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schism-dev / schism

Semi-implicit Cross-scale Hydroscience Integrated System Model (SCHISM)
http://ccrm.vims.edu/schismweb/
Apache License 2.0
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Question about the meaning of "wetted cross section length" error #105

Closed SorooshMani-NOAA closed 1 year ago

SorooshMani-NOAA commented 1 year ago

@josephzhang8 @cuill I have a question about an error I encountered. I'm using the same OCSMesh-PySCHISM-SCHISM workflow as before, but on a new platform and I get this error:

0: ABORT:  STEP: wetted cross section length on open bnd <=0; boundary ndx=1 , length=  0.000000000000000E+000

I was wondering if you could help me understand the meaning of this so that I can proceed with debugging what resulted in this.

Does this mean that the first open boundary segment (first two nodes in the boundary segment of my hgrid.grd) has length zero? Or is it about something else? Does it look like an issue with meshing?

feiye-vims commented 1 year ago

Hi Soroosh,

This means one of your open boundaries is completely dry.

Fei

SorooshMani-NOAA commented 1 year ago

Thank you @feiye-vims, that's strange because I didn't really change my meshing (subsetting) method. Could this be related to interpolating DEMs on my mesh if you have to guess?

Also which nodes should I look at the first nodes of the first open boundary segment? Based on ndx=1?

feiye-vims commented 1 year ago

I think that means all modes of the first open bnd are dry. This could be related to DEM interpolation. You may want to check the depths of those nodes in the hgrid.

SorooshMani-NOAA commented 1 year ago

This is very odd, the first couple of elevations in the boundary (from hgrid.grd file) are (coordinates comments manually added for easier read):

1 ! total number of ocean boundaries
268 ! total number of ocean boundary nodes
268 ! number of nodes for ocean_boundary_0
249994 ! -59.99968778 43.43439751 1003.01256100
250403 ! -59.99994778 43.37117561 1240.92041020
250797 ! -59.99979179 43.29860084 1584.45312500
251209 ! -59.99981273 43.18319423 2014.39843750
.
.
.

And since the elevation is positive down, these already should be wet, right?

feiye-vims commented 1 year ago

Yes.

Did the crash happen at the first time step?

SorooshMani-NOAA commented 1 year ago

It seems to be happening during the second timestep:

 time stepping begins...           1        1152
 before GetGAHMFields
 maxTrackRecords:          170
 Working on time frame:    150.000000000000     
 Requested output time:    150.000000000000      
 , skipping generating data for this time;   151200.000000000     
   172800.000000000        194400.000000000        216000.000000000     
   237600.000000000        259200.000000000        280800.000000000     
   302400.000000000        324000.000000000        345600.000000000     
   367200.000000000        388800.000000000        410400.000000000     
   432000.000000000        453600.000000000        475200.000000000     
   496800.000000000        518400.000000000        540000.000000000     
   561600.000000000        583200.000000000        604800.000000000     
   626400.000000000        648000.000000000        669600.000000000     
   691200.000000000        712800.000000000        734400.000000000     
   756000.000000000        777600.000000000        799200.000000000     
   820800.000000000        842400.000000000        864000.000000000     
   885600.000000000        907200.000000000        928800.000000000     
   950400.000000000        972000.000000000        993600.000000000     
   1015200.00000000        1036800.00000000        1058400.00000000     
   1080000.00000000        1101600.00000000        1123200.00000000     
   1144800.00000000        1166400.00000000        1188000.00000000     
   1209600.00000000        1231200.00000000        1252800.00000000     
   1274400.00000000        1296000.00000000        1317600.00000000     
   1339200.00000000        1360800.00000000        1382400.00000000     
   1404000.00000000        1425600.00000000        1447200.00000000     
   1465200.00000000        1468800.00000000        1490400.00000000     
   1512000.00000000        1533600.00000000        1555200.00000000     
   1576800.00000000        1598400.00000000        1620000.00000000     
   1641600.00000000        1663200.00000000        1684800.00000000     
   1706400.00000000        1728000.00000000        1749600.00000000     
   1771200.00000000        1792800.00000000        1814400.00000000     
 after GetGAHMFields
 done adjusting wind stress ...
 done flow b.c.
 done hvis... 
 done backtracking
 done 1st preparation
 done 2nd preparation
 done solver; etatot=   300570572.613247      ; average |eta|=
   538.075471512410     
 done solving momentum eq...
 done solving w
 done solving transport equation
 done recomputing levels...
 done density and flux calculation...
TIME STEP=            1;  TIME=           150.000000
 before GetGAHMFields
 Working on time frame:    300.000000000000     
 Requested output time:    300.000000000000      
 , skipping generating data for this time;   151200.000000000     
   172800.000000000        194400.000000000        216000.000000000     
   237600.000000000        259200.000000000        280800.000000000     
   302400.000000000        324000.000000000        345600.000000000     
   367200.000000000        388800.000000000        410400.000000000     
   432000.000000000        453600.000000000        475200.000000000     
   496800.000000000        518400.000000000        540000.000000000     
   561600.000000000        583200.000000000        604800.000000000     
   626400.000000000        648000.000000000        669600.000000000     
   691200.000000000        712800.000000000        734400.000000000     
   756000.000000000        777600.000000000        799200.000000000     
   820800.000000000        842400.000000000        864000.000000000     
   885600.000000000        907200.000000000        928800.000000000     
   950400.000000000        972000.000000000        993600.000000000     
   1015200.00000000        1036800.00000000        1058400.00000000     
   1080000.00000000        1101600.00000000        1123200.00000000     
   1144800.00000000        1166400.00000000        1188000.00000000     
   1209600.00000000        1231200.00000000        1252800.00000000     
   1274400.00000000        1296000.00000000        1317600.00000000     
   1339200.00000000        1360800.00000000        1382400.00000000     
   1404000.00000000        1425600.00000000        1447200.00000000     
   1465200.00000000        1468800.00000000        1490400.00000000     
   1512000.00000000        1533600.00000000        1555200.00000000     
   1576800.00000000        1598400.00000000        1620000.00000000     
   1641600.00000000        1663200.00000000        1684800.00000000     
   1706400.00000000        1728000.00000000        1749600.00000000     
   1771200.00000000        1792800.00000000        1814400.00000000     
 after GetGAHMFields
 done adjusting wind stress ...
josephzhang8 commented 1 year ago

I suspect PaHM may be generating some junk wind that dries up the bnd? Can u try turning off PaHM?

-Joseph

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

From: Soroosh Mani @.> Sent: Friday, June 2, 2023 12:26 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/schism] Question about the meaning of "wetted cross section length" error (Issue #105)

[EXTERNAL to VIMS received message]

It seems to be happening during the second timestep:

time stepping begins... 1 1152

before GetGAHMFields

maxTrackRecords: 170

Working on time frame: 150.000000000000

Requested output time: 150.000000000000

, skipping generating data for this time; 151200.000000000

172800.000000000 194400.000000000 216000.000000000

237600.000000000 259200.000000000 280800.000000000

302400.000000000 324000.000000000 345600.000000000

367200.000000000 388800.000000000 410400.000000000

432000.000000000 453600.000000000 475200.000000000

496800.000000000 518400.000000000 540000.000000000

561600.000000000 583200.000000000 604800.000000000

626400.000000000 648000.000000000 669600.000000000

691200.000000000 712800.000000000 734400.000000000

756000.000000000 777600.000000000 799200.000000000

820800.000000000 842400.000000000 864000.000000000

885600.000000000 907200.000000000 928800.000000000

950400.000000000 972000.000000000 993600.000000000

1015200.00000000 1036800.00000000 1058400.00000000

1080000.00000000 1101600.00000000 1123200.00000000

1144800.00000000 1166400.00000000 1188000.00000000

1209600.00000000 1231200.00000000 1252800.00000000

1274400.00000000 1296000.00000000 1317600.00000000

1339200.00000000 1360800.00000000 1382400.00000000

1404000.00000000 1425600.00000000 1447200.00000000

1465200.00000000 1468800.00000000 1490400.00000000

1512000.00000000 1533600.00000000 1555200.00000000

1576800.00000000 1598400.00000000 1620000.00000000

1641600.00000000 1663200.00000000 1684800.00000000

1706400.00000000 1728000.00000000 1749600.00000000

1771200.00000000 1792800.00000000 1814400.00000000

after GetGAHMFields

done adjusting wind stress ...

done flow b.c.

done hvis...

done backtracking

done 1st preparation

done 2nd preparation

done solver; etatot= 300570572.613247 ; average |eta|=

538.075471512410

done solving momentum eq...

done solving w

done solving transport equation

done recomputing levels...

done density and flux calculation...

TIME STEP= 1; TIME= 150.000000

before GetGAHMFields

Working on time frame: 300.000000000000

Requested output time: 300.000000000000

, skipping generating data for this time; 151200.000000000

172800.000000000 194400.000000000 216000.000000000

237600.000000000 259200.000000000 280800.000000000

302400.000000000 324000.000000000 345600.000000000

367200.000000000 388800.000000000 410400.000000000

432000.000000000 453600.000000000 475200.000000000

496800.000000000 518400.000000000 540000.000000000

561600.000000000 583200.000000000 604800.000000000

626400.000000000 648000.000000000 669600.000000000

691200.000000000 712800.000000000 734400.000000000

756000.000000000 777600.000000000 799200.000000000

820800.000000000 842400.000000000 864000.000000000

885600.000000000 907200.000000000 928800.000000000

950400.000000000 972000.000000000 993600.000000000

1015200.00000000 1036800.00000000 1058400.00000000

1080000.00000000 1101600.00000000 1123200.00000000

1144800.00000000 1166400.00000000 1188000.00000000

1209600.00000000 1231200.00000000 1252800.00000000

1274400.00000000 1296000.00000000 1317600.00000000

1339200.00000000 1360800.00000000 1382400.00000000

1404000.00000000 1425600.00000000 1447200.00000000

1465200.00000000 1468800.00000000 1490400.00000000

1512000.00000000 1533600.00000000 1555200.00000000

1576800.00000000 1598400.00000000 1620000.00000000

1641600.00000000 1663200.00000000 1684800.00000000

1706400.00000000 1728000.00000000 1749600.00000000

1771200.00000000 1792800.00000000 1814400.00000000

after GetGAHMFields

done adjusting wind stress ...

- Reply to this email directly, view it on GitHubhttps://github.com/schism-dev/schism/issues/105#issuecomment-1574008976, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFBKNZ7T2F42BUP25JDAY7LXJIH2ZANCNFSM6AAAAAAYXOO2LM. You are receiving this because you were mentioned.Message ID: @.**@.>>

SorooshMani-NOAA commented 1 year ago

I turned off meteo forcing (by setting nws=0), but I still run into the same error:

102: ABORT:  STEP: wetted cross section length on open bnd <=0; boundary ndx=           1 , length=  0.000000000000000E+000
 time stepping begins...           1        1152              
 done adjusting wind stress ...                               
 done flow b.c.                                               
 done hvis...                                                 
 done backtracking                                            
 done 1st preparation                                         
 done 2nd preparation                                         
 done solver; etatot=   300570572.613247      ; average |eta|=
   538.075471512410                                           
 done solving momentum eq...                                  
 done solving w                                               
 done solving transport equation                              
 done recomputing levels...                                   
 done density and flux calculation...                         
TIME STEP=            1;  TIME=           150.000000          
 done adjusting wind stress ...

Now that I know approximately where I should look for the issue, let me spend some more time on my own to see if I can get more info about why it's erroring out. Maybe it's something very simple that I'm missing ...

josephzhang8 commented 1 year ago

Thx for the info. U can send us the setup if u still cannot figure it out...

-Joseph

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

From: Soroosh Mani @.> Sent: Friday, June 2, 2023 3:03 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/schism] Question about the meaning of "wetted cross section length" error (Issue #105)

[EXTERNAL to VIMS received message]

I turned off meteo forcing (by setting nws=0), but I still run into the same error:

102: ABORT: STEP: wetted cross section length on open bnd <=0; boundary ndx= 1 , length= 0.000000000000000E+000

time stepping begins... 1 1152

done adjusting wind stress ...

done flow b.c.

done hvis...

done backtracking

done 1st preparation

done 2nd preparation

done solver; etatot= 300570572.613247 ; average |eta|=

538.075471512410

done solving momentum eq...

done solving w

done solving transport equation

done recomputing levels...

done density and flux calculation...

TIME STEP= 1; TIME= 150.000000

done adjusting wind stress ...

Now that I know approximately where I should look for the issue, let me spend some more time on my own to see if I can get more info about why it's erroring out. Maybe it's something very simple that I'm missing ...

- Reply to this email directly, view it on GitHubhttps://github.com/schism-dev/schism/issues/105#issuecomment-1574183368, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFBKNZ4PGNNSC7BOE4VEEQ3XJI2EZANCNFSM6AAAAAAYXOO2LM. You are receiving this because you were mentioned.Message ID: @.**@.>>

SorooshMani-NOAA commented 1 year ago

@josephzhang8 @feiye-vims, I'd like to take you up on your kind offer to pass the setup that fails for me to you for help. You can download it from here: https://drive.google.com/file/d/1TgiTBEj--WqfAmKYy9Zk4A5gJCHg8OCZ/view?usp=sharing

Thanks again

josephzhang8 commented 1 year ago

I'll take a look...

-Joseph

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

From: Soroosh Mani @.> Sent: Monday, June 5, 2023 12:32 PM To: schism-dev/schism @.> Cc: Y. Joseph Zhang @.>; Mention @.> Subject: Re: [schism-dev/schism] Question about the meaning of "wetted cross section length" error (Issue #105)

[EXTERNAL to VIMS received message]

@josephzhang8https://github.com/josephzhang8 @feiye-vimshttps://github.com/feiye-vims, I'd like to take you up on your kind offer to pass the setup that fails for me to you for help. You can download it from here: https://drive.google.com/file/d/1TgiTBEj--WqfAmKYy9Zk4A5gJCHg8OCZ/view?usp=sharing

Thanks again

- Reply to this email directly, view it on GitHubhttps://github.com/schism-dev/schism/issues/105#issuecomment-1577116393, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFBKNZ5LSPUOBJ2WIS4E2V3XJYCYBANCNFSM6AAAAAAYXOO2LM. You are receiving this because you were mentioned.Message ID: @.**@.>>

josephzhang8 commented 1 year ago

@SoroosH; your elev.ic has large negative values in ocean so you seemed to set elec_ic=-dp. So the total depths are 0 or negative.

-Joseph

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

From: Y. Joseph Zhang Sent: Monday, June 5, 2023 1:00 PM To: schism-dev/schism @.>; schism-dev/schism @.> Cc: Mention @.***> Subject: RE: [schism-dev/schism] Question about the meaning of "wetted cross section length" error (Issue #105)

I'll take a look...

-Joseph

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

From: Soroosh Mani @.**@.>> Sent: Monday, June 5, 2023 12:32 PM To: schism-dev/schism @.**@.>> Cc: Y. Joseph Zhang @.**@.>>; Mention @.**@.>> Subject: Re: [schism-dev/schism] Question about the meaning of "wetted cross section length" error (Issue #105)

[EXTERNAL to VIMS received message]

@josephzhang8https://github.com/josephzhang8 @feiye-vimshttps://github.com/feiye-vims, I'd like to take you up on your kind offer to pass the setup that fails for me to you for help. You can download it from here: https://drive.google.com/file/d/1TgiTBEj--WqfAmKYy9Zk4A5gJCHg8OCZ/view?usp=sharing

Thanks again

- Reply to this email directly, view it on GitHubhttps://github.com/schism-dev/schism/issues/105#issuecomment-1577116393, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AFBKNZ5LSPUOBJ2WIS4E2V3XJYCYBANCNFSM6AAAAAAYXOO2LM. You are receiving this because you were mentioned.Message ID: @.**@.>>

SorooshMani-NOAA commented 1 year ago

Thank you @josephzhang8! I use pyschism through coupledmodeldriver to setup the model. I can try a basic script directly in pyschism and if I see the same problem, maybe this issue can be moved to pyschism repo.

While I'm testing, @cuill do you know if anything related to default elevation IC has changed in recent versions of pyschism?

cuill commented 1 year ago

@SorooshMani-NOAA Yes, I made changes for elev_ic, which uses the original depth info from hgrid.gr3 not reversed values.

branch 5b5ded0d98ffb0776a1a99538cb33f99d1ffa1a8

SorooshMani-NOAA commented 1 year ago

OK I see, I'll update the client scripts then, thanks!