<reponame>image-tester/custodian<filename>custodian/qchem/jobs.py
# coding: utf-8

from __future__ import unicode_literals, division
import glob
import shlex

"""
This module implements basic kinds of jobs for QChem runs.
"""

import os
from monty.io import zopen
import shutil
import copy
import subprocess
from pymatgen.io.qchemio import QcInput
from custodian.custodian import Job, gzip_dir

__author__ = "<NAME>"
__version__ = "0.1"
__maintainer__ = "<NAME>"
__email__ = "<EMAIL>"
__status__ = "Alpha"
__date__ = "12/03/13"


class QchemJob(Job):
    """
    A basic QChem Job.
    """

    def __init__(self, qchem_cmd, input_file="mol.qcinp",
                 output_file="mol.qcout", chk_file=None, qclog_file=None,
                 gzipped=False, backup=True, alt_cmd=None,
                 large_static_mem=False):
        """
        This constructor is necessarily complex due to the need for
        flexibility. For standard kinds of runs, it's often better to use one
        of the static constructors.

        Args:
            qchem_cmd ([str]): Command to run QChem as a list args (without
                input/output file name). For example: ["qchem", "-np", "24"]
            input_file (str): Name of the QChem input file.
            output_file (str): Name of the QChem output file.
            chk_file (str): Name of the QChem check point file. None means no
                checkpoint point file. Defaults to None.
            qclog_file (str): Name of the file to redirect the standard output
                to. None means not to record the standard output. Defaults to
                None.
            gzipped (bool): Whether to gzip the final output. Defaults to False.
            backup (bool): Whether to backup the initial input files. If True,
                the input files will be copied with a ".orig" appended.
                Defaults to True.
            alt_cmd (dict of list): Alternate commands.
                For example: {"openmp": ["qchem", "-seq", "-nt", "24"]
                              "half_cpus": ["qchem", "-np", "12"]}
            large_static_mem: use ultra large static memory
        """
        self.qchem_cmd = copy.deepcopy(qchem_cmd)
        self.input_file = input_file
        self.output_file = output_file
        self.chk_file = chk_file
        self.qclog_file = qclog_file
        self.gzipped = gzipped
        self.backup = backup
        self.current_command = self.qchem_cmd
        self.current_command_name = "general"
        self.large_static_mem = large_static_mem
        self._set_qchem_memory()
        self.alt_cmd = copy.deepcopy(alt_cmd)

    def _set_qchem_memory(self, qcinp=None):
        if not qcinp:
            qcinp = QcInput.from_file(self.input_file)
        if "PBS_JOBID" in os.environ:
            if "hopque" in os.environ["PBS_JOBID"]:
                # on Hopper
                for j in qcinp.jobs:
                    if self.current_command_name == "general":
                        if self.large_static_mem:
                            j.set_memory(total=1100, static=300)
                        else:
                            j.set_memory(total=1100, static=100)
                    elif self.current_command_name == "half_cpus":
                        if self.large_static_mem:
                            j.set_memory(total=2200, static=500)
                        else:
                            j.set_memory(total=2200, static=100)
                    elif self.current_command_name == "openmp":
                        if self.large_static_mem:
                            j.set_memory(total=28000, static=10000)
                        else:
                            j.set_memory(total=28000, static=3000)
            elif "edique" in os.environ["PBS_JOBID"]:
                # on Edison
                for j in qcinp.jobs:
                    if self.current_command_name == "general":
                        if self.large_static_mem:
                            j.set_memory(total=2500, static=500)
                        else:
                            j.set_memory(total=2500, static=100)
                    elif self.current_command_name == "half_cpus":
                        if self.large_static_mem:
                            j.set_memory(total=5000, static=1000)
                        else:
                            j.set_memory(total=5000, static=200)
                    elif self.current_command_name == "openmp":
                        if self.large_static_mem:
                            j.set_memory(total=60000, static=20000)
                        else:
                            j.set_memory(total=60000, static=5000)
        qcinp.write_file(self.input_file)

    def select_command(self, cmd_name, qcinp=None):
        """
        Set the command to run QChem by name. "general" set to the default one.
            Args:
                cmd_name: the command name to change to.
                qcinp: the QcInput object to operate on.

        Returns:
            True: success
            False: failed
        """
        available_commands = ["general"]
        if self.alt_cmd:
            available_commands.extend(self.alt_cmd.keys())
        if cmd_name not in available_commands:
            raise Exception("Command mode \"", cmd_name, "\" is not available")
        if cmd_name == "general":
            self.current_command = self.qchem_cmd
        else:
            self.current_command = self.alt_cmd[cmd_name]
        self.current_command_name = cmd_name
        self._set_qchem_memory(qcinp)
        return True

    def setup(self):
        if self.backup:
            i = 0
            while os.path.exists("{}.{}.orig".format(self.input_file, i)):
                i += 1
            shutil.copy(self.input_file,
                        "{}.{}.orig".format(self.input_file, i))
            if self.chk_file and os.path.exists(self.chk_file):
                shutil.copy(self.chk_file,
                            "{}.{}.orig".format(self.chk_file, i))
            if os.path.exists(self.output_file):
                shutil.copy(self.output_file,
                            "{}.{}.orig".format(self.output_file, i))
            if self.qclog_file and os.path.exists(self.qclog_file):
                shutil.copy(self.qclog_file,
                            "{}.{}.orig".format(self.qclog_file, i))

    def run(self):
        if "edique" in os.environ["PBS_JOBID"] or "hopque" in os.environ["PBS_JOBID"]:
            tmp_creation_cmd = shlex.split("aprun -n1 -N1 mkdir /tmp/eg_qchem")
            tmp_clean_cmd = shlex.split("aprun -n1 -N1 rm -rf /tmp/eg_qchem")
        else:
            tmp_clean_cmd = None
            tmp_creation_cmd = None
        cmd = copy.deepcopy(self.current_command)
        cmd += [self.input_file, self.output_file]
        if self.chk_file:
            cmd.append(self.chk_file)
        if self.qclog_file:
            with open(self.qclog_file, "w") as filelog:
                subprocess.call(tmp_clean_cmd, stdout=filelog)
                subprocess.call(tmp_creation_cmd, stdout=filelog)
                returncode = subprocess.call(cmd, stdout=filelog)
                subprocess.call(tmp_clean_cmd, stdout=filelog)
        else:
            returncode = subprocess.call(cmd)
        return returncode

    def postprocess(self):
        if self.gzipped:
            if "edique" in os.environ["PBS_JOBID"] or "hopque" in os.environ["PBS_JOBID"]:
                cur_dir = os.getcwd()
                file_list = [os.path.join(cur_dir, name) for name in glob.glob("*")]
                gzip_cmd = shlex.split("aprun -n1 -N1 gzip") + file_list
                subprocess.call(gzip_cmd)
            else:
                gzip_dir(".")

# coding: utf-8

from __future__ import unicode_literals, division
import glob
import shlex

"""
This module implements basic kinds of jobs for QChem runs.
"""

import os
from monty.io import zopen
import shutil
import copy
import subprocess
from pymatgen.io.qchemio import QcInput
from custodian.custodian import Job, gzip_dir

__author__ = "<NAME>"
__version__ = "0.1"
__maintainer__ = "<NAME>"
__email__ = "<EMAIL>"
__status__ = "Alpha"
__date__ = "12/03/13"


class QchemJob(Job):
    """
    A basic QChem Job.
    """

    def __init__(self, qchem_cmd, input_file="mol.qcinp",
                 output_file="mol.qcout", chk_file=None, qclog_file=None,
                 gzipped=False, backup=True, alt_cmd=None,
                 large_static_mem=False):
        """
        This constructor is necessarily complex due to the need for
        flexibility. For standard kinds of runs, it's often better to use one
        of the static constructors.

        Args:
            qchem_cmd ([str]): Command to run QChem as a list args (without
                input/output file name). For example: ["qchem", "-np", "24"]
            input_file (str): Name of the QChem input file.
            output_file (str): Name of the QChem output file.
            chk_file (str): Name of the QChem check point file. None means no
                checkpoint point file. Defaults to None.
            qclog_file (str): Name of the file to redirect the standard output
                to. None means not to record the standard output. Defaults to
                None.
            gzipped (bool): Whether to gzip the final output. Defaults to False.
            backup (bool): Whether to backup the initial input files. If True,
                the input files will be copied with a ".orig" appended.
                Defaults to True.
            alt_cmd (dict of list): Alternate commands.
                For example: {"openmp": ["qchem", "-seq", "-nt", "24"]
                              "half_cpus": ["qchem", "-np", "12"]}
            large_static_mem: use ultra large static memory
        """
        self.qchem_cmd = copy.deepcopy(qchem_cmd)
        self.input_file = input_file
        self.output_file = output_file
        self.chk_file = chk_file
        self.qclog_file = qclog_file
        self.gzipped = gzipped
        self.backup = backup
        self.current_command = self.qchem_cmd
        self.current_command_name = "general"
        self.large_static_mem = large_static_mem
        self._set_qchem_memory()
        self.alt_cmd = copy.deepcopy(alt_cmd)

    def _set_qchem_memory(self, qcinp=None):
        if not qcinp:
            qcinp = QcInput.from_file(self.input_file)
        if "PBS_JOBID" in os.environ:
            if "hopque" in os.environ["PBS_JOBID"]:
                # on Hopper
                for j in qcinp.jobs:
                    if self.current_command_name == "general":
                        if self.large_static_mem:
                            j.set_memory(total=1100, static=300)
                        else:
                            j.set_memory(total=1100, static=100)
                    elif self.current_command_name == "half_cpus":
                        if self.large_static_mem:
                            j.set_memory(total=2200, static=500)
                        else:
                            j.set_memory(total=2200, static=100)
                    elif self.current_command_name == "openmp":
                        if self.large_static_mem:
                            j.set_memory(total=28000, static=10000)
                        else:
                            j.set_memory(total=28000, static=3000)
            elif "edique" in os.environ["PBS_JOBID"]:
                # on Edison
                for j in qcinp.jobs:
                    if self.current_command_name == "general":
                        if self.large_static_mem:
                            j.set_memory(total=2500, static=500)
                        else:
                            j.set_memory(total=2500, static=100)
                    elif self.current_command_name == "half_cpus":
                        if self.large_static_mem:
                            j.set_memory(total=5000, static=1000)
                        else:
                            j.set_memory(total=5000, static=200)
                    elif self.current_command_name == "openmp":
                        if self.large_static_mem:
                            j.set_memory(total=60000, static=20000)
                        else:
                            j.set_memory(total=60000, static=5000)
        qcinp.write_file(self.input_file)

    def select_command(self, cmd_name, qcinp=None):
        """
        Set the command to run QChem by name. "general" set to the default one.
            Args:
                cmd_name: the command name to change to.
                qcinp: the QcInput object to operate on.

        Returns:
            True: success
            False: failed
        """
        available_commands = ["general"]
        if self.alt_cmd:
            available_commands.extend(self.alt_cmd.keys())
        if cmd_name not in available_commands:
            raise Exception("Command mode \"", cmd_name, "\" is not available")
        if cmd_name == "general":
            self.current_command = self.qchem_cmd
        else:
            self.current_command = self.alt_cmd[cmd_name]
        self.current_command_name = cmd_name
        self._set_qchem_memory(qcinp)
        return True

    def setup(self):
        if self.backup:
            i = 0
            while os.path.exists("{}.{}.orig".format(self.input_file, i)):
                i += 1
            shutil.copy(self.input_file,
                        "{}.{}.orig".format(self.input_file, i))
            if self.chk_file and os.path.exists(self.chk_file):
                shutil.copy(self.chk_file,
                            "{}.{}.orig".format(self.chk_file, i))
            if os.path.exists(self.output_file):
                shutil.copy(self.output_file,
                            "{}.{}.orig".format(self.output_file, i))
            if self.qclog_file and os.path.exists(self.qclog_file):
                shutil.copy(self.qclog_file,
                            "{}.{}.orig".format(self.qclog_file, i))

    def run(self):
        if "edique" in os.environ["PBS_JOBID"] or "hopque" in os.environ["PBS_JOBID"]:
            tmp_creation_cmd = shlex.split("aprun -n1 -N1 mkdir /tmp/eg_qchem")
            tmp_clean_cmd = shlex.split("aprun -n1 -N1 rm -rf /tmp/eg_qchem")
        else:
            tmp_clean_cmd = None
            tmp_creation_cmd = None
        cmd = copy.deepcopy(self.current_command)
        cmd += [self.input_file, self.output_file]
        if self.chk_file:
            cmd.append(self.chk_file)
        if self.qclog_file:
            with open(self.qclog_file, "w") as filelog:
                subprocess.call(tmp_clean_cmd, stdout=filelog)
                subprocess.call(tmp_creation_cmd, stdout=filelog)
                returncode = subprocess.call(cmd, stdout=filelog)
                subprocess.call(tmp_clean_cmd, stdout=filelog)
        else:
            returncode = subprocess.call(cmd)
        return returncode

    def postprocess(self):
        if self.gzipped:
            if "edique" in os.environ["PBS_JOBID"] or "hopque" in os.environ["PBS_JOBID"]:
                cur_dir = os.getcwd()
                file_list = [os.path.join(cur_dir, name) for name in glob.glob("*")]
                gzip_cmd = shlex.split("aprun -n1 -N1 gzip") + file_list
                subprocess.call(gzip_cmd)
            else:
                gzip_dir(".")
# coding: utf-8 This module implements basic kinds of jobs for QChem runs. A basic QChem Job. This constructor is necessarily complex due to the need for         flexibility. For standard kinds of runs, it's often better to use one         of the static constructors.          Args:             qchem_cmd ([str]): Command to run QChem as a list args (without                 input/output file name). For example: ["qchem", "-np", "24"]             input_file (str): Name of the QChem input file.             output_file (str): Name of the QChem output file.             chk_file (str): Name of the QChem check point file. None means no                 checkpoint point file. Defaults to None.             qclog_file (str): Name of the file to redirect the standard output                 to. None means not to record the standard output. Defaults to                 None.             gzipped (bool): Whether to gzip the final output. Defaults to False.             backup (bool): Whether to backup the initial input files. If True,                 the input files will be copied with a ".orig" appended.                 Defaults to True.             alt_cmd (dict of list): Alternate commands.                 For example: {"openmp": ["qchem", "-seq", "-nt", "24"]                               "half_cpus": ["qchem", "-np", "12"]}             large_static_mem: use ultra large static memory # on Hopper # on Edison Set the command to run QChem by name. "general" set to the default one.             Args:                 cmd_name: the command name to change to.                 qcinp: the QcInput object to operate on.          Returns:             True: success             False: failed