How to Run an Evolutionary Algorithm with a Custom Workflow?

[hyesol]

Hi! I’m using the simmate in developer mode and trying to run an evolutionary algorithm with a custom workflow I created. As shown in the screenshot, I’ve modified fixed_composition.py - "relaxation.vasp.staged" to "relaxation.vasp.warren-lab-staged" (this is the workflow I code, and it works fine on its own!).

However, I’m encountering an error that says only "relaxation.vasp.staged" can be used for fixed-composition searching. Is there a way to bypass this error and run the evolutionary algorithm with the workflow I want?

[jacksund]

I don't allow different workflows yet because there are several assumptions I've made about the workflow involved -- and the search may fail without them. For example, the ability to export specific types of figures is something associated with the staged workflow, and the whole evo search will fail if your new workflow doesn't have those methods.

More work needs to be done on the search to allow any workflow, and I unfortunately won't have the time to do that this month... But since you are using things in developer mode, you are welcome to test out your workflow and implement the necessary fixes for it to run. The error you see occurs here, so you can remove this line to begin testing:

simmate/src/simmate/apps/evolution/models/chemical_system.py

Line 71 in e03f34f

"Only `relaxation.vasp.staged` is supported in early testing"

Sorry this isn't the answer you were hoping for! I do have plans for updating the evo search to support this -- but the timeline just happens to be longer than what your project probably needs

[hyesol]

No worries! I am encountering another problem though, when I try to run simmate workflows run search.yaml in general (not using the developer mode) I get this error code.

2024-10-09 14:33:08 INFO     Configuring database and workflows 🛠                                                                                       
2024-10-09 18:33:10 INFO     Configuration complete 🚀                                                                                                  
                    INFO     Starting 'structure-prediction.toolkit.fixed-composition'                                                                  
2024-10-09 18:33:11 INFO     Setting up evolutionary search for Co10 O20                                                                                
                    INFO     Generating fingerprints for past structures...                                                                             
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/command_line/ │
│ workflows.py:299 in run                                                                          │
│                                                                                                  │
│   296 │                                                                                          │
│   297 │   from simmate.engine import Workflow                                                    │
│   298 │                                                                                          │
│ ❱ 299 │   Workflow.run_from_file(filename).result()                                              │
│   300                                                                                            │
│   301                                                                                            │
│   302 @workflows_app.command()                                                                   │
│                                                                                                  │
│ ╭─────────────────────── locals ────────────────────────╮                                        │
│ │ filename = PosixPath('search.yaml')                   │                                        │
│ │ Workflow = <class 'simmate.engine.workflow.Workflow'> │                                        │
│ ╰───────────────────────────────────────────────────────╯                                        │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/engine/workfl │
│ ow.py:358 in run_from_file                                                                       │
│                                                                                                  │
│    355 │   │   Runs a workflow locally where parameters are loaded from a yaml or toml file      │
│    356 │   │   """                                                                               │
│    357 │   │   workflow, parameters = cls._load_settings_file(filename)                          │
│ ❱  358 │   │   state = workflow.run(**parameters)                                                │
│    359 │   │   return state                                                                      │
│    360 │                                                                                         │
│    361 │   @classmethod                                                                          │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │        cls = <class 'simmate.engine.workflow.Workflow'>                                      │ │
│ │   filename = PosixPath('search.yaml')                                                        │ │
│ │ parameters = {                                                                               │ │
│ │              │   'composition': 'Co10O20',                                                   │ │
│ │              │   'subworkflow_kwargs': {                                                     │ │
│ │              │   │   'command': 'mpirun -n 4 vasp_std > vasp.out',                           │ │
│ │              │   │   'compress_output': True,                                                │ │
│ │              │   │   'tags': ['fixed']                                                       │ │
│ │              │   },                                                                          │ │
│ │              │   'directory': 'Co10O20_fixed'                                                │ │
│ │              }                                                                               │ │
│ │   workflow = <class                                                                          │ │
│ │              'simmate.apps.evolution.workflows.fixed_composition.StructurePrediction__Toolk… │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/engine/workfl │
│ ow.py:178 in run                                                                                 │
│                                                                                                  │
│    175 │   │   """                                                                               │
│    176 │   │   # Note: this is a separate method and wrapper around run_full because             │
│    177 │   │   # we want to allow Prefect executor to overwrite this method.                     │
│ ❱  178 │   │   result = cls._run_full(**kwargs)                                                  │
│    179 │   │   state = DummyState(result)                                                        │
│    180 │   │   return state                                                                      │
│    181                                                                                           │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │    cls = <class                                                                              │ │
│ │          'simmate.apps.evolution.workflows.fixed_composition.StructurePrediction__Toolkit__… │ │
│ │ kwargs = {                                                                                   │ │
│ │          │   'composition': 'Co10O20',                                                       │ │
│ │          │   'subworkflow_kwargs': {                                                         │ │
│ │          │   │   'command': 'mpirun -n 4 vasp_std > vasp.out',                               │ │
│ │          │   │   'compress_output': True,                                                    │ │
│ │          │   │   'tags': ['fixed']                                                           │ │
│ │          │   },                                                                              │ │
│ │          │   'directory': 'Co10O20_fixed'                                                    │ │
│ │          }                                                                                   │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/engine/workfl │
│ ow.py:242 in _run_full                                                                           │
│                                                                                                  │
│    239 │   │   # Finally run the core part of the workflow. This should return a                 │
│    240 │   │   # dictionary object if we have "use_database=True", but can be                    │
│    241 │   │   # any python object if "use_database=False"                                       │
│ ❱  242 │   │   results = cls.run_config(**kwargs_cleaned)                                        │
│    243 │   │                                                                                     │
│    244 │   │   # save the result to the database                                                 │
│    245 │   │   if cls.use_database:                                                              │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │             cls = <class                                                                     │ │
│ │                   'simmate.apps.evolution.workflows.fixed_composition.StructurePrediction__… │ │
│ │ compress_output = False                                                                      │ │
│ │       directory = 'Co10O20_fixed'                                                            │ │
│ │          kwargs = {                                                                          │ │
│ │                   │   'composition': 'Co10O20',                                              │ │
│ │                   │   'subworkflow_kwargs': {                                                │ │
│ │                   │   │   'command': 'mpirun -n 4 vasp_std > vasp.out',                      │ │
│ │                   │   │   'compress_output': True,                                           │ │
│ │                   │   │   'tags': ['fixed']                                                  │ │
│ │                   │   }                                                                      │ │
│ │                   }                                                                          │ │
│ │  kwargs_cleaned = {                                                                          │ │
│ │                   │   'run_id': '65fe1566-290a-4c12-9b4e-e217390dd345',                      │ │
│ │                   │   'directory':                                                           │ │
│ │                   PosixPath('/media/synology/user/hyesol/Cobalt/CoO/test/Co10O20_fixed'),    │ │
│ │                   │   'compress_output': False,                                              │ │
│ │                   │   'source': None,                                                        │ │
│ │                   │   'started_at': datetime.datetime(2024, 10, 9, 18, 33, 10, 911239,       │ │
│ │                   tzinfo=datetime.timezone.utc),                                             │ │
│ │                   │   'composition': Comp: Co10 O20,                                         │ │
│ │                   │   'subworkflow_kwargs': {                                                │ │
│ │                   │   │   'command': 'mpirun -n 4 vasp_std > vasp.out',                      │ │
│ │                   │   │   'compress_output': True,                                           │ │
│ │                   │   │   'tags': ['fixed']                                                  │ │
│ │                   │   },                                                                     │ │
│ │                   │   'subworkflow_name': 'relaxation.vasp.staged',                          │ │
│ │                   │   'fitness_field': 'energy_per_atom',                                    │ │
│ │                   │   'convergence_cutoff': 0.001,                                           │ │
│ │                   │   ... +10                                                                │ │
│ │                   }                                                                          │ │
│ │          run_id = None                                                                       │ │
│ │          source = None                                                                       │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/apps/evolutio │
│ n/workflows/fixed_composition.py:118 in run_config                                               │
│                                                                                                  │
│   115 │   │   # the pool up front. This is acheive just by accessing the validator.              │
│   116 │   │   # This also makes sure the Fingerprints are all up to date before                  │
│   117 │   │   # submitting workers below                                                         │
│ ❱ 118 │   │   search_datatable.validator                                                         │
│   119 │   │                                                                                      │
│   120 │   │   logging.info("Finished setup")                                                     │
│   121 │   │   logging.info(                                                                      │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │ best_survival_cutoff = 1800                                                                  │ │
│ │                  cls = <class                                                                │ │
│ │                        'simmate.apps.evolution.workflows.fixed_composition.StructurePredict… │ │
│ │          composition = Comp: Co10 O20                                                        │ │
│ │   convergence_cutoff = 0.001                                                                 │ │
│ │            directory = PosixPath('/media/synology/user/hyesol/Cobalt/CoO/test/Co10O20_fixed… │ │
│ │        fitness_field = 'energy_per_atom'                                                     │ │
│ │               kwargs = {                                                                     │ │
│ │                        │   'compress_output': False,                                         │ │
│ │                        │   'source': None,                                                   │ │
│ │                        │   'started_at': datetime.datetime(2024, 10, 9, 18, 33, 10, 911239,  │ │
│ │                        tzinfo=datetime.timezone.utc)                                         │ │
│ │                        }                                                                     │ │
│ │       max_structures = 19036                                                                 │ │
│ │ min_structures_exact = 900                                                                   │ │
│ │                    n = 30.0                                                                  │ │
│ │    nfirst_generation = 15                                                                    │ │
│ │         nsteadystate = 40                                                                    │ │
│ │               run_id = '65fe1566-290a-4c12-9b4e-e217390dd345'                                │ │
│ │     search_datatable = <FixedCompositionSearch: FixedCompositionSearch object (1)>           │ │
│ │      selector_kwargs = {}                                                                    │ │
│ │        selector_name = 'TournamentSelection'                                                 │ │
│ │   singleshot_sources = ['third_parties', 'prototypes']                                       │ │
│ │           sleep_step = 10                                                                    │ │
│ │  steadystate_sources = {                                                                     │ │
│ │                        │   'RandomSymStructure': 0.55,                                       │ │
│ │                        │   'from_ase.Heredity': 0.25,                                        │ │
│ │                        │   'from_ase.MirrorMutation': 0.05,                                  │ │
│ │                        │   'from_ase.RotationalMutation': 0.05,                              │ │
│ │                        │   'from_ase.AtomicPermutation': 0.05,                               │ │
│ │                        │   'from_ase.CoordinatePerturbation': 0.05                           │ │
│ │                        }                                                                     │ │
│ │   subworkflow_kwargs = {                                                                     │ │
│ │                        │   'command': 'mpirun -n 4 vasp_std > vasp.out',                     │ │
│ │                        │   'compress_output': True,                                          │ │
│ │                        │   'tags': ['fixed']                                                 │ │
│ │                        }                                                                     │ │
│ │     subworkflow_name = 'relaxation.vasp.staged'                                              │ │
│ │     validator_kwargs = {'distance_tolerance': 0.2, 'use_database': True}                     │ │
│ │       validator_name = 'PartialCrystalNNFingerprint'                                         │ │
│ │  write_summary_files = True                                                                  │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/apps/evolutio │
│ n/models/fixed_composition.py:587 in validator                                                   │
│                                                                                                  │
│   584 │   │   validator_class = getattr(validator_module, self.validator_name)                   │
│   585 │   │                                                                                      │
│   586 │   │   logging.info("Generating fingerprints for past structures...")                     │
│ ❱ 587 │   │   fingerprint_validator = validator_class(                                           │
│   588 │   │   │   composition=Composition(self.composition),                                     │
│   589 │   │   │   structure_pool=self.individuals_completed.order_by(self.fitness_field),        │
│   590 │   │   │   **self.validator_kwargs,                                                       │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │            self = <FixedCompositionSearch: FixedCompositionSearch object (1)>                │ │
│ │ validator_class = <class                                                                     │ │
│ │                   'simmate.toolkit.validators.fingerprint.pcrystalnn.PartialCrystalNNFinger… │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/toolkit/valid │
│ ators/fingerprint/base.py:44 in __init__                                                         │
│                                                                                                  │
│    41 │   │   self.distance_tolerance = distance_tolerance or self.distance_tolerance            │
│    42 │   │                                                                                      │
│    43 │   │   # setup featurizer with the given composition                                      │
│ ❱  44 │   │   self.featurizer = self.get_featurizer(**kwargs)                                    │
│    45 │   │                                                                                      │
│    46 │   │   # see if we are working with a list of toolkit structures or a queryset            │
│    47 │   │   if isinstance(structure_pool, list):                                               │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │ distance_tolerance = 0.2                                                                     │ │
│ │             kwargs = {'composition': Comp: Co10 O20}                                         │ │
│ │               self = <simmate.toolkit.validators.fingerprint.pcrystalnn.PartialCrystalNNFin… │ │
│ │                      object at 0x7f2c5ce62a90>                                               │ │
│ │     structure_pool = <SearchResults []>                                                      │ │
│ │       use_database = True                                                                    │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/simmate/toolkit/valid │
│ ators/fingerprint/pcrystalnn.py:36 in get_featurizer                                             │
│                                                                                                  │
│   33 │   │   else:                                                                               │
│   34 │   │   │   # We change x_diff_weight to 3 here because we want the coordation              │
│   35 │   │   │   # to be atom-dependent (best we can do is oxidation-state dependent here)       │
│ ❱ 36 │   │   │   sitefingerprint_method = cnnf.from_preset(                                      │
│   37 │   │   │   │   "ops", distance_cutoffs=None, x_diff_weight=3                               │
│   38 │   │   │   )                                                                               │
│   39                                                                                             │
│                                                                                                  │
│ ╭──────────────── locals ─────────────────╮                                                      │
│ │       composition = Comp: Co10 O20      │                                                      │
│ │ crystalnn_options = {}                  │                                                      │
│ │      stat_options = ['mean', 'std_dev'] │                                                      │
│ ╰─────────────────────────────────────────╯                                                      │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/matminer/featurizers/ │
│ site/fingerprint.py:389 in from_preset                                                           │
│                                                                                                  │
│   386 │   │   │   return CrystalNNFingerprint(op_types, **kwargs)                                │
│   387 │   │                                                                                      │
│   388 │   │   elif preset == "ops":                                                              │
│ ❱ 389 │   │   │   cn_target_motif_op = load_cn_target_motif_op()                                 │
│   390 │   │   │   op_types = copy.deepcopy(cn_target_motif_op)                                   │
│   391 │   │   │   for k in range(24):                                                            │
│   392 │   │   │   │   if k + 1 in op_types:                                                      │
│                                                                                                  │
│ ╭──────────────────────── locals ─────────────────────────╮                                      │
│ │ kwargs = {'distance_cutoffs': None, 'x_diff_weight': 3} │                                      │
│ │ preset = 'ops'                                          │                                      │
│ ╰─────────────────────────────────────────────────────────╯                                      │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/matminer/featurizers/ │
│ site/fingerprint.py:889 in load_cn_target_motif_op                                               │
│                                                                                                  │
│   886 │   │   (dict)                                                                             │
│   887 │   """                                                                                    │
│   888 │   with open(os.path.join(os.path.dirname(__file__), "cn_target_motif_op.yaml")) as f:    │
│ ❱ 889 │   │   return yaml.safe_load(f)                                                           │
│   890                                                                                            │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │ f = <_io.TextIOWrapper                                                                       │ │
│ │     name='/home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/matmin… │ │
│ │     mode='r' encoding='UTF-8'>                                                               │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/ruamel/yaml/main.py:1 │
│ 105 in safe_load                                                                                 │
│                                                                                                  │
│   1102 │   and produce the corresponding Python object.                                          │
│   1103 │   Resolve only basic YAML tags.                                                         │
│   1104 │   """                                                                                   │
│ ❱ 1105 │   error_deprecation('safe_load', 'load', arg="typ='safe', pure=True")                   │
│   1106                                                                                           │
│   1107                                                                                           │
│   1108 def safe_load_all(stream: StreamTextType, version: Optional[VersionType] = None) -> Any:  │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │  stream = <_io.TextIOWrapper                                                                 │ │
│ │           name='/home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/… │ │
│ │           mode='r' encoding='UTF-8'>                                                         │ │
│ │ version = None                                                                               │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
│                                                                                                  │
│ /home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/ruamel/yaml/main.py:1 │
│ 039 in error_deprecation                                                                         │
│                                                                                                  │
│   1036 │   if sys.version_info < (3, 10):                                                        │
│   1037 │   │   raise AttributeError(s)                                                           │
│   1038 │   else:                                                                                 │
│ ❱ 1039 │   │   raise AttributeError(s, name=None)                                                │
│   1040                                                                                           │
│   1041                                                                                           │
│   1042 _error_dep_arg = "typ='rt'"                                                               │
│                                                                                                  │
│ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │
│ │     arg = "typ='safe', pure=True"                                                            │ │
│ │ comment = 'instead of'                                                                       │ │
│ │ context = '        return yaml.safe_load(f)\n'                                               │ │
│ │     fun = 'safe_load'                                                                        │ │
│ │    info = Traceback(filename='/home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/… │ │
│ │           lineno=889, function='load_cn_target_motif_op', code_context=['        return      │ │
│ │           yaml.safe_load(f)\n'], index=0, positions=Positions(lineno=889, end_lineno=889,    │ │
│ │           col_offset=15, end_col_offset=32))                                                 │ │
│ │ inspect = <module 'inspect' from                                                             │ │
│ │           '/home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/inspect.py'>         │ │
│ │  method = 'load'                                                                             │ │
│ │       s = '\n"safe_load()" has been removed, use\n\n  yaml = YAML(typ=\'safe\', pure=True)\n │ │
│ │           yam'+192                                                                           │ │
│ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
AttributeError: 
"safe_load()" has been removed, use

  yaml = YAML(typ='safe', pure=True)
  yaml.load(...)

instead of file "/home/WarrenLab/miniconda3/envs/hyesol_nested/lib/python3.11/site-packages/matminer/featurizers/site/fingerprint.py", line 889

        return yaml.safe_load(f)

This is my .yaml file

workflow_name: structure-prediction.toolkit.fixed-composition
composition: Co10O20

subworkflow_kwargs:
    command: mpirun -n 4 vasp_std > vasp.out
    compress_output: true
    tags:
        - fixed

directory: Co10O20_fixed

I am not sure if this is a bug on simmate end or if I am doing something wrong.

[jacksund]

looks like an update in the yaml package, so it might be an issue with how you installed things. Could you run the command conda list yaml with your env active and let me know the output

[hyesol]

yes, it gives me this!

(hyesol_newdb) [WarrenLab@WarWulf hyesol]$ conda list yaml
# packages in environment at /home/WarrenLab/miniconda3/envs/hyesol_newdb:
#
# Name                    Version                   Build  Channel
pyyaml                    6.0.1           py311h459d7ec_1    conda-forge
ruamel.yaml               0.18.6          py311h459d7ec_0    conda-forge
ruamel.yaml.clib          0.2.8           py311h459d7ec_0    conda-forge
yaml                      0.2.5                h7f98852_2    conda-forge

[jacksund]

looks like thats the output for the hyesol_newdb env while your error trackback shows you using hyesol_nested.

Also after taking a closer look at the traceback, the error is either from matminer or yaml since the error is happening in the matminer.featurizers.site.fingerprint module when it calls yaml.safe_load. So this is almost certainly an installation issue (maybe pip installing where you shouldn't...? or the matminer conda being broken).

[hyesol]

😂 idk why I keep doing this, but I had this problem with all of the environments that I was working on (sorry for the confusion!) After some digging, I managed to run simmate workflows run search.yaml by downgrading ruamel.yaml to ruamel.yaml==0.17.36 ... and at least it works for now... (I followed this page)
But always, thank you so much!