Installation query

[makeabhishek]

Hi,
I installed seisflows following the latest instructions.

git clone --branch devel https://github.com/adjtomo/seisflows.git
cd seisflows
conda env create -f environment.yml
conda activate seisflows
pip install -e .

I'm aware that SPECFEM is not the part of seisflow. But I want to confirm if we need to install SPECFEM separately?
Does SPECFEM directory need to be inside seisflows or anywhere is fine?

Thanks
Abhi

[bch0w]

Hi @makeabhishek, great question. Yes, SPECFEM will need to be installed and compiled separately for your machine, and you will have to choose which version of SPECFEM (2D/3D/3D_GLOBE) you need for your application.

SPECFEM does not need to be within SeisFlows. In the SeisFlows parameter file, you will just need to specify paths to the bin/, DATA/ and DATABASES_MPI/ directories of SPECFEM.

One caveat of this is that the example problems are capable of downloading and compiling SPECFEM2D on a workstation, however in most cases I'd recommend the User do this themselves as it gives more flexibility and control over how SPECFEM is compiled.

[makeabhishek]

Thanks @bch0w for the guidance. I was trying to run pytest for seisflows. But I got the following error.

(seisflows) teamacoustics@teamacoutics:~/Documents/seisflows/seisflows/tests$ pytest
============================= test session starts ==============================
platform linux -- Python 3.11.0, pytest-7.2.2, pluggy-1.0.0
rootdir: /home/teamacoustics/Documents/seisflows
collected 32 items                                                             

test_optimize.py ..........                                              [ 31%]
test_preprocess.py ........                                              [ 56%]
test_seisflows.py .....                                                  [ 71%]
test_solver.py F..                                                       [ 81%]
test_system.py ....                                                      [ 93%]
test_tools.py ..                                                         [100%]

=================================== FAILURES ===================================
______________________________ test_source_names _______________________________

    def test_source_names():
        """
        Check that source names are established correctly
        """
        # Establish solver that looks for CMTSOLUTIONS with NTASK==1
        sources = os.path.join(TEST_DATA, "sources")
        solver = Specfem(path_specfem_data=sources, source_prefix="CMTSOLUTION")
        assert(len(solver.source_names) == 1)
    
        # Set NTASK==2 to grab both source files
        solver = Specfem(path_specfem_data=sources, source_prefix="CMTSOLUTION",
                         ntask=2)
        source_names = glob(os.path.join(sources, "CMTSOLUTION*"))
        source_names = [_.split("_")[-1] for _ in source_names]
    
>       assert(source_names == solver.source_names)
E       AssertionError: assert ['002', '001'] == ['001', '002']
E         At index 0 diff: '002' != '001'
E         Use -v to get more diff

/home/teamacoustics/Documents/seisflows/seisflows/tests/test_solver.py:31: AssertionError
=============================== warnings summary ===============================
../../../../anaconda3/envs/seisflows/lib/python3.11/site-packages/pkg_resources/__init__.py:121
  /home/teamacoustics/anaconda3/envs/seisflows/lib/python3.11/site-packages/pkg_resources/__init__.py:121: DeprecationWarning: pkg_resources is deprecated as an API
    warnings.warn("pkg_resources is deprecated as an API", DeprecationWarning)

../../../../anaconda3/envs/seisflows/lib/python3.11/site-packages/pkg_resources/__init__.py:2870
  /home/teamacoustics/anaconda3/envs/seisflows/lib/python3.11/site-packages/pkg_resources/__init__.py:2870: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

seisflows/tests/test_preprocess.py: 24 warnings
  /home/teamacoustics/anaconda3/envs/seisflows/lib/python3.11/site-packages/pyasdf/asdf_data_set.py:282: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    self._loose_asdf_format_version = LooseVersion(

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED test_solver.py::test_source_names - AssertionError: assert ['002', '001'] == ['001', '002']
================== 1 failed, 31 passed, 26 warnings in 58.09s ==================
(seisflows) teamacoustics@teamacoutics:~/Documents/seisflows/seisflows/tests$ 

[bch0w]

Thanks for catching that, @makeabhishek! Interestingly that test passes on my workstation, I guess that's why they caution that lists in Python are liable to change! I will make sure to fix that test in the next update. Just leaving a to-do here so that I remember.

To Do:

• sort source names before assertion in test_solver.test_source_names()