
        model
Message-ID: <6D603562-0FC2-41B5-B16D-54635A408690 at ucsd.edu>
Content-Type: text/plain; charset="utf-8"

Hi Yue

The MITgcm doesn?t do any compression.
You will have to compress (e.g. zip) after the MITgcm I/O.

Matt


> On Mar 18, 2025, at 9:17 PM, WU Yue <vywu at ust.hk> wrote:
>
> Dear MITgcm team,
>
> I?m running a regional model based on LLC1080 grid (the domain of Face 1 shown in Fig.1). The original version uses sNx = 90, sNy = 90 with 320 active tiles (also 320 processors used) for the entire domain, which takes around 6 days to run 2 experimental years. To focus more on a smaller region and for resource-saving, I masked southern part of the domain (new Face 1 in Fig.2) then uses sNx = 90 and sNy = 60 with 317 active tiles. The new version runs around 4 days for 2 years, which seems good to me that reducing grid number per tile to 2/3 of the origional version, the running time should speed by 1/3 in time.
>
> However, I noticed that the output data size remains the same between the old and new versions. It appears to have values in the region with active tiles, but for those in inactive tiles the model keep assigning to zeros (see two Figs). In that sense, the new version only saves in time but doesn?t save the storage.
>
> Does anyone know whether the processors are used to computing active tiles whilst allocating zeros to inactive tiles? Or is the model do the allocation? (or other?) Are these zeros will definitely exist?
>
> Best wishes,
> Yue
>
> <Fig1.png><Fig2.png>_______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fmailman.mitgcm.org%2Fmailman%2Flistinfo%2Fmitgcm-support__%3B!!Mih3wA!DkYkZRo09RtuSD2Fp2ylcFkslD1nCFQBPtLAMtxWg3j99aN9PTymIqZ58WLpAy3VYA1RWTq9QDlntA%24&data=05%7C02%7Cvywu%40ust.hk%7C6f826ca220de49d6ce8b08dd66f1a77f%7Cc917f3e2932249269bb3daca730413ca%7C1%7C0%7C638779910271360858%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=lzIw5UouZS9wjqNF16iGt3GV%2Fo5grHte8WuyPj9IluI%3D&reserved=0<https://urldefense.com/v3/__http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!Mih3wA!DkYkZRo09RtuSD2Fp2ylcFkslD1nCFQBPtLAMtxWg3j99aN9PTymIqZ58WLpAy3VYA1RWTq9QDlntA$>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.mitgcm.org%2Fpipermail%2Fmitgcm-support%2Fattachments%2F20250319%2F3cf57ae3%2Fattachment-0001.html&data=05%7C02%7Cvywu%40ust.hk%7C6f826ca220de49d6ce8b08dd66f1a77f%7Cc917f3e2932249269bb3daca730413ca%7C1%7C0%7C638779910271369436%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=z9Y8rXOe1R%2BPpkliwuDFMNI9FUBJblemDvEk%2FZQdpfM%3D&reserved=0<http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20250319/3cf57ae3/attachment-0001.html>>

------------------------------

Message: 2
Date: Wed, 19 Mar 2025 15:22:49 +0100
From: Martin Losch <Martin.Losch at awi.de>
To: MITgcm Support <mitgcm-support at mitgcm.org>
Subject: Re: [MITgcm-support] Zeros in inactive tiles in the regional
        model
Message-ID: <0B16A2B8-E0D6-4990-8230-589CEB17B2B6 at awi.de>
Content-Type: text/plain; charset="utf-8"

Hi Yue,

I am not sure, if I understand the issue properly, but if you use ?blank tiles? via ?blankList? in ?eedata?, then the inactive tiles in this list will not be computed (no processor assigned), but still part of the output field (just zeros, as you have found out yourself). This is useful, when you try to mask out parts in the middle of the domain, that do not contain any ocean (in your case maybe some tiles in the eastern part of the domain over Scandinavia or Russia), but if all grid points from j = 1 to 900 are supposed to be masked, it may make more sense to redefine the grid to start only at your j=900.

Martin

> On 19. Mar 2025, at 14:52, Matthew Mazloff <mmazloff at ucsd.edu> wrote:
>
> Hi Yue
>
> The MITgcm doesn?t do any compression.
> You will have to compress (e.g. zip) after the MITgcm I/O.
>
> Matt
>
>
>> On Mar 18, 2025, at 9:17 PM, WU Yue <vywu at ust.hk <mailto:vywu at ust.hk>> wrote:
>>
>> Dear MITgcm team,
>>
>> I?m running a regional model based on LLC1080 grid (the domain of Face 1 shown in Fig.1). The original version uses sNx = 90, sNy = 90 with 320 active tiles (also 320 processors used) for the entire domain, which takes around 6 days to run 2 experimental years. To focus more on a smaller region and for resource-saving, I masked southern part of the domain (new Face 1 in Fig.2) then uses sNx = 90 and sNy = 60 with 317 active tiles. The new version runs around 4 days for 2 years, which seems good to me that reducing grid number per tile to 2/3 of the origional version, the running time should speed by 1/3 in time.
>>
>> However, I noticed that the output data size remains the same between the old and new versions. It appears to have values in the region with active tiles, but for those in inactive tiles the model keep assigning to zeros (see two Figs). In that sense, the new version only saves in time but doesn?t save the storage.
>>
>> Does anyone know whether the processors are used to computing active tiles whilst allocating zeros to inactive tiles? Or is the model do the allocation? (or other?) Are these zeros will definitely exist?
>>
>> Best wishes,
>> Yue
>>
>> <Fig1.png><Fig2.png>_______________________________________________
>> MITgcm-support mailing list
>> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
>> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2F%2Fmailman.mitgcm.org%2Fmailman%2Flistinfo%2Fmitgcm-support__%3B!!Mih3wA!DkYkZRo09RtuSD2Fp2ylcFkslD1nCFQBPtLAMtxWg3j99aN9PTymIqZ58WLpAy3VYA1RWTq9QDlntA%24&data=05%7C02%7Cvywu%40ust.hk%7C6f826ca220de49d6ce8b08dd66f1a77f%7Cc917f3e2932249269bb3daca730413ca%7C1%7C0%7C638779910271377794%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=mLoBXLReWCpQFy%2BsdTNXLPcZUgDrry%2BlRy5P8FTYUHM%3D&reserved=0<https://urldefense.com/v3/__http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support__;!!Mih3wA!DkYkZRo09RtuSD2Fp2ylcFkslD1nCFQBPtLAMtxWg3j99aN9PTymIqZ58WLpAy3VYA1RWTq9QDlntA$>
>
> _______________________________________________
> MITgcm-support mailing list
> MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
> https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.mitgcm.org%2Fmailman%2Flistinfo%2Fmitgcm-support&data=05%7C02%7Cvywu%40ust.hk%7C6f826ca220de49d6ce8b08dd66f1a77f%7Cc917f3e2932249269bb3daca730413ca%7C1%7C0%7C638779910271386175%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=r0lv4YdvHM98V5%2FLuxybMmWwZ2s8fZxA2qeHMS2R%2BP0%3D&reserved=0<http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.mitgcm.org%2Fpipermail%2Fmitgcm-support%2Fattachments%2F20250319%2F73e47af9%2Fattachment.html&data=05%7C02%7Cvywu%40ust.hk%7C6f826ca220de49d6ce8b08dd66f1a77f%7Cc917f3e2932249269bb3daca730413ca%7C1%7C0%7C638779910271394304%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=RjKHiYt59zEW7TcS4TjXA6YRct9HXmG8lRPIbadvRm4%3D&reserved=0<http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20250319/73e47af9/attachment.html>>

------------------------------

Subject: Digest Footer

_______________________________________________
MITgcm-support mailing list
MITgcm-support at mitgcm.org
https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmailman.mitgcm.org%2Fmailman%2Flistinfo%2Fmitgcm-support&data=05%7C02%7Cvywu%40ust.hk%7C6f826ca220de49d6ce8b08dd66f1a77f%7Cc917f3e2932249269bb3daca730413ca%7C1%7C0%7C638779910271402295%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&sdata=hy8u%2Fv3JeI04%2BPL%2BJSMJ7%2B5CJQe%2BlW6ak0aRhkfgxvU%3D&reserved=0<http://mailman.mitgcm.org/mailman/listinfo/mitgcm-support>


------------------------------

End of MITgcm-support Digest, Vol 261, Issue 7
**********************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.mitgcm.org/pipermail/mitgcm-support/attachments/20250320/d5be13d7/attachment-0001.html>

More information about the MITgcm-support mailing list