This module depends on the Custodian class in the custodian project, which is a wrapper that manages jobs running on computing clusters. The custodian module is part of The Materials Project.
This module extends the Custodian class by creating the subclass SSHCustodian, which adds the functionality to copy the temporary directory created via monty to the scratch partitions on slave compute nodes, provided that the cluster's file-system is configured in this way. The implementation invokes a sub-process to utilize the ssh executable installed on the cluster, so it is not particularly elegant or platform independent, nor is this solution likely to be general to all clusters. This is why this modification has not been submitted as a pull request to the main Custodian project.
You use SSHCustodian in the same way as the Custodian class, and it should
integrate in with your existing scripts. The SSHCustodian class takes two
additional arguments when creating a new instance, scratch_dir_node_only
and pbs_nodefile
:
scratch_dir_node_only (bool): If set to True, custodian will grab the list of nodes in the file path provided to pbs_nodefile and use copy the temp_dir to the scratch_dir on each node over ssh. This is necessary on cluster setups where each node has its own independent scratch partition. pbs_nodefile (str): The filepath to the list of nodes to be used in a calculation. If this path does not point to a valid file, then scratch_dir_node_only will be automatically set to False.
The subclass SSHVaspJob was also created, which overrides the setup method to
also check the environment variable PBS_NUM_PPN
when auto_npar =
True
. This is necessary to implement for using compute node scratch
partitions on PBS-based queueing systems, as the generic method of using
multiprocessing.cpu_count()
to count the number of cores will include
hyperthreads, which will overestimate the number of physical cores and lead to
NPAR being set too large. One consequence of setting NPAR too high is that a
VASP job will hang, consuming resources but not doing anything useful. If you
are using this kind of scratch directory, be careful about setting NPAR.
On many clusters, the filepath for the list of compute nodes is in the
environment variable PBS_NODEFILE
, which can be accessed in bash as
$PBS_NODEFILE
and in python using the os
module. An example of
how SSHCustodian can be used in a script is the following:
import logging import os from sshcustodian.sshcustodian import SSHCustodian from custodian.vasp.handlers import (VaspErrorHandler, UnconvergedErrorHandler, MeshSymmetryErrorHandler, NonConvergingErrorHandler, PotimErrorHandler) from custodian.vasp.validators import VasprunXMLValidator from sshcustodian.vasp.sshjobs import SSHVaspJob from pymatgen.io.vasp import VaspInput FORMAT = '%(asctime)s %(message)s' logging.basicConfig(format=FORMAT, level=logging.INFO, filename="run.log") class VaspInputArgs: def __init__(self): """ Set the default values for running a VASP job. """ self.static_kpoint = 1 def import_dict(self, in_dict): """ Create and update self variables using dictionary. """ for (key, value) in iteritems(in_dict): if key == "command": self.command = value if key == "static_kpoint": self.static_kpoint = value if key == "jobs": self.jobs = value def get_runs(args): vasp_command = args.command.split() njobs = len(args.jobs) for i, job in enumerate(args.jobs): final = False if i != njobs - 1 else True if any(c.isdigit() for c in job): suffix = "." + job else: suffix = ".{}{}".format(job, i + 1) settings = [] backup = True if i == 0 else False copy_magmom = False vinput = VaspInput.from_directory(".") if i > 0: settings.append( {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}) job_type = job.lower() auto_npar = True if job_type.startswith("static"): m = [i * args.static_kpoint for i in vinput["KPOINTS"].kpts[0]] settings.extend([ {"dict": "INCAR", "action": {"_set": {"NSW": 0}}}, {'dict': 'KPOINTS', 'action': {'_set': {'kpoints': [m]}}}]) yield SSHVaspJob(vasp_command, final=final, suffix=suffix, backup=backup, settings_override=settings, copy_magmom=copy_magmom, auto_npar=auto_npar) scratch_root = os.path.abspath("/scratch") pbs_nodefile = os.environ.get("PBS_NODEFILE") job_args = VaspInputArgs() job_dict = {"command": "pvasp", "jobs": ["static"]} job_args.import_dict(job_dict) handlers = [VaspErrorHandler(), MeshSymmetryErrorHandler(), UnconvergedErrorHandler(), NonConvergingErrorHandler(), PotimErrorHandler()] validators = [VasprunXMLValidator()] logging.info("Handlers used are {0}".format(handlers)) c = SSHCustodian(handlers, get_runs(job_args), validators, checkpoint=True, scratch_dir=scratch_root, scratch_dir_node_only=True, pbs_nodefile=pbs_nodefile) c.run()
Note that depending on how your cluster is configured, the "command":
"pvasp"
will need to be changed to however you invoke a parallel job.
For further information on how to use custodian, consult the custodian project documentation.