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Model setup with Tide + River open boundaries
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TOPIC: Model setup with Tide + River open boundaries

Model setup with Tide + River open boundaries 3 years 10 months ago #37545

  • Kurum
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Hi,

The setup below works (with appropriate changes to it) fine when I use a cli file with only the tidal open boundary described with 5 6 6. I have added the 4 5 5 discharge boundary into the cli file (attached cli file) and made the changes below to the cas file and I receive an MPI ABORT error. I read the forum and the manual as much as I can to no avail. I checked the log files and they don't have any messages, they abruptly end. I also attached the partel_T2DGEO.log which seems to be telling me the boundaries are read correctly.
I should also note that I did not compile with MUMPS - could this be the issue?

Any help would be appreciated. Cheers
relevant part of cas:
BINARY DATABASE 1 FOR TIDE               = './DATA/h_tpxo7.2'
BINARY DATABASE 2 FOR TIDE               = './DATA/u_tpxo7.2'
ORIGINAL DATE OF TIME                    = 2020;01;01
ORIGINAL HOUR OF TIME                    = 0;0;0       
COEFFICIENT TO CALIBRATE TIDAL RANGE     = 1.0
COEFFICIENT TO CALIBRATE SEA LEVEL       = 0.0
/OPTION FOR LIQUID BOUNDARIES            = 1
OPTION FOR LIQUID BOUNDARIES             = 1;1
PRESCRIBED ELEVATIONS 			 = 0;0 / dummy initiation
LIQUID BOUNDARIES FILE                   = Q_ramp.bc
OPTION FOR TIDAL BOUNDARY CONDITIONS     = 1
OPTION FOR TIDAL BOUNDARY CONDITIONS     = 1;0
TIDAL DATA BASE                          = 2
MINOR CONSTITUENTS INFERENCE             = YES
Q_ramp.bc file:
# Ramping Discharge	
T Q(1)	
s m3/s	
0	0
3600	2000
7200	4000
10800	6000
14400	8000
18000	10000
Error message:
*************************************
                     *    END OF MEMORY ORGANIZATION:    *
                     *************************************

 INITIALIZING TELEMAC2D FOR
 INBIEF (BIEF): NOT A VECTOR MACHINE (ACCORDING TO YOUR DATA)
 FONSTR : FRICTION COEFFICIENTS READ IN THE
          GEOMETRY FILE
 STRCHE (BIEF): NO MODIFICATION OF FRICTION

 NUMBER OF LIQUID BOUNDARIES:           2

 CORFON (TELEMAC2D): NO MODIFICATION OF BOTTOM

 INITIALISATION BASED ON TPXO:
 C_ID(           1 ) = m2
 C_ID(           2 ) = s2
 C_ID(           3 ) = n2
 C_ID(           4 ) = k2
 C_ID(           5 ) = k1
 C_ID(           6 ) = o1
 C_ID(           7 ) = p1
 C_ID(           8 ) = q1
 C_ID(           9 ) = mf
 C_ID(          10 ) = mm
 C_ID(          11 ) = m4
 C_ID(          12 ) = ms4
 C_ID(          13 ) = mn4
  - ACQUIRING LEVELS
  - INTERPOLATING LEVELS
  - ACQUIRING VELOCITIES
  - INTERPOLATING VELOCITIES
 END OF TPXO INITIALISATION

================================================================================
 ITERATION        0    TIME:   0.0000 S
 TELEMAC2D INITIALIZED
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
with errorcode 2.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[Workhorse-Linux:896889] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[Workhorse-Linux:896889] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Traceback (most recent call last):
  File "/home/workhorse/v8p2/scripts/python3/telemac2d.py", line 7, in <module>
    main('telemac2d')
  File "/home/workhorse/v8p2/scripts/python3/runcode.py", line 271, in main
    run_study(cas_file, code_name, options)
  File "/home/workhorse/v8p2/scripts/python3/execution/run_cas.py", line 157, in run_study
    run_local_cas(my_study, options)
  File "/home/workhorse/v8p2/scripts/python3/execution/run_cas.py", line 65, in run_local_cas
    my_study.run(options)
  File "/home/workhorse/v8p2/scripts/python3/execution/study.py", line 612, in run
    self.run_local()
  File "/home/workhorse/v8p2/scripts/python3/execution/study.py", line 440, in run_local
    run_code(self.run_cmd, self.sortie_file)
  File "/home/workhorse/v8p2/scripts/python3/execution/run.py", line 182, in run_code
    raise TelemacException('Fail to run\n'+exe)
utils.exceptions.TelemacException: Fail to run
/usr/local/openmpi-4/bin/mpiexec -np 26 /home/workhorse/TestRun_v8p2/t2d_TestRun_Tide_Q_test.cas_2021-01-06-23h47min07s/out_telemac2d

end of one of the log files - they are all similar with no additional information
.......
                    *************************************
                     *    END OF MEMORY ORGANIZATION:    *
                     *************************************

 INITIALIZING TELEMAC2D FOR        
 INBIEF (BIEF): NOT A VECTOR MACHINE (ACCORDING TO YOUR DATA)
 FONSTR : FRICTION COEFFICIENTS READ IN THE
          GEOMETRY FILE
 STRCHE (BIEF): NO MODIFICATION OF FRICTION

  
 NUMBER OF LIQUID BOUNDARIES:           2

 CORFON (TELEMAC2D): NO MODIFICATION OF BOTTOM

 INITIALISATION BASED ON TPXO:
 C_ID(           1 ) = m2  
 C_ID(           2 ) = s2  
 C_ID(           3 ) = n2  
 C_ID(           4 ) = k2  
 C_ID(           5 ) = k1  
 C_ID(           6 ) = o1  
 C_ID(           7 ) = p1  
 C_ID(           8 ) = q1  
 C_ID(           9 ) = mf
Attachments:
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Model setup with Tide + River open boundaries 3 years 10 months ago #37546

  • c.coulet
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If the diver discharge is on boundary 1, this means tide is on boundary 2 so option for tidal boundary condition is wrong !
This should be 0;1 instead of 1;0
Christophe
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Model setup with Tide + River open boundaries 3 years 10 months ago #37549

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Hi,

I tried that but it gives me the following error:
"If the diver discharge is on boundary 1..." do you say this because of Q(1) in the Q_ramp.bc file? I tried it with Q(2) as well same error as before.
 USER_CORRXY (BIEF):NO MODIFICATION OF COORDINATES

 MESH: MESH   ALLOCATED
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 21 in communicator MPI_COMM_WORLD
with errorcode 2.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] PMIX ERROR: UNREACHABLE in file server/pmix_server.c at line 2198
[Workhorse-Linux:982611] 12 more processes have sent help message help-mpi-api.txt / mpi-abort
[Workhorse-Linux:982611] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Traceback (most recent call last):
  File "/home/workhorse/v8p2/scripts/python3/telemac2d.py", line 7, in <module>
    main('telemac2d')
  File "/home/workhorse/v8p2/scripts/python3/runcode.py", line 271, in main
    run_study(cas_file, code_name, options)
  File "/home/workhorse/v8p2/scripts/python3/execution/run_cas.py", line 157, in run_study
    run_local_cas(my_study, options)
  File "/home/workhorse/v8p2/scripts/python3/execution/run_cas.py", line 65, in run_local_cas
    my_study.run(options)
  File "/home/workhorse/v8p2/scripts/python3/execution/study.py", line 612, in run
    self.run_local()
  File "/home/workhorse/v8p2/scripts/python3/execution/study.py", line 440, in run_local
    run_code(self.run_cmd, self.sortie_file)
  File "/home/workhorse/v8p2/scripts/python3/execution/run.py", line 182, in run_code
    raise TelemacException('Fail to run\n'+exe)
utils.exceptions.TelemacException: Fail to run
/usr/local/openmpi-4/bin/mpiexec -np 26 /home/workhorse/TestRun_v8p2/t2d_TestRun_Tide_Q_test.cas_2021-01-07-03h04min01s/out_telemac2d
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Model setup with Tide + River open boundaries 3 years 10 months ago #37550

  • c.coulet
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Could you check the model start well if you run it on only 1 processor?
Christophe
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Model setup with Tide + River open boundaries 3 years 10 months ago #37551

  • Kurum
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Interesting when I use the mpiexec -np 1 I got more about the problem (I think).
                     *************************************
                     *    END OF MEMORY ORGANIZATION:    *
                     *************************************

 INITIALIZING TELEMAC2D FOR
 INBIEF (BIEF): NOT A VECTOR MACHINE (ACCORDING TO YOUR DATA)
 FONSTR : FRICTION COEFFICIENTS READ IN THE
          GEOMETRY FILE
 STRCHE (BIEF): NO MODIFICATION OF FRICTION

 THERE IS     2 LIQUID BOUNDARIES:

 BOUNDARY    1 :
  BEGINS AT BOUNDARY POINT:     4176 , WITH GLOBAL NUMBER:      3953
  AND COORDINATES:     439125.4           3285322.
  ENDS AT BOUNDARY POINT:     1792 , WITH GLOBAL NUMBER:      1746
  AND COORDINATES:     1261519.           3302380.

 BOUNDARY    2 :
  BEGINS AT BOUNDARY POINT:     3447 , WITH GLOBAL NUMBER:        91
  AND COORDINATES:     673248.4           3367014.
  ENDS AT BOUNDARY POINT:     3453 , WITH GLOBAL NUMBER:        85
  AND COORDINATES:     672679.8           3367245.

 THERE IS     2 SOLID BOUNDARIES:

 BOUNDARY    1 :
  BEGINS AT BOUNDARY POINT:     1792 , WITH GLOBAL NUMBER:      1746
  AND COORDINATES:     1261519.           3302380.
  ENDS AT BOUNDARY POINT:     3447 , WITH GLOBAL NUMBER:        91
  AND COORDINATES:     673248.4           3367014.

 BOUNDARY    2 :
  BEGINS AT BOUNDARY POINT:     3453 , WITH GLOBAL NUMBER:        85
  AND COORDINATES:     672679.8           3367245.
  ENDS AT BOUNDARY POINT:     4176 , WITH GLOBAL NUMBER:      3953
  AND COORDINATES:     439125.4           3285322.

 CORFON (TELEMAC2D): NO MODIFICATION OF BOTTOM

 INITIALISATION BASED ON TPXO:
 C_ID(           1 ) = m2
 C_ID(           2 ) = s2
 C_ID(           3 ) = n2
 C_ID(           4 ) = k2
 C_ID(           5 ) = k1
 C_ID(           6 ) = o1
 C_ID(           7 ) = p1
 C_ID(           8 ) = q1
 C_ID(           9 ) = mf
 C_ID(          10 ) = mm
 C_ID(          11 ) = m4
 C_ID(          12 ) = ms4
 C_ID(          13 ) = mn4
  - ACQUIRING LEVELS
  - INTERPOLATING LEVELS
  - ACQUIRING VELOCITIES
  - INTERPOLATING VELOCITIES
 END OF TPXO INITIALISATION

================================================================================
 ITERATION        0    TIME:   0.0000 S
 TELEMAC2D INITIALIZED
 THE LIQUID BOUNDARIES FILE CONTAINS
         161  LINES WITH:
 Q(2) 

 VIT : MORE PRESCRIBED VELOCITIES ARE REQUIRED
       IN THE PARAMETER FILE
       AT LEAST      1 MUST BE GIVEN

 PLANTE: PROGRAM STOPPED AFTER AN ERROR
 RETURNING EXIT CODE:            2
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 2.

So I added PRESCRIBED VELOCITIES = 0;0 into the cas and I got the following error:
ITERATION        0    TIME:   0.0000 S
 TELEMAC2D INITIALIZED
 THE LIQUID BOUNDARIES FILE CONTAINS
         161  LINES WITH:
 Q(2)

 Q : MORE PRESCRIBED FLOWRATES
     ARE REQUIRED IN THE PARAMETER FILE
     AT LEAST      2 MUST BE GIVEN

So I added PRESCRIBED FLOWRATES = 0;0 to the cas and it "works".
Final cas looks like this:
BINARY DATABASE 1 FOR TIDE               = './DATA/h_tpxo7.2'
BINARY DATABASE 2 FOR TIDE               = './DATA/u_tpxo7.2'
ORIGINAL DATE OF TIME                    = 2020;01;01
ORIGINAL HOUR OF TIME                    = 0;0;0       
COEFFICIENT TO CALIBRATE TIDAL RANGE     = 1.0
COEFFICIENT TO CALIBRATE SEA LEVEL       = 0.0
/OPTION FOR LIQUID BOUNDARIES            = 1
OPTION FOR LIQUID BOUNDARIES             = 1;1
PRESCRIBED ELEVATIONS 					 = 0;0 / dummy initiation
PRESCRIBED VELOCITIES 					 = 0;0 / dummy initiation
PRESCRIBED FLOWRATES 					 = 0;0 / dummy initiation
LIQUID BOUNDARIES FILE                   = Q_ramp.bc / Q(2)
OPTION FOR TIDAL BOUNDARY CONDITIONS     = 1
OPTION FOR TIDAL BOUNDARY CONDITIONS     = 1;0
TIDAL DATA BASE                          = 2
MINOR CONSTITUENTS INFERENCE             = YES


Finally I tried with more than 1 cores and that works too. Is this the proper way of setting it though? I will check the results and report back.

Edit:
I just noticed that the discharge and tide seems to be working fine.
FLUX BOUNDARY    1:     142850.6     M3/S  ( >0 : ENTERING  <0 : EXITING )
     FLUX BOUNDARY    2:     5991.667     M3/S  ( >0 : ENTERING  <0 : EXITING )

Flux Boundary 2 is the discharge boundary and increasing as it should.
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Model setup with Tide + River open boundaries 3 years 10 months ago #37553

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Using the sequential run allow you to be sure the model start then switching to parallel computation will work except if a partitioning problem occur or if you use your own fortran file in which your own program is not parallel compatible...
Christophe
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Model setup with Tide + River open boundaries 3 years 10 months ago #37556

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Thank you c.coulet - this definitely helped me. I was able to fix all issues with my files it's running fine now. I hope it helps others. Cheers
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Model setup with Tide + River open boundaries 3 years 10 months ago #37581

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Hello,

Just a clarification of the LIQUID BOUNDARIES FILE to complete Christophe answer:
You need to add at least as many values for PRESCRIBED ELEVATIONS, PRESCRIBED FLOWRATES and/or PRESCRIBED VELOCITIES, as the number of open boundaries defined in the LIQUID BOUNDARIES FILE. Indeed if there are not as many open boundaries defined in this last file as the real number of open boundaries defined in the BOUNDARY CONDITIONS FILE, the other values to be prescribed are taken from the steering file.

Hope this is clearer for you now.

Chi-Tuan
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Model setup with Tide + River open boundaries 3 years 10 months ago #37609

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Hi Chi-Tuan,

yes everything is clear now and working fine.
Here is the final working setup for a case with 2 open boundaries:

Boundary 1 = Tidal Boundary (5 6 6)
Boundary 2 = River Discharge Boundary (4 5 5)

cas:
BINARY DATABASE 1 FOR TIDE = './DATA/h_tpxo7.2'
BINARY DATABASE 2 FOR TIDE = './DATA/u_tpxo7.2'
ORIGINAL DATE OF TIME = 2020;01;01
ORIGINAL HOUR OF TIME = 0;0;0
COEFFICIENT TO CALIBRATE TIDAL RANGE = 1.0
COEFFICIENT TO CALIBRATE SEA LEVEL = 0.5
/OPTION FOR LIQUID BOUNDARIES = 1
OPTION FOR LIQUID BOUNDARIES = 1;1
PRESCRIBED ELEVATIONS = 0;0
PRESCRIBED VELOCITIES = 0;0
PRESCRIBED FLOWRATES = 0;0
LIQUID BOUNDARIES FILE = Q_ramp.bc
OPTION FOR TIDAL BOUNDARY CONDITIONS = 1
OPTION FOR TIDAL BOUNDARY CONDITIONS = 1;0
TIDAL DATA BASE = 2
MINOR CONSTITUENTS INFERENCE = YES

Q_ramp.bc looks like this:
# Ramping Discharge
T Q(2)
s m3/s
0 0
3600 2000
7200 4000
10800 6000


I hope this helps someone else.
Cheers
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