Help with this error: Given indices do not match output variable rank! #17

BryanSouzaM · 2021-06-11T15:31:05Z

BryanSouzaM
Jun 11, 2021

Hello everybody.
Congratulations on developing the mHM. I'm trying to apply it to a basin in Brazil, but I find this error during the process.
I tried to change as little as possible of the mhm file (converted to .txt) mhm.txt

But now i'm stuck in this error, which i couldn't identify the reason. Can you help me?

P.s.: I'm not using any of the optional data in the model. (et.nc, neutrons.nc, Q_bkfl.nc, sm.nc, twsa.nc)

----------------------------------------------------------------------
              mHM-UFZ

    MULTISCALE HYDROLOGIC MODEL
           Version: 5.11.2-dev0
           Date:    2021-06-10

Originally by L. Samaniego & R. Kumar
----------------------------------------------------------------------

Openmp not used.
MPI not used.
Start at 11.06.2021 12:23:43.
Working directory: /root/velhas
Using main file mhm_driver.f90 and namelists:
     mhm.nml
     mhm_parameter.nml
     mhm_outputs.nml


Read namelist file: mhm.nml
Read namelist file: mhm_parameter.nml
Read namelist file: mhm_outputs.nml
 INFO: Process (10, neutrons) is deactivated, so output will be suppressed.

domain 1:
resolution Hydrology (domain 1)     = 25.000
resolution Routing (domain 1)       = 25.000

Resolution of routing and hydrological modeling are equal!

Following output will be written:
  NetCDF deflate level: 6
  NetCDF output precision: double
  STATES:
    interceptional storage                          (L1_inter) [mm]
    soil water content in the single layers     (L1_soilMoist) [mm]
    volumetric soil moisture in the single layers              [mm/mm]
    mean volum. soil moisture averaged over all soil layers    [mm/mm]
    waterdepth in reservoir of sealed areas       (L1_sealSTW) [mm]
    waterdepth in reservoir of unsat. soil zone  (L1_unsatSTW) [mm]
  FLUXES:

FINISHED reading config

  Inititalize mRM

    Following output will be written:
    NetCDF deflate level: 6
    NetCDF output precision: double
    FLUXES:
      routed streamflow      (L11_qMod)                [m3 s-1]
      river temperature      (RivTemp)                 [deg C]

    FINISHED reading config


# of domains:                  1

  Input data directories:
  --------------
      DOMAIN                    1
  --------------
    Morphological directory:      test_domain/input/morph/ (found)
    Land cover directory:         test_domain/input/luse/ (found)
    Precipitation directory:      test_domain/input/meteo/pre/ (found)
    Temperature directory:        test_domain/input/meteo/tavg/ (found)
    PET directory:                test_domain/input/meteo/pet/ (found)
    Output directory:             test_domain/output_b1/ (found)


  Read data ...
  Reading data ...
    Reading dem and lcover ...
      Reading dem for domain: 1 ...
      Reading lcover for domain: 1 ...

Tillage layers: the tillage horizons are modelled
                upto mHM layers:          1
    Reading data for domain: 1 ...
      Reading slope ...
      Reading aspect ...
      Reading soil ids ...
      Reading LAI ...
      Reading latitude/logitude ...
    in   114.658 seconds.
  in   158.575 seconds.
***WARNING: Geological unit 2
            is not appearing in study domain.
***WARNING: Geological unit 6
            is not appearing in study domain.
***WARNING: Geological unit 8
            is not appearing in study domain.
***WARNING: Geological unit -9999
            is not appearing in study domain.
    in   158.575 seconds.
  Initialize domains ...
 Given indices do not match output variable rank!

Answered by pallavhydro

Jun 11, 2021

Hi Bryan

I may not be able to point out the issue directly, but I have concerns over the following based on your mhm.nml -

You want mhm to run at 25m x 25m grid. Is that correct? You have selected iFlag_cordinate_sys as x, y system (in m) and entered resolution_Hydrology and resolution_Routing as 25 i.e. 25 m.
In mhm, there are three resolutions viz. L0, L1 (also L11) and L2. L0 - morphology (dem, etc.), L1 - hydrology (model resolution), L11 - routing (use same as L1 if not sure) and L2 - meteorology. Usually we set L0 < L1/L11 <= L2. Your L1 is 25 m. What is the L0 dataset resolution that you are using? Perhaps using larger L1 and L11 (say 25000 i.e. 25 km) makes sense.
If you are…

View full answer

StephanThober · 2021-06-11T21:11:11Z

StephanThober
Jun 11, 2021
Maintainer

Dear Bryan, Great to hear that you are using mHM and sorry to see that you run into problems. Please report your issue on https://github.com/mhm-ufz/mhm/discussions and paste your mhm.nml so that we can help you to sort this out. Kind regards, Stephan

…

-------------------------------------------------------------------------------------------- Dr. Stephan Thober Senior scientist Department Computational Hydrosystems Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482324 ***@***.***, www.ufz.de/index.php?en=38099 Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzende des Aufsichtsrats/Chairwoman of the Supervisory Board: MinDirig'in Oda Keppler Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König

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

On 11. Jun 2021, at 17:31, Bryan Souza ***@***.***> wrote: Hello everybody. Congratulations on developing the mHM. I'm trying to apply it to a basin in Brazil, but I find this error during the process. I tried to change as little as possible of the mhm file (converted to .txt) mhm.txt But now i'm stuck in this error, which i couldn't identify the reason. Can you help me? ---------------------------------------------------------------------- mHM-UFZ MULTISCALE HYDROLOGIC MODEL Version: 5.11.2-dev0 Date: 2021-06-10 Originally by L. Samaniego & R. Kumar ---------------------------------------------------------------------- Openmp not used. MPI not used. Start at 11.06.2021 12:23:43. Working directory: /root/velhas Using main file mhm_driver.f90 and namelists: mhm.nml mhm_parameter.nml mhm_outputs.nml Read namelist file: mhm.nml Read namelist file: mhm_parameter.nml Read namelist file: mhm_outputs.nml INFO: Process (10, neutrons) is deactivated, so output will be suppressed. domain 1: resolution Hydrology (domain 1) = 25.000 resolution Routing (domain 1) = 25.000 Resolution of routing and hydrological modeling are equal! Following output will be written: NetCDF deflate level: 6 NetCDF output precision: double STATES: interceptional storage (L1_inter) [mm] soil water content in the single layers (L1_soilMoist) [mm] volumetric soil moisture in the single layers [mm/mm] mean volum. soil moisture averaged over all soil layers [mm/mm] waterdepth in reservoir of sealed areas (L1_sealSTW) [mm] waterdepth in reservoir of unsat. soil zone (L1_unsatSTW) [mm] FLUXES: FINISHED reading config Inititalize mRM Following output will be written: NetCDF deflate level: 6 NetCDF output precision: double FLUXES: routed streamflow (L11_qMod) [m3 s-1] river temperature (RivTemp) [deg C] FINISHED reading config # of domains: 1 Input data directories: -------------- DOMAIN 1 -------------- Morphological directory: test_domain/input/morph/ (found) Land cover directory: test_domain/input/luse/ (found) Precipitation directory: test_domain/input/meteo/pre/ (found) Temperature directory: test_domain/input/meteo/tavg/ (found) PET directory: test_domain/input/meteo/pet/ (found) Output directory: test_domain/output_b1/ (found) Read data ... Reading data ... Reading dem and lcover ... Reading dem for domain: 1 ... Reading lcover for domain: 1 ... Tillage layers: the tillage horizons are modelled upto mHM layers: 1 Reading data for domain: 1 ... Reading slope ... Reading aspect ... Reading soil ids ... Reading LAI ... Reading latitude/logitude ... in 114.658 seconds. in 158.575 seconds. ***WARNING: Geological unit 2 is not appearing in study domain. ***WARNING: Geological unit 6 is not appearing in study domain. ***WARNING: Geological unit 8 is not appearing in study domain. ***WARNING: Geological unit -9999 is not appearing in study domain. in 158.575 seconds. Initialize domains ... Given indices do not match output variable rank! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.

1 reply

BryanSouzaM Jun 11, 2021
Author

Hey Stephan! ty for your answer.
Isn't that the discussion channel?

StephanThober · 2021-06-11T21:29:30Z

StephanThober
Jun 11, 2021
Maintainer

Hi Bryan, No this channel is for all sorts of issues that user might run into like the one you stumbled upon. Best, Stephan

…

-------------------------------------------------------------------------------------------- Dr. Stephan Thober Senior scientist Department Computational Hydrosystems Helmholtz-Zentrum für Umweltforschung GmbH - UFZ Helmholtz Centre for Environmental Research GmbH - UFZ Permoserstraße 15, 04318 Leipzig, Germany Phone +49 341 235 482324 ***@***.***, www.ufz.de/index.php?en=38099 Sitz der Gesellschaft/Registered Office: Leipzig Registergericht/Registration Office: Amtsgericht Leipzig Handelsregister Nr./Trade Register Nr.: B 4703 Vorsitzende des Aufsichtsrats/Chairwoman of the Supervisory Board: MinDirig'in Oda Keppler Wissenschaftlicher Geschäftsführer/Scientific Managing Director: Prof. Dr. Georg Teutsch Administrative Geschäftsführerin/Administrative Managing Director: Dr. Sabine König

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

On 11. Jun 2021, at 23:16, Bryan Souza ***@***.***> wrote: Hey Stephan! ty for your answer. Isn't that the execution channel? — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe.

2 replies

BryanSouzaM Jun 11, 2021
Author

So, i'm in the right place, correct?

StephanThober Jun 11, 2021
Maintainer

yes, sorry for the confusion.

pallavhydro · 2021-06-11T22:30:53Z

pallavhydro
Jun 11, 2021

Hi Bryan

I may not be able to point out the issue directly, but I have concerns over the following based on your mhm.nml -

You want mhm to run at 25m x 25m grid. Is that correct? You have selected iFlag_cordinate_sys as x, y system (in m) and entered resolution_Hydrology and resolution_Routing as 25 i.e. 25 m.
In mhm, there are three resolutions viz. L0, L1 (also L11) and L2. L0 - morphology (dem, etc.), L1 - hydrology (model resolution), L11 - routing (use same as L1 if not sure) and L2 - meteorology. Usually we set L0 < L1/L11 <= L2. Your L1 is 25 m. What is the L0 dataset resolution that you are using? Perhaps using larger L1 and L11 (say 25000 i.e. 25 km) makes sense.
If you are using L1,L11 = 25m resolution, have you prepared the corresponding latlon file (latlon.nc) for your model setup?
Also I suppose you have your basin data placed under test_domain folder structure? May I suggest you to perhaps use a separate folder with your basin name to avoid confusion. At the moment, looking at the mhm.nml, it looks as if you are using the test domain data.

Cheers
Pallav

4 replies

BryanSouzaM Jun 11, 2021
Author

Hey!

You want mhm to run at 25m x 25m grid. Is that correct? What is the L0 dataset resolution that you are using?
Yes, all my input data are at 25m resolution.

If you are using L1,L11 = 25m resolution, have you prepared the corresponding latlon file (latlon.nc) for your model setup?
Perhaps here is the error. I'm only using one latlon grid file since I'm only using one resolution for the entire model.
I create a new latlon file, for different levels but with the same header. I will give it a try !!
Also I suppose you have your basin data placed under test_domain folder structure?
yes, I tried renaming my files to the same names as the test basin to avoid errors.

BryanSouzaM Jun 11, 2021
Author

Update:

The error disappeared. Now I'm facing another... apparently for lack of space. I think I will have to change the resolution of level 2.

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

pallavhydro Jun 12, 2021

Hi Bryan

Great. So for the reference of readers of this discussion blog, the solution was correct latlon file in line with the resolutions being used.

Next issue: Seg. Fault. Few comments -

This is a generic error message (not mhm specific) and the debugging of the issue would need more info/ strategy. Since this is now a different issue, I would say it would make more sense if you open a different discussion topic and we continue there.
While we continue this discussion as a new topic, I would suggest you (as already mentioned by @StephanThober ) to again post your latest mhm.nml and the runtime output of the error. This will give us some clues already. But unlike last time, try posting mhm.nml content as code as well. Let's see whether this becomes the better way to share the namelist file or just obstructs readability.

Cheers
Pallav

BryanSouzaM Jun 12, 2021
Author

Thanks a lot Pallav.

First, I will try to solve the problem myself. I believe it has something to do with memory allocation during cmake. If I can, I'll post the solution here. Otherwise, I will ask for help. Thanks for the support!

Bryan

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Help with this error: Given indices do not match output variable rank! #17

BryanSouzaM Jun 11, 2021

Replies: 3 comments · 7 replies

StephanThober Jun 11, 2021 Maintainer

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BryanSouzaM
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