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oceanmodeling / ufs-weather-model

This repo is forked from ufs-weather-model, and contains the model code and external links needed to build the UFS coastal model executable and model components, including the ROMS, FVCOM, ADCIRC and SCHISM plus WaveWatch III model components.
https://github.com/oceanmodeling/ufs-coastal-app
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SCHISM integration #2

Open uturuncoglu opened 1 year ago

uturuncoglu commented 1 year ago

@platipodium @saeed-moghimi-noaa @pvelissariou1 I am creating this issue to communicate the SCHISM related developments. I am planing to do the same for each component. So, we could focus specific component in each issue. Anyway here is my update about the ongoing development regarding to SCHISM:

saeed-moghimi-noaa commented 1 year ago

Thanks @uturuncoglu . For schism I also tag @josephzhang8 .

uturuncoglu commented 1 year ago

Maybe I could go with ike_shinnecock.sch. I think this is SCHISM forced by data atmosphere that requires only u and v wind components. I need to find data for 2008-08-23 and maybe could use CDEPS ATMMESH data mode but I need CFS data for it. @pvelissariou1 Can you also send me CFS data for those dates. It seems forecast length is 120 hours for this case.

uturuncoglu commented 1 year ago

ike_shinnecock.sch seems standalone test. So maybe it is good to start with it without worrying data atmosphere etc. Let me start with it and maybe I could define it as RT under UFS.

uturuncoglu commented 1 year ago

@platipodium @saeed-moghimi-noaa @pvelissariou1 @josephzhang8 ike_shinnecock.sch seems working now. Is there any simple script or tool that I could use to create 2d maps etc. to check the results.

platipodium commented 1 year ago

Thanks @uturuncoglu ... quite a beast to download :=).

On my M1 the command should be "./compile.sh macosx.gnu-DAPP=COASTALS -DNO_PARMETIS=ON -DOLDIO=ON" coastal YES NO. I got as far as missing PIO...

platipodium commented 1 year ago

Thanks @uturuncoglu ... quite a beast to download :=).

On my M1 the command should be "./compile.sh macosx.gnu-DAPP=COASTALS -DNO_PARMETIS=ON -DOLDIO=ON" coastal YES NO. I got as far as missing PIO...

New issue #3

The CMAKE_FIND package does not locate my installed PIO, I'll make a new issue

josephzhang8 commented 1 year ago

The easiest way to visualize SCHISM results may be via the matlab scripts in the source code bundle:

../schism/src/Utility/VisMatlab/SCHISM*2.m (I assume you used the new version with scribed I/O, i.e. no OLDIO turned on)

We also have schismview, a python script that needs some documentation but I can ask my staff to send you the instructions.

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 2:08 AM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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uturuncoglu commented 1 year ago

@josephzhang8 The exiting CoastalApp was using OLDIO (-DOLDIO=ON) and I used that tooin my case but it is easy to test it by turning it off. Let me try.

uturuncoglu commented 1 year ago

@josephzhang8 I tried to compile without OLDIO but I am getting following error when I run the model,

3: 3: ABORT: INIT: Too few scribes (0). Please specify atleast equal to number of output variables (1)

So, maybe the configuration needs to be adjusted to run in this case. Let me know if I need to change any option in the ike_shinnecock.sch case.

josephzhang8 commented 1 year ago

If you use OLDIO on, you should viz using SCHISM_*.m (no '2').

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 12:07 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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josephzhang8 commented 1 year ago

When running with new I/O, you need to specify # of I/O 'scribe' processes; see

https://schism-dev.github.io/schism/master/getting-started/running-model.html

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 12:19 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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3: 3: ABORT: INIT: Too few scribes (0). Please specify atleast equal to number of output variables (1)

So, maybe the configuration needs to be adjusted to run in this case. Let me know if I need to change any option in the ike_shinnecock.sch case.

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uturuncoglu commented 1 year ago

@josephzhang8 Okay. I'll check the documentation. Thanks for your help.

josephzhang8 commented 1 year ago

Anytime, Ufuk! Thank you for helping us.

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 12:47 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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uturuncoglu commented 1 year ago

Hi All,

I added new RT under tests/rt_coastal.conf (in the same branch)

./rt.sh -l rt_coastal.conf -k -n coastal_ike_shinnecock_sch

It is running in my side (still uses old I/O, once I test new one I'll fix the configuration). To run ufs_coastal related RT, you need to copy input directories and make minor change in the rt.sh to point your new input directory. Let me know if you need to access them. They are on Cheyenne.

What is next? I am plaining to continue to work and run one coupled schism configuration. It seems ike_shinnecock.atm2sch uses data atmosphere. So, running first with NUOPC connector and then with CMEPS would be good to see if we have issue with CMPES like we had in ADCIRC component. It would be also nice to sync with UFS Weather Model since lots of development done after we fork it. So, this would be a good test for syncing ufs-coastal.

@pvelissariou1 If you don't mind, could you send me CFS data for 2008-08-23? I am not sure this configuration also covers the same region like florence_hsofs.atm2adc (maybe that test name needs to be florence_cfs.atm2adc since we are facing with CFS) but if you provide a file for me I could create ESMF mesh file for it if it is required.

saeed-moghimi-noaa commented 1 year ago

@uturuncoglu @pvelissariou1 @josephzhang8 @platipodium

Very good progress indeed. I agree with staying with schism to include more of the tests. For the pull request I have no idea when would be the best time. I feel like it make sense if we start a regular weekly tag-up (perhaps just 30 min) for now only with schism developers. We are still waiting to hear back from adcirc folks. FVCOM also just finished their tests for nems-fvcom and nems-ww3-fvcom. They are also actively working with us right now. As another avenue to take if adcirc folks stayed unresponsive.

pvelissariou1 commented 1 year ago

Saeed, Ufuk

Joannes just scheduled a meeting next Tuesday to discuss the CoastalApp/ADCIRC CMEPS issues. He used one of their regular meetings where all parties are participating.

Takis

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Physical Scientist - Project Lead cell: (205) 227-9141 email: @.***

On Fri, Mar 31, 2023 at 12:58 PM Saeed Moghimi @.***> wrote:

@uturuncoglu https://github.com/uturuncoglu @pvelissariou1 https://github.com/pvelissariou1 @josephzhang8 https://github.com/josephzhang8 @platipodium https://github.com/platipodium

Very good progress indeed. I agree with staying with schism to include more of the tests. For the pull request I have no idea when would be the best time. I feel like it make sense if we start a regular weekly tag-up (perhaps just 30 min) for now only with schism developers. We are still waiting to hear back from adcirc folks. FVCOM also just finished their tests for nems-fvcom and nems-ww3-fvcom. They are also actively working with us right now. As another avenue to take if adcirc folks stayed unresponsive.

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josephzhang8 commented 1 year ago

When I tried to clone ufs-coastal, it took >1 hr and still running, with a lot 'y'.

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 1:47 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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Hi All,

I added new RT under tests/rt_coastal.conf (in the same branch)

./rt.sh -l rt_coastal.conf -k -n coastal_ike_shinnecock_sch

It is running in my side (still uses old I/O, once I test new one I'll fix the configuration). To run ufs_coastal related RT, you need to copy input directories and make minor change in the rt.sh to point your new input directory. Let me know if you need to access them. They are on Cheyenne.

What is next? I am plaining to continue to work and run one coupled schism configuration. It seems ike_shinnecock.atm2schhttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnoaa-ocs-modeling%2FCoastalApp-testsuite%2Ftree%2Fdevelop%2Fike_shinnecock.atm2sch&data=05%7C01%7Cyjzhang%40vims.edu%7C77eac092417246d5e32508db320ff3f9%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638158816330066916%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4zjzBrJI9kRpFrSwFDVGy6xiGG%2F5tYfwUzpRAf63Z20%3D&reserved=0 uses data atmosphere. So, running first with NUOPC connector and then with CMEPS would be good to see if we have issue with CMPES like we had in ADCIRC component. It would be also nice to sync with UFS Weather Model since lots of development done after we fork it. So, this would be a good test for syncing ufs-coastal.

@pvelissariou1https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fpvelissariou1&data=05%7C01%7Cyjzhang%40vims.edu%7C77eac092417246d5e32508db320ff3f9%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638158816330066916%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=OlqW7GT8RhX%2FmPL8VqOxsNIg8CFfgSYu79Cr%2BnxuJ4k%3D&reserved=0 If you don't mind, could you send me CFS data for 2008-08-23? I am not sure this configuration also covers the same region like florence_hsofs.atm2adc (maybe that test name needs to be florence_cfs.atm2adc since we are facing with CFS) but if you provide a file for me I could create ESMF mesh file for it if it is required.

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uturuncoglu commented 1 year ago

@josephzhang8 let me test in my side. If there is some issue with .gitmodules file that could create issue.

uturuncoglu commented 1 year ago

@saeed-moghimi-noaa Just to clarify. I will not have PR in UFS Weather Model side. I am just planing to bring their updates to our fork (and to branch). That is all. So we could keep up-to-date along with the development in UFS Weather Model side. I think we decided not to push anything to UFS Weather Model authoritative repository yet in our last call.

saeed-moghimi-noaa commented 1 year ago

@uturuncoglu Thanks for the clarification. Understood.

uturuncoglu commented 1 year ago

@josephzhang8 Following command works for me (I named the directory as TEST).

git clone --recursive -b feature/coastal_app https://github.com/oceanmodeling/ufs-coastal.git TEST

BTW, since ADCIRC is private repository, they need to add you (maybe you are already in that group) and enter password when git asks.

josephzhang8 commented 1 year ago

Yup it works. So we'll stay in this branch for the time being.

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 4:24 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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git clone --recursive -b feature/coastal_app https://github.com/oceanmodeling/ufs-coastal.githttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Foceanmodeling%2Fufs-coastal.git&data=05%7C01%7Cyjzhang%40vims.edu%7C0fdc6f1064b644406d0508db3225cd99%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638158910176907713%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=XGazmufDXrTEoN3c0PPQD0QXyPOs5CgXlYd062aPnJg%3D&reserved=0 TEST

BTW, since ADCIRC is private repository, they need to add you (maybe you are already in that group) and enter password when git asks.

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uturuncoglu commented 1 year ago

@josephzhang8 Yes that is the plan but we will keep it up-to-date with authoritative repository. I could also make this branch default so you don't need to specify branch in the clone but we could decide it later. I am plaining to keep develop up-to-date with authoritative repository. Anyway, we could discuss these details in the next call.

josephzhang8 commented 1 year ago

Understood; thx Ufuk!

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 4:40 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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uturuncoglu commented 1 year ago

@josephzhang8 @platipodium I set <# scribes> as following in my job submission script,

mpiexec_mpt -p %g: -np 4 omplace ./fv3.exe 1

but still getting same error. I think this is because of not building src/Driver. The UFS driver does not have similar code like following,

https://github.com/uturuncoglu/schism/blob/639d57a17f22d33d82d422b494e41c1cd99cd29e/src/Driver/schism_driver.F90#L91

I think we make this as an option in ESMF config file (under OCN_attributes:: group) and pass to the model with this way. I could modify the schism cap but maybe you might want to follow different approach. I think this was not used with the exiting CoastalApp since it was building with OLDIO. Anyway, let me know what you think. We could also open an another ticket for this issue.

josephzhang8 commented 1 year ago

Thx Ufuk. I think you are right; Carsten and I have not looked at the cap for new I/O. I'll work with him on this... meanwhile you can continue with OLDIO. Thx.

Regards,

Joseph Zhang (804)684 7595 (office) SCHISM web: http://ccrm.vims.edu/schism/ From: Ufuk Turunçoğlu @.> Sent: Friday, March 31, 2023 5:32 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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mpiexec_mpt -p %g: -np 4 omplace ./fv3.exe 1

but still getting same error. I think this is because of not building src/Driver. The UFS driver does not have similar code like following,

https://github.com/uturuncoglu/schism/blob/639d57a17f22d33d82d422b494e41c1cd99cd29e/src/Driver/schism_driver.F90#L91https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Futuruncoglu%2Fschism%2Fblob%2F639d57a17f22d33d82d422b494e41c1cd99cd29e%2Fsrc%2FDriver%2Fschism_driver.F90%23L91&data=05%7C01%7Cyjzhang%40vims.edu%7C18d0a07b4a9c4ebaffca08db322f6c1f%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638158951495839859%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=uZKAf6mQNHeiBU8tbsKH%2FzTeinCK1ygGk6dvmPH3T10%3D&reserved=0

I think we make this as an option in ESMF config file (under OCN_attributes:: group) and pass to the model with this way. I could modify the schism cap but maybe you might want to follow different approach. I think this was not used with the exiting CoastalApp since it was building with OLDIO. Anyway, let me know what you think. We could also open an another ticket for this issue.

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uturuncoglu commented 1 year ago

@josephzhang8 Sure. That sounds fine.

platipodium commented 1 year ago

Go ahead with making that an option. We did not so far because in principle none of the models should do I/O, but rather a dedicated I/O server....

uturuncoglu commented 1 year ago

@platipodium you mean having an option in ESMF config file (in our case nems.configure). If so, I could easily implement to see how it works.

uturuncoglu commented 1 year ago

@platipodium @josephzhang8 I have implemented a way to get nscribes from nems.configure. It is in the following fork and branch,

https://github.com/uturuncoglu/schism-esmf/tree/feature/coastal_app

you could see diff in here,

https://github.com/schism-dev/schism-esmf/compare/master...uturuncoglu:schism-esmf:feature/coastal_app?expand=1

but it seems that the model is hanging in MeshCreate call. In my case the configuration uses 4 core and I set nscribes to 1. So, do I need to assign 1 more processor to the application for I/O? It was using 4 task but maybe I need to use 5 with new I/O. Anyway, let me know what you think?

I also realized that you did not implement the finalize routine for SCHISM and if I understand correctly from following code,

https://github.com/uturuncoglu/schism/blob/639d57a17f22d33d82d422b494e41c1cd99cd29e/src/Driver/schism_driver.F90#L166

The new IO has also some code that needs to be run during finalization. Anyway, I am not sure this is an urgent issue but I think that you need to be aware of it.

uturuncoglu commented 1 year ago

Okay. I tried with 5 task and still failing. Maybe I missed some code that needs to be ported from SCHISM to cap. Anyway, continue to look at it.

uturuncoglu commented 1 year ago

I also tried to print out task_id s

0: task_id =            1
1: task_id =            1
2: task_id =            1
3: task_id =            2

It is something like following. Maybe it is hanging because only task_id = 1 calls schism_init and last one calls scribe_init. So, definitely there is some logic over there that I did not catch yet.

josephzhang8 commented 1 year ago

Hi Ufuk:

If you did not specify iof_hydro(25) in your param.nml, the code's default is on (1) b/c this is needed for visIT. You can turn it off explicitly, or increase nscriebs to 2.

RE: scribe finalize, I did not add any code b/c the last statement in the main program should take care of that.

call schism_main call parallel_finalize

Does this make sense? Thx.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Ufuk Turunçoğlu @.> Sent: Monday, April 3, 2023 4:52 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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https://github.com/uturuncoglu/schism-esmf/tree/feature/coastal_apphttps://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Futuruncoglu%2Fschism-esmf%2Ftree%2Ffeature%2Fcoastal_app&data=05%7C01%7Cyjzhang%40vims.edu%7C4eed5e754d8b40f1d11b08db34854d97%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638161519379661183%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=x%2BJO3xvpDAXtkGQ%2FIS5OvvM7HOFmC2%2BA%2FkUXGwEk%2Ftc%3D&reserved=0

you could see diff in here,

https://github.com/schism-dev/schism-esmf/compare/master...uturuncoglu:schism-esmf:feature/coastal_app?expand=1https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fschism-dev%2Fschism-esmf%2Fcompare%2Fmaster...uturuncoglu%3Aschism-esmf%3Afeature%2Fcoastal_app%3Fexpand%3D1&data=05%7C01%7Cyjzhang%40vims.edu%7C4eed5e754d8b40f1d11b08db34854d97%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638161519379661183%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=DiIvE1AWM5BDmB0yvrOb1Mfavc1GZUEkoM2Sx7yoiHk%3D&reserved=0

but it seems that the model is hanging in MeshCreate call. In my case the configuration uses 4 core and I set nscribes to 1. So, do I need to assign 1 more processor to the application for I/O? It was using 4 task but maybe I need to use 5 with new I/O. Anyway, let me know what you think?

I also realized that you did not implement the finalize routine for SCHISM and if I understand correctly from following code,

https://github.com/uturuncoglu/schism/blob/639d57a17f22d33d82d422b494e41c1cd99cd29e/src/Driver/schism_driver.F90#L166https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Futuruncoglu%2Fschism%2Fblob%2F639d57a17f22d33d82d422b494e41c1cd99cd29e%2Fsrc%2FDriver%2Fschism_driver.F90%23L166&data=05%7C01%7Cyjzhang%40vims.edu%7C4eed5e754d8b40f1d11b08db34854d97%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638161519379661183%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sEYUFVqXIHlrQ4nR30btoNF3IaACdcoWMeb67gYq6Xg%3D&reserved=0

The new IO has also some code that needs to be run during finalization. Anyway, I am not sure this is an urgent issue but I think that you need to be aware of it.

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josephzhang8 commented 1 year ago

I suspect there is something we need to add for the cap under new I/O. Could u try directly running it without cap, i.e. SCHISM stand-alone? This should definitely work...

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Ufuk Turunçoğlu @.> Sent: Monday, April 3, 2023 5:13 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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I also tried to print out task_id s

0: task_id = 1

1: task_id = 1

2: task_id = 1

3: task_id = 2

It is something like following. Maybe it is hanging because only task_id = 1 calls schism_init and last one calls scribe_init. So, definitely there is some logic over there that I did not catch yet.

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uturuncoglu commented 1 year ago

@josephzhang8 In my case, I have following,

iof_hydro(25) = 0 !horizontal vel vector [m/s]

So, it think I need to use scribe = 1 for this configuration. I started to think about the MPI Communicator. Maybe subset of it needs to passed to cap but not sure. I am looking to schism_mpi_comm at this point. I did not try to run the model standalone without cap with new I/O. CoastalApp is using old I/O by default.

uturuncoglu commented 1 year ago

Okay. I think I found the issue, there are some logic in the following code,

https://github.com/uturuncoglu/schism/blob/639d57a17f22d33d82d422b494e41c1cd99cd29e/src/Core/schism_msgp.F90#L403

and sets last task (if you set scribe = 1, it could be more based on this number) as I/O task. I think we need to create sub communicator for the component and use this sub communicator (that excludes the I/O tasks) for cap.

uturuncoglu commented 1 year ago

Little bit down more interesting things are happening,

https://github.com/uturuncoglu/schism/blob/639d57a17f22d33d82d422b494e41c1cd99cd29e/src/Core/schism_msgp.F90#L415

So, there could be a communicator mismatch issue between model and the cap. Not sure.

josephzhang8 commented 1 year ago

Maybe Carsten, you and I need to meet on this? I need to look at the relevant cap code... thx.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Ufuk Turunçoğlu @.> Sent: Monday, April 3, 2023 5:45 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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Little bit down more interesting things are happening,

https://github.com/uturuncoglu/schism/blob/639d57a17f22d33d82d422b494e41c1cd99cd29e/src/Core/schism_msgp.F90#L415https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Futuruncoglu%2Fschism%2Fblob%2F639d57a17f22d33d82d422b494e41c1cd99cd29e%2Fsrc%2FCore%2Fschism_msgp.F90%23L415&data=05%7C01%7Cyjzhang%40vims.edu%7C87eb46081887434e861408db348cb5f7%7C8cbcddd9588d4e3b9c1e2367dbdf1740%7C0%7C0%7C638161551180129866%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=oKSKinGNlzwe10fN%2B4helW9padVvNpoHj0CCIdAGGuM%3D&reserved=0

So, there could be a communicator mismatch issue between model and the cap. Not sure.

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uturuncoglu commented 1 year ago

Let me investigate little bit more. If I could not fix it, we could meet about it. Testing new I/O without coupling could be also beneficial. At least, it eliminates some possibilities. I'll try to run that case too.

uturuncoglu commented 1 year ago

@pvelissariou1 I need data for 2008-08-23 to use under CDEPS ATMMESH data mode. If you don't mind could you send me the data (forecast length is 120 hours). If you send me some information, then I could create the data by myself.

uturuncoglu commented 1 year ago

As I see from the netcdf history. The data is downloaded from NCAR - CISL RDA. I checked CFSv2 (https://rda.ucar.edu/datasets/ds094.0/) and I think it does not go back to 2008. Maybe we need to use another dataset such as ERA5 etc.

platipodium commented 1 year ago

Dear @uturuncoglu thanks for your analysis. I am not very experienced with splitting communicators, and I don't believe we need to do so in the cap, as the resources for the cap should be allocated by the driver, giving the cap/component a set subset of MPI_COMM_WORLD to operate on.

If there is a split within schism to separate out I/O from compute, this should also not affect the cap. I may be entirely wrong, though, and of course we can make any necessary changes.

platipodium commented 1 year ago

@uturuncoglu So far there was no need to do anything in a Finalize() routine from the side of the cap, but we (I) can for sure implement this.

What are the things needed in Finalisze() and how do you approach this? In MOSSCO, we tagged every deep object with a "creator" attribute when this object was created, such that we could easily traverse through all objects of component in Finalize(), destroying everything tagged with the same "creator" attribute.

That is very MOSSCO-specific, so I wonder how Coastalapp/ufs-coastal would approach this. I there an implicit tagging of who created an object already in NUOPC infrastructure?

platipodium commented 1 year ago

@uturuncoglu @josephzhang8 I reviewed https://github.com/schism-dev/schism/compare/master...uturuncoglu:schism:feature/coastal_app?expand=1.

It seems fine (thank you for the NEtCDF elaboration!). We did not previously implement this as building the driver pschism did not hurt. For the cap, we would only use the SCHISM libraries (libhydro, libcore ..., repackaged into one libschism) anyway. The naming BLD_STANDALONE may have to be reconsidered (at a later stage). It would be nice to have this along the already more established line of USE_XXX, possibly USE_STANDALONE=ON or USE_DRIVER...

uturuncoglu commented 1 year ago

@platipodium I'll discuss with ESMF core team about handling I/O. The PEs that only do I/O might need to be defined as I/O or write component (like UFS) but I am not sure that is the beast approach. I think supporting new I/O capability is not urgent at this point. Anyway, I'll update you about it and may be it would be nice to open a ticket in SCHISM side about it to keep track of it.

I think it is more important when you use new I/O since it requires to call specific routine in the finalize step. I am not sure how I/O works but in finalize it might write some information to the file/s. Under ufs-coastal each component is responsible to call their own finalize routine. So, SCHISM also needs to implement it with its own way.

josephzhang8 commented 1 year ago

At the moment we don't have anything to finalize in the scribe I/O part, but we can always add something there like you said. Note there is a mpi_barrier call to make sure scribe and compute processes go into mpi_finalize together.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Ufuk Turunçoğlu @.> Sent: Tuesday, April 4, 2023 12:01 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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I think it is more important when you use new I/O since it requires to call specific routine in the finalize step. I am not sure how I/O works but in finalize it might write some information to the file/s. Under ufs-coastal each component is responsible to call their own finalize routine. So, SCHISM also needs to implement it with its own way.

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pvelissariou1 commented 1 year ago

@Ufuk The data for 2008 (Ike) are in /work/noaa/nosofs/pvelissa/for_Ufuk_atm_data/Ike_CFSR.nc This dataset covers the whole globe (0.5 degree resolution). Somehow the subsetting functionality is not currently working at rda.ucar.edu. Let me know if this dataset works for you.

Panagiotis Velissariou, Ph.D., P.E. UCAR Scientist National Ocean and Atmospheric Administration National Ocean Service Office of Coast Survey CSDL/CMMB Physical Scientist - Project Lead cell: (205) 227-9141 email: @.***

On Tue, Apr 4, 2023 at 11:05 AM Joseph Zhang @.***> wrote:

At the moment we don't have anything to finalize in the scribe I/O part, but we can always add something there like you said. Note there is a mpi_barrier call to make sure scribe and compute processes go into mpi_finalize together.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Ufuk Turunçoğlu @.> Sent: Tuesday, April 4, 2023 12:01 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

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I think it is more important when you use new I/O since it requires to call specific routine in the finalize step. I am not sure how I/O works but in finalize it might write some information to the file/s. Under ufs-coastal each component is responsible to call their own finalize routine. So, SCHISM also needs to implement it with its own way.

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uturuncoglu commented 1 year ago

@pvelissariou1 Thanks. I will try with that too. It seems I could provide ERA5 data now which allow me to test the mediator.

uturuncoglu commented 1 year ago

@platipodium @josephzhang8 @saeed-moghimi-noaa @pvelissariou1 Okay. I could successfully run ike_shinnecock.atm2sch (CDEPS+SCHISM) test cases with connectors. I did not check the results yet since I have still issue with analyzing the results. I'll also define this case as RT under UFS Weather Model.

Anyway, I also tried to test CMEPS and as I expected I am getting same error with ADCIRC. Since SCHISM also provides the mesh and fields on nodes it creates incompatibility issue with CMEPS. Anyway, as I remember there was an option in the SCHISM side that uses elements other then nodes. Right? Is it possible to activate that option again. It could be runtime option in the SCHISM cap. Anyway let me know what you think and if you need we could have a call about it.

20230404 145539.068 ERROR            PET1 ESMF_FieldRegrid.F90:4102 ESMF_FieldRegridGetArea Invalid argument  - Can't currently calculate area on a mesh location other than elements
20230404 145539.068 ERROR            PET1 med.F90:2323 Invalid argument  - Passing error in return code
20230404 145539.068 ERROR            PET1 med.F90:1686 Invalid argument  - Passing error in return code
20230404 145539.068 ERROR            PET1 MED:src/addon/NUOPC/src/NUOPC_ModelBase.F90:1639 Invalid argument  - Passing error in return code
20230404 145539.068 ERROR            PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:2577 Invalid argument  - Phase 'IPDv03p7' Initialize for modelComp 3: MED did not return ESMF_SUCCESS
20230404 145539.068 ERROR            PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:2408 Invalid argument  - Passing error in return code
20230404 145539.068 ERROR            PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:2192 Invalid argument  - Passing error in return code
20230404 145539.068 ERROR            PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:463 Invalid argument  - Passing error in return code
20230404 145539.068 ERROR            PET1 UFS.F90:386 Invalid argument  - Aborting UFS
20230404 145539.068 INFO             PET1 Finalizing ESMF
josephzhang8 commented 1 year ago

That's great to know, Ufuk.

Carsten can resurrect the code using elem based partitioning. As I explained, this is the native partitioning used by SCHISM, and we had to change it at the request of Robert O. to get the cap working. @@.**@.>: let me know if you need my help in the routine. Thx.

-Joseph

Y. Joseph Zhang Web: schism.wiki Office: 804 684 7466

From: Ufuk Turunçoğlu @.> Sent: Tuesday, April 4, 2023 5:03 PM To: oceanmodeling/ufs-coastal @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [oceanmodeling/ufs-coastal] SCHISM integration (Issue #2)

[EXTERNAL to VIMS received message]

@platipodiumhttps://github.com/platipodium @josephzhang8https://github.com/josephzhang8 @saeed-moghimi-noaahttps://github.com/saeed-moghimi-noaa @pvelissariou1https://github.com/pvelissariou1 Okay. I could successfully run ike_shinnecock.atm2sch (CDEPS+SCHISM) test cases with connectors. I did not check the results yet since I have still issue with analyzing the results. I'll also define this case as RT under UFS Weather Model.

Anyway, I also tried to test CMEPS and as I expected I am getting same error with ADCIRC. Since SCHISM also provides the mesh and fields on nodes it creates incompatibility issue with CMEPS. Anyway, as I remember there was an option in the SCHISM side that uses elements other then nodes. Right? Is it possible to activate that option again. It could be runtime option in the SCHISM cap. Anyway let me know what you think and if you need we could have a call about it.

20230404 145539.068 ERROR PET1 ESMF_FieldRegrid.F90:4102 ESMF_FieldRegridGetArea Invalid argument - Can't currently calculate area on a mesh location other than elements

20230404 145539.068 ERROR PET1 med.F90:2323 Invalid argument - Passing error in return code

20230404 145539.068 ERROR PET1 med.F90:1686 Invalid argument - Passing error in return code

20230404 145539.068 ERROR PET1 MED:src/addon/NUOPC/src/NUOPC_ModelBase.F90:1639 Invalid argument - Passing error in return code

20230404 145539.068 ERROR PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:2577 Invalid argument - Phase 'IPDv03p7' Initialize for modelComp 3: MED did not return ESMF_SUCCESS

20230404 145539.068 ERROR PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:2408 Invalid argument - Passing error in return code

20230404 145539.068 ERROR PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:2192 Invalid argument - Passing error in return code

20230404 145539.068 ERROR PET1 UFS Driver Grid Comp:src/addon/NUOPC/src/NUOPC_Driver.F90:463 Invalid argument - Passing error in return code

20230404 145539.068 ERROR PET1 UFS.F90:386 Invalid argument - Aborting UFS

20230404 145539.068 INFO PET1 Finalizing ESMF

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