Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/mpi.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """Experimental support for MPI.""" |
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2 import inspect |
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3 import os |
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4 import re |
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5 from typing import List, Mapping, MutableMapping, Optional, Type, TypeVar, Union |
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6 |
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7 from ruamel import yaml |
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8 |
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9 MpiConfigT = TypeVar("MpiConfigT", bound="MpiConfig") |
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10 |
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11 MPIRequirementName = "http://commonwl.org/cwltool#MPIRequirement" |
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12 |
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13 |
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14 class MpiConfig: |
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15 def __init__( |
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16 self, |
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17 runner: str = "mpirun", |
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18 nproc_flag: str = "-n", |
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19 default_nproc: Union[int, str] = 1, |
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20 extra_flags: Optional[List[str]] = None, |
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21 env_pass: Optional[List[str]] = None, |
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22 env_pass_regex: Optional[List[str]] = None, |
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23 env_set: Optional[Mapping[str, str]] = None, |
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24 ) -> None: |
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25 """ |
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26 Initialize from the argument mapping. |
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27 |
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28 Defaults are: |
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29 runner: "mpirun" |
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30 nproc_flag: "-n" |
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31 default_nproc: 1 |
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32 extra_flags: [] |
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33 env_pass: [] |
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34 env_pass_regex: [] |
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35 env_set: {} |
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36 |
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37 Any unknown keys will result in an exception. |
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38 """ |
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39 self.runner = runner |
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40 self.nproc_flag = nproc_flag |
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41 self.default_nproc = int(default_nproc) |
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42 self.extra_flags = extra_flags or [] |
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43 self.env_pass = env_pass or [] |
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44 self.env_pass_regex = env_pass_regex or [] |
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45 self.env_set = env_set or {} |
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46 |
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47 @classmethod |
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48 def load(cls: Type[MpiConfigT], config_file_name: str) -> MpiConfigT: |
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49 """Create the MpiConfig object from the contents of a YAML file. |
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50 |
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51 The file must contain exactly one object, whose attributes must |
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52 be in the list allowed in the class initialiser (all are |
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53 optional). |
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54 """ |
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55 with open(config_file_name) as cf: |
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56 data = yaml.main.round_trip_load(cf) |
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57 try: |
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58 return cls(**data) |
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59 except TypeError as e: |
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60 unknown = set(data.keys()) - set(inspect.signature(cls).parameters) |
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61 raise ValueError(f"Unknown key(s) in MPI configuration: {unknown}") |
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62 |
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63 def pass_through_env_vars(self, env: MutableMapping[str, str]) -> None: |
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64 """Take the configured list of environment variables and pass them to the executed process.""" |
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65 for var in self.env_pass: |
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66 if var in os.environ: |
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67 env[var] = os.environ[var] |
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68 |
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69 for var_re in self.env_pass_regex: |
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70 r = re.compile(var_re) |
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71 for k in os.environ: |
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72 if r.match(k): |
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73 env[k] = os.environ[k] |
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74 |
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75 def set_env_vars(self, env: MutableMapping[str, str]) -> None: |
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76 """Set some variables to the value configured.""" |
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77 env.update(self.env_set) |