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addressing adjtomo#138 broke out 'Model' class from the specfem tools…
… into its own tool for faster imports SeisFlows command line tool moved heavier imports into functions to speed up call times for other functions that don't need it fixed import statements and all tests pass
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,85 @@ | ||
| #!/usr/bin/env python3 | ||
| """ | ||
| This class provides utilities for the Seisflows solver interactions with | ||
| Specfem3D Cartesian, specifically to run on Chinook. | ||
| """ | ||
| import sys | ||
| import subprocess | ||
| from seisflows import logger | ||
| from seisflows.tools import unix, msg | ||
| from seisflows.solver.specfem3d import Specfem3D | ||
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| class Specfem3D_Chinook(Specfem3D): | ||
| """ | ||
| Solver SPECFEM3D | ||
| ---------------- | ||
| SPECFEM3D-specific alterations to the base SPECFEM module | ||
| Parameters | ||
| ---------- | ||
| Paths | ||
| ----- | ||
| *** | ||
| """ | ||
| __doc__ = Specfem3D.__doc__ + __doc__ | ||
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| def _run_binary(self, executable, stdout="solver.log", with_mpi=True): | ||
| """ | ||
| Calls MPI solver executable to run solver binaries, used by individual | ||
| processes to run the solver on system. If the external solver returns a | ||
| non-zero exit code (failure), this function will return a negative | ||
| boolean. | ||
| .. note:: | ||
| This function ASSUMES it is being run from a SPECFEM working | ||
| directory, i.e., that the executables are located in ./bin/ | ||
| .. note:: | ||
| This is essentially an error-catching wrapper of subprocess.run() | ||
| :type executable: str | ||
| :param executable: executable function to call. May or may not start | ||
| E.g., acceptable calls for the solver would './bin/xspecfem2D'. | ||
| Also accepts additional command line arguments such as: | ||
| 'xcombine_sem alpha_kernel kernel_paths...' | ||
| :type stdout: str | ||
| :param stdout: where to redirect stdout | ||
| :type with_mpi: bool | ||
| :param with_mpi: If `mpiexec` is given, use MPI to run the executable. | ||
| Some executables (e.g., combine_vol_data_vtk) must be run in | ||
| serial so this flag allows them to turn off MPI running. | ||
| :raises SystemExit: If external numerical solver return any failure | ||
| code while running | ||
| """ | ||
| # Executable may come with additional sub arguments, we only need to | ||
| # check that the actually executable exists | ||
| if not unix.which(executable.split(" ")[0]): | ||
| logger.critical(msg.cli(f"executable '{executable}' does not exist", | ||
| header="external solver error", border="=")) | ||
| sys.exit(-1) | ||
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| # Prepend with `mpiexec` if we are running with MPI | ||
| # looks something like: `mpirun -n 4 ./bin/xspecfem2d` | ||
| if self._mpiexec and with_mpi: | ||
| executable = f"{self._mpiexec} -n {self.nproc} {executable}" | ||
| logger.debug(f"running executable with cmd: '{executable}'") | ||
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||
| try: | ||
| with open(stdout, "w") as f: | ||
| subprocess.run(executable, shell=True, check=True, stdout=f, | ||
| stderr=f) | ||
| except (subprocess.CalledProcessError, OSError) as e: | ||
| logger.critical( | ||
| msg.cli("The external numerical solver has returned a " | ||
| "nonzero exit code (failure). Consider stopping any " | ||
| "currently running jobs to avoid wasted " | ||
| "computational resources. Check 'scratch/solver/" | ||
| f"mainsolver/{stdout}' for the solvers stdout log " | ||
| "message. The failing command and error message are:", | ||
| items=[f"exc: {executable}", f"err: {e}"], | ||
| header="external solver error", | ||
| border="=") | ||
| ) | ||
| sys.exit(-1) |
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