annotate env/lib/python3.9/site-packages/cwltool/mpi.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author shellac
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)