|
| 1 | +import os |
| 2 | +import typing as ty |
| 3 | +import logging |
| 4 | +from pathlib import Path |
| 5 | +import re |
| 6 | +import subprocess as sp |
| 7 | + |
| 8 | +import attrs |
| 9 | +from pydra.compose import shell |
| 10 | +from pydra.environments import base |
| 11 | +from pydra.utils.general import ensure_list |
| 12 | + |
| 13 | + |
| 14 | +logger = logging.getLogger("pydra") |
| 15 | + |
| 16 | +if ty.TYPE_CHECKING: |
| 17 | + from pydra.engine.job import Job |
| 18 | + |
| 19 | + |
| 20 | +@attrs.define |
| 21 | +class Lmod(base.Environment): |
| 22 | + """Lmod environment.""" |
| 23 | + |
| 24 | + modules: list[str] = attrs.field(converter=ensure_list) |
| 25 | + |
| 26 | + @modules.validator |
| 27 | + def _validate_modules(self, _, value: ty.Any) -> None: |
| 28 | + if not value: |
| 29 | + raise ValueError("At least one module must be specified") |
| 30 | + if not all(isinstance(v, str) for v in value): |
| 31 | + raise ValueError("All module names must be strings") |
| 32 | + |
| 33 | + def execute(self, job: "Job[shell.Task]") -> dict[str, int | str]: |
| 34 | + env_src = self.run_lmod_cmd("python", "load", *self.modules) |
| 35 | + env = {} |
| 36 | + for key, value in re.findall( |
| 37 | + r"""os\.environ\[['"](.*?)['"]\]\s*=\s*['"](.*?)['"]""", env_src |
| 38 | + ): |
| 39 | + env[key] = value |
| 40 | + cmd_args = job.task._command_args(values=job.inputs) |
| 41 | + values = base.execute(cmd_args, env=env) |
| 42 | + return_code, stdout, stderr = values |
| 43 | + if return_code: |
| 44 | + msg = f"Error running '{job.name}' job with {cmd_args}:" |
| 45 | + if stderr: |
| 46 | + msg += "\n\nstderr:\n" + stderr |
| 47 | + if stdout: |
| 48 | + msg += "\n\nstdout:\n" + stdout |
| 49 | + raise RuntimeError(msg) |
| 50 | + return {"return_code": return_code, "stdout": stdout, "stderr": stderr} |
| 51 | + |
| 52 | + @classmethod |
| 53 | + def modules_are_installed(cls) -> bool: |
| 54 | + return "MODULESHOME" in os.environ |
| 55 | + |
| 56 | + @classmethod |
| 57 | + def run_lmod_cmd(cls, *args: str) -> str: |
| 58 | + if not cls.modules_are_installed(): |
| 59 | + raise RuntimeError( |
| 60 | + "Could not find Lmod installation, please ensure it is installed and MODULESHOME is set" |
| 61 | + ) |
| 62 | + lmod_exec = Path(os.environ["MODULESHOME"]) / "libexec" / "lmod" |
| 63 | + |
| 64 | + try: |
| 65 | + output_bytes, error_bytes = sp.Popen( |
| 66 | + [str(lmod_exec)] + list(args), |
| 67 | + stdout=sp.PIPE, |
| 68 | + stderr=sp.PIPE, |
| 69 | + ).communicate() |
| 70 | + except (sp.CalledProcessError, OSError) as e: |
| 71 | + raise RuntimeError(f"Error running 'lmod': {e}") |
| 72 | + |
| 73 | + output = output_bytes.decode("utf-8") |
| 74 | + error = error_bytes.decode("utf-8") |
| 75 | + |
| 76 | + if output == "_mlstatus = False\n": |
| 77 | + raise RuntimeError(f"Error running module cmd '{' '.join(args)}':\n{error}") |
| 78 | + |
| 79 | + return output |
| 80 | + |
| 81 | + |
| 82 | +# Alias so it can be referred to as lmod.Environment |
| 83 | +Environment = Lmod |
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