Run examples as out of box

[mnagaso]

Hi,

I found that there is a missing information for new users to run the first example, which is for creation of parameters.yaml.

It should be done with seisflows init (but not seisflows setup with current devel), but I could not find an instruction for this step (sorry if I have just been missing it).

So I put some line to create a default parameter file automatically if it does not exist, when the setup function is called. I added some parameters to allow seisflows check to work.

Please let me know if it would be ok, or would be better to add more parameters in the default file e.g.

• path_specfem_bin ...

Because I think that it would be useful if the first examples can be run with the out-of-box state, otherwise new users resign to use the library instead of digging around the correct way to do.

[bch0w]

Thanks for raising this @mnagaso, I swapped the names of two command line parameters init and setup to be more inline with their actual functionality in this big PR (https://github.com/adjtomo/seisflows/pull/181), but did not update the examples or the documentation to match. I think what is needed here is just a simple update to the namespace in the example. I can have a look at this real quick and see if the fix is that simple.

[mnagaso]

Thank you very much @bch0w ! Yes I tried to just replace the setup and init as my last commit by following your guide, then it worked like a charm!

In the later part of this example (seisflows examples run 1), I got the error below. It seems that data/001 directory is not created. I am checking this on my side for understanding seisflows, but it would be great if you could give me any idea on this error?

================================================================================
COMPLETE EXAMPLE SETUP
================================================================================

================================================================================
RUNNING SEISFLOWS EXAMPLE WORKFLOW
================================================================================
2024-02-22 20:41:39 [INFO] | setup Inversion workflow
2024-02-22 20:41:48 [DEBU] | running setup for module 'system.Workstation'
2024-02-22 20:41:51 [DEBU] | running setup for module 'solver.Specfem2D'
2024-02-22 20:41:51 [INFO] | initializing 1 solver directories
2024-02-22 20:41:51 [DEBU] | mkdir 001
2024-02-22 20:41:55 [DEBU] | linking source '001' as 'mainsolver'
2024-02-22 20:41:57 [DEBU] | running setup for module 'preprocess.Default'
2024-02-22 20:41:57 [DEBU] | running setup for module 'optimize.Gradient'
2024-02-22 20:41:59 [INFO] | no optimization checkpoint found, assuming first run
2024-02-22 20:42:01 [INFO] | 
////////////////////////////////////////////////////////////////////////////////
                              RUNNING ITERATION 01                              
////////////////////////////////////////////////////////////////////////////////
2024-02-22 20:42:01 [INFO] | 
================================================================================
                           RUNNING INVERSION WORKFLOW                           
================================================================================
2024-02-22 20:42:01 [INFO] | 
////////////////////////////////////////////////////////////////////////////////
                      EVALUATING MISFIT FOR INITIAL MODEL                       
////////////////////////////////////////////////////////////////////////////////
2024-02-22 20:42:01 [INFO] | evaluating misfit for model in `path_model_init`
2024-02-22 20:42:01 [INFO] | checking model parameters:
2024-02-22 20:42:01 [INFO] | vp: min=5800.000; mean=5800.000; max=5800.000
2024-02-22 20:42:01 [INFO] | vs: min=3500.000; mean=3500.000; max=3500.000
2024-02-22 20:42:01 [INFO] | preparing observation data for source 001
2024-02-22 20:42:01 [DEBU] | looking for data in: '/home/mnagaso/workspace/MINES/seisflows_projects/test/data/001/*'
2024-02-22 20:42:01 [CRIT] | 
================================================================================
                               DATA IMPORT ERROR                                
                               /////////////////                                
001 found no `obs` data with wildcard:
'/home/mnagaso/workspace/MINES/seisflows_projects/test/data/001/*'. Please check
`path_data` or manually import data and re-submit
================================================================================

================================================================================
EXAMPLE FAILED

Command 'seisflows submit' returned non-zero exit status 255.
================================================================================

[mnagaso]

I close this PR because there is a dedicated development on the branch https://github.com/adjtomo/seisflows/tree/bugfix-example_namspace_change

[bch0w]

Thanks @mnagaso, yes I started working on that branch last week but did not have time to finish. There are a few critical changes I had made that need to be fixed before the example can run, should hopefully PR that early this week!

[mnagaso]

Hi @bch0w, Thanks you very much for this mention and updating the example class! It will be helpful for me to understand the structure of seisflow.