def functional(indiv, outdir=None, value=False, **kwargs):
from pylada.misc import local_path
from pickle import dump
outdir = local_path(outdir)
outdir.ensure(dir=True)
dump((indiv, value), outdir.join('OUTCAR').open('wb'))
return Extract(str(outdir))
def functional(indiv, outdir=None, value=False, **kwargs):
from pylada.misc import local_path
from pickle import dump
outdir = local_path(outdir)
outdir.ensure(dir=True)
dump((indiv, value), outdir.join('OUTCAR').open('wb'))
return Extract(str(outdir))
def completer(self, event):
""" Completer for %record magic function. """
from pylada.misc import local_path
from pickle import load
from os.path import isdir, exists
result = []
data = event.line.split()[1:]
if (len(event.symbol) == 0 and len(data) > 0 and data[-1] == "--n") \
or (len(event.symbol) > 0 and len(data) > 1 and data[-2] == "--n") \
or (len(event.symbol) == 0 and len(data) > 0 and data[-1] == "--namespace") \
or (len(event.symbol) > 0 and len(data) > 1 and data[-2] == "--namespace"):
return [key for key, value in self.api.user_ns.items()
if key[0] != '_' and hasattr(value, '__dict__')]
if (len(event.symbol) == 0 and len(data) > 0 and data[-1] == "--file") \
or (len(event.symbol) > 0 and len(data) > 1 and data[-2] == "--file"):
other = event.symbol
string = '%mglob "cont:This is a record." {0}*'.format(other)
result = [u for u in self.api.magic(string)]
string = '%mglob dir:{0}*'.format(other)
result.extend([u for u in self.api.magic(string)])
if isdir(other) and other[-1] != '/':
string = '%mglob "cont:This is a record." {0}/*'.format(other)
result.extend([u for u in self.api.magic(string)])
return result
if '--file' not in data:
result.append('--file')
options = {'--list', '--view', '--load', '--remove', '--update'}
if '-n' in data or '--namespace' in data and '--load' not in data:
result.append('--load')
elif '--load' in data and '-n' not in data and '--namespace' not in data:
result.append('--namespace')
elif len(options.intersection(set(data))) == 0:
result.extend(['--list', '--view', '--load', '--remove', '--namespace', '--update'])
if len(set(['--load', '--remove', '--view']).intersection(set(data))) != 0:
path = '.pylada_record'
known = [u for u in data]
if '--file' in data:
index = data.index('--file')
assert len(data) > index + 1
path = str(local_path(data[index + 1]))
known.pop(index + 1)
if exists(path):
with open(path) as file:
keys = load(file)
if '--namespace' in known:
index = known.index('--namespace')
if len(known) > index + 1:
known.pop(index + 1)
if '-n' in known:
index = known.index('-n')
if len(known) > index + 1:
known.pop(index + 1)
result.extend(keys - set(known))
else:
result.extend([u for u in self.api.user_ns.keys() if u[0] != '_'])
return result
def call_functional(indiv, outdir=None, value=False, **kwargs):
from pylada.misc import local_path
from pickle import dump
path = local_path(outdir)
path.ensure(dir=True)
dump((indiv, value), path.join("OUTCAR").open("wb"))
return Extract(outdir)
def run_with_restart(outdir="restarting"):
""" Example of running relaxation with cell-shape """
from pylada.misc import local_path
from numpy.random import random
outdir = local_path(outdir)
structure = diamond_structure()
pwscf = diamond_pwscf()
structure[1].pos += random(3) * 0.01 - 0.005
structure.cell += random((3, 3)) * 0.01 - 0.005
pwscf.control.calculation = 'vc-relax'
pwscf.cell.factor = 2.0
result = pwscf(structure, outdir=outdir.join('first'))
result = pwscf(structure, outdir=outdir.join('second'), restart=result)
def functional(structure, outdir=None, value=False, **kwargs):
""" A dummy functional """
from copy import deepcopy
from pickle import dump
from random import random
from pylada.misc import local_path
structure = deepcopy(structure)
structure.value = value
outdir = local_path(outdir)
outdir.ensure(dir=True)
dump((random(), structure, value, functional), outdir.join('OUTCAR').open('wb'))
return Extract(outdir)
return structure
def Extract(outdir=None):
""" An extraction function for a dummy functional """
from os import getcwd
from collections import namedtuple
from pickle import load
from pylada.misc import local_path
if outdir == None:
outdir = getcwd()
Extract = namedtuple('Extract', ['success', 'directory',
'energy', 'structure', 'value', 'functional'])
outdir = local_path(outdir)
if not outdir.check():
return Extract(False, str(outdir), None, None, None, None)
if not outdir.join('OUTCAR').check(file=True):
return Extract(False, str(outdir), None, None, None, None)
with local_path.join('OUTCAR').open('r') as file:
structure, energy, value, functional = load(file)
return Extract(True, outdir, energy, structure, value, functional)
def Extract(outdir=None):
from os.path import exists
from os import getcwd
from collections import namedtuple
from pickle import load
from pylada.misc import local_path
if outdir == None:
outdir = getcwd()
Extract = namedtuple('Extract', ['success', 'directory', 'indiv', 'functional'])
if not exists(outdir):
return Extract(False, outdir, None, functional)
outdir = local_path(outdir)
if not outdir.join('OUTCAR').check(file=True):
return Extract(False, str(outdir), None, functional)
indiv, value = load(outdir.join('OUTCAR').open('rb'))
return Extract(True, outdir, indiv, functional)
def Extract(outdir=None):
from os.path import exists
from os import getcwd
from collections import namedtuple
from pickle import load
from pylada.misc import local_path
if outdir == None:
outdir = getcwd()
Extract = namedtuple('Extract',
['success', 'directory', 'indiv', 'functional'])
if not exists(outdir):
return Extract(False, outdir, None, functional)
outdir = local_path(outdir)
if not outdir.join('OUTCAR').check(file=True):
return Extract(False, str(outdir), None, functional)
indiv, value = load(outdir.join('OUTCAR').open('rb'))
return Extract(True, outdir, indiv, functional)
def Extract(outdir=None):
from os.path import exists
from os import getcwd
from collections import namedtuple
from pickle import load
from pylada.misc import local_path
if outdir == None:
outdir = getcwd()
Extract = namedtuple("Extract",
["success", "directory", "indiv", "functional"])
if not exists(outdir):
return Extract(False, outdir, None, functional)
outdir = local_path(outdir)
if not outdir.join("OUTCAR").check(file=True):
return Extract(False, str(outdir), None, functional)
indiv, value = load(outdir.join("OUTCAR").open("rb"))
return Extract(True, outdir, indiv, functional_call)
def __init__(self, directory):
from pylada.misc import local_path
self.directory = str(local_path(directory))
def test_icharg():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR, CHGCAR
from pylada.vasp import Vasp
from pylada.misc import local_path
from pylada.error import ValueError
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['icharg']
d = {'ICharg': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory):
rmtree(directory)
makedirs(directory)
try:
assert a.icharg == 'auto'
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
local_path(restartdir).ensure(dir=True)
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# do not copy if empty
with open(join(restartdir, CHGCAR), 'w') as file:
pass
with open(join(restartdir, WAVECAR), 'w') as file:
pass
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# now copy only CHGCAR
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy only CHGCAR with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '11'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy both
a.nonscf = False
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now copy both with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '10'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now check that latest is copied
remove(join(restartdir, CHGCAR))
remove(join(directory, CHGCAR))
sleep(1.2)
with open(join(directory, WAVECAR), 'w') as file:
file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file:
pass # Buffering issues..
a.nonscf = False
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello'
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello world'
# makes sure requests are honored
# tries request. Should fail since CHGCAR does not exist.
remove(join(directory, WAVECAR))
a.icharg = 'chgcar'
assert a.icharg == 'chgcar'
try:
o.output_map(vasp=a, outdir=directory)
except ValueError:
pass
else:
raise Exception()
# now try for gold.
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
assert eval(repr(o), d).value == 'chgcar'
assert loads(dumps(o)).value == 'chgcar'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
def launch_program(cmdl, comm=None, formatter=None, env=None,
stdout=None, stderr=None, stdin=None, outdir=None):
""" Command used to launch a program.
This function launches external programs for Pylada. It is included as a
global so that it can be adapted to different computing environment. It
also makes it easier to debug Pylada's mpi configuration when installing on
a new machine.
.. note::
The number one configuration problem is an incorrect
:py:data:`~pylada.mpirun_exe`.
.. note::
The number two configuration problem is mpi-placement (eg how to launch
two different mpi program simultaneously in one PBS/SLURM job). First
read the manual for the mpi environment on the particular machine Pylada
is installed on. Then adapt
:py:function:`~pylada.machine_dependent_call_modifier` by redeclaring it
in $HOME/.pylada.
:param str cmld:
Command-line string. It will be formatted using ``formatter`` or
``comm`` if either are present. Otherwise, it should be exactly the
(bash) command-prompt.
:param comm:
Should contain everythin needed to launch an mpi call.
In practice, it is copied from :py:data:`~pylada.default_comm` and
modified for the purpose of a particular call (e.g. could use fewer
than all available procs)
:type comm: :py:class:`~pylada.process.mpi.Communicator`
:param dict formatter:
Dictionary with which to format the communicator. If ``comm`` is
present, then it will be updated with ``comm``'s input.
:param dict env:
Dictionary containing the environment variables in which to do call.
:param stdout:
File object to which to hook-up the standard output. See Popen_.
:param stderr:
File object to which to hook-up the standard error. See Popen_.
:param str outdir:
Path to the working directory.
.. _Popen:: http://docs.python.org/library/subprocess.html#popen-constructor
"""
from shlex import split as shlex_split
from subprocess import Popen
from pylada import machine_dependent_call_modifier
from pylada.misc import local_path
# At this point formatter is {"program": vasp}
# and cmdl is "mpirun -n {n} {placement} {program}"
# Set in formatter: 'placement': '', 'ppn': 8, 'n': 8
# make sure that the formatter contains stuff from the communicator, eg the
# number of processes.
if comm is not None and formatter is not None:
formatter.update(comm)
# Set in formatter: 'placement': '-machinefile /home.../pylada_commtempfile'
# Stuff that will depend on the supercomputer.
machine_dependent_call_modifier(formatter, comm, env)
# if a formatter exists, then use it on the cmdl string.
if formatter is not None:
cmdl = cmdl.format(**formatter)
# otherwise, if comm is not None, use that.
elif comm is not None:
cmdl = cmdl.format(**comm)
# Split command from string to list
cmdl = shlex_split(cmdl)
# makes sure the directory exists:
local_path(outdir).ensure(dir=True)
# Finally, start the process.
popen = Popen(cmdl, stdout=stdout, stderr=stderr, stdin=stdin,
cwd=outdir, env=env)
popen.wait()
#if testValidProgram: popen.wait()
return popen
def test_icharg():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR, CHGCAR
from pylada.vasp import Vasp
from pylada.misc import local_path
from pylada.error import ValueError
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['icharg']
d = {'ICharg': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory):
rmtree(directory)
makedirs(directory)
try:
assert a.icharg == 'auto'
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
local_path(restartdir).ensure(dir=True)
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# do not copy if empty
with open(join(restartdir, CHGCAR), 'w') as file:
pass
with open(join(restartdir, WAVECAR), 'w') as file:
pass
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '2'
assert not exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
# now copy only CHGCAR
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy only CHGCAR with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '11'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
remove(join(directory, CHGCAR))
# now copy both
a.nonscf = False
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now copy both with scf
a.nonscf = True
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '10'
assert exists(join(directory, CHGCAR))
assert exists(join(directory, WAVECAR))
# now check that latest is copied
remove(join(restartdir, CHGCAR))
remove(join(directory, CHGCAR))
sleep(1.2)
with open(join(directory, WAVECAR), 'w') as file:
file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file:
pass # Buffering issues..
a.nonscf = False
a.restart = Extract(restartdir, True)
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello'
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '0'
assert exists(join(directory, WAVECAR))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() != 'hello world'
# makes sure requests are honored
# tries request. Should fail since CHGCAR does not exist.
remove(join(directory, WAVECAR))
a.icharg = 'chgcar'
assert a.icharg == 'chgcar'
try:
o.output_map(vasp=a, outdir=directory)
except ValueError:
pass
else:
raise Exception()
# now try for gold.
with open(join(restartdir, CHGCAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['icharg'] == '1'
assert exists(join(directory, CHGCAR))
assert not exists(join(directory, WAVECAR))
assert eval(repr(o), d).value == 'chgcar'
assert loads(dumps(o)).value == 'chgcar'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
def test_istart():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR
from pylada.vasp import Vasp
from pylada.misc import local_path
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['istart']
d = {'IStart': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory):
rmtree(directory)
makedirs(directory)
try:
assert a.istart == 'auto'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
local_path(restartdir).ensure(dir=True)
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# do not copy if file is empty
a.restart = Extract(restartdir, True)
with open(join(restartdir, WAVECAR), 'w') as file:
pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# now should copy
assert a.istart == 'auto'
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
# check it copies only latest file.
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
file.flush()
with open(join(restartdir, WAVECAR), 'r') as file:
pass
sleep(1.5)
with open(join(directory, WAVECAR), 'w') as file:
file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file:
pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
sleep(0.2)
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
# check if scratch is required
remove(join(directory, WAVECAR))
a.istart = 'scratch'
assert a.istart == 'scratch'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'scratch'
assert loads(dumps(o)).value == 'scratch'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
def completer(self, event):
""" Completer for %record magic function. """
from pylada.misc import local_path
from pickle import load
from os.path import isdir, exists
result = []
data = event.line.split()[1:]
if (len(event.symbol) == 0 and len(data) > 0 and data[-1] == "--n") \
or (len(event.symbol) > 0 and len(data) > 1 and data[-2] == "--n") \
or (len(event.symbol) == 0 and len(data) > 0 and data[-1] == "--namespace") \
or (len(event.symbol) > 0 and len(data) > 1 and data[-2] == "--namespace"):
return [
key for key, value in self.api.user_ns.items()
if key[0] != '_' and hasattr(value, '__dict__')
]
if (len(event.symbol) == 0 and len(data) > 0 and data[-1] == "--file") \
or (len(event.symbol) > 0 and len(data) > 1 and data[-2] == "--file"):
other = event.symbol
string = '%mglob "cont:This is a record." {0}*'.format(other)
result = [u for u in self.api.magic(string)]
string = '%mglob dir:{0}*'.format(other)
result.extend([u for u in self.api.magic(string)])
if isdir(other) and other[-1] != '/':
string = '%mglob "cont:This is a record." {0}/*'.format(other)
result.extend([u for u in self.api.magic(string)])
return result
if '--file' not in data:
result.append('--file')
options = {'--list', '--view', '--load', '--remove', '--update'}
if '-n' in data or '--namespace' in data and '--load' not in data:
result.append('--load')
elif '--load' in data and '-n' not in data and '--namespace' not in data:
result.append('--namespace')
elif len(options.intersection(set(data))) == 0:
result.extend([
'--list', '--view', '--load', '--remove', '--namespace', '--update'
])
if len(set(['--load', '--remove', '--view']).intersection(set(data))) != 0:
path = '.pylada_record'
known = [u for u in data]
if '--file' in data:
index = data.index('--file')
assert len(data) > index + 1
path = str(local_path(data[index + 1]))
known.pop(index + 1)
if exists(path):
with open(path) as file:
keys = load(file)
if '--namespace' in known:
index = known.index('--namespace')
if len(known) > index + 1:
known.pop(index + 1)
if '-n' in known:
index = known.index('-n')
if len(known) > index + 1:
known.pop(index + 1)
result.extend(keys - set(known))
else:
result.extend([u for u in self.api.user_ns.keys() if u[0] != '_'])
return result
def test_istart():
from time import sleep
from collections import namedtuple
from pickle import loads, dumps
from os import remove, makedirs
from os.path import join, exists
from shutil import rmtree
from tempfile import mkdtemp
from pylada.vasp.files import WAVECAR
from pylada.vasp import Vasp
from pylada.misc import local_path
Extract = namedtuple("Extract", ['directory', 'success'])
a = Vasp()
o = a._input['istart']
d = {'IStart': o.__class__}
directory = mkdtemp()
if directory in ['/tmp/test', '/tmp/test/']:
if exists(directory):
rmtree(directory)
makedirs(directory)
try:
assert a.istart == 'auto'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'auto'
assert loads(dumps(o)).value == 'auto'
restartdir = join(directory, 'restart')
local_path(restartdir).ensure(dir=True)
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
# do not copy if not successful
a.restart = Extract(restartdir, False)
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# do not copy if file is empty
a.restart = Extract(restartdir, True)
with open(join(restartdir, WAVECAR), 'w') as file:
pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert not exists(join(directory, 'WAVECAR'))
# now should copy
assert a.istart == 'auto'
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
# check it copies only latest file.
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
file.flush()
with open(join(restartdir, WAVECAR), 'r') as file:
pass
sleep(1.5)
with open(join(directory, WAVECAR), 'w') as file:
file.write('hello world')
with open(join(directory, WAVECAR), 'r') as file:
pass
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello world'
sleep(0.2)
with open(join(restartdir, WAVECAR), 'w') as file:
file.write('hello')
assert o.output_map(vasp=a, outdir=directory)['istart'] == '1'
assert exists(join(directory, 'WAVECAR'))
with open(join(directory, WAVECAR), 'r') as file:
assert file.read().rstrip().lstrip() == 'hello'
# check if scratch is required
remove(join(directory, WAVECAR))
a.istart = 'scratch'
assert a.istart == 'scratch'
assert o.output_map(vasp=a, outdir=directory)['istart'] == '0'
assert eval(repr(o), d).value == 'scratch'
assert loads(dumps(o)).value == 'scratch'
finally:
if directory not in ['/tmp/test', '/tmp/test/'] and exists(directory):
rmtree(directory)
def __init__(self, directory):
from pylada.misc import local_path
self.directory = str(local_path(directory))
def launch_program(cmdl,
comm=None,
formatter=None,
env=None,
stdout=None,
stderr=None,
stdin=None,
outdir=None):
""" Command used to launch a program.
This function launches external programs for Pylada. It is included as a
global so that it can be adapted to different computing environment. It
also makes it easier to debug Pylada's mpi configuration when installing on
a new machine.
.. note::
The number one configuration problem is an incorrect
:py:data:`~pylada.mpirun_exe`.
.. note::
The number two configuration problem is mpi-placement (eg how to launch
two different mpi program simultaneously in one PBS/SLURM job). First
read the manual for the mpi environment on the particular machine Pylada
is installed on. Then adapt
:py:function:`~pylada.machine_dependent_call_modifier` by redeclaring it
in $HOME/.pylada.
:param str cmld:
Command-line string. It will be formatted using ``formatter`` or
``comm`` if either are present. Otherwise, it should be exactly the
(bash) command-prompt.
:param comm:
Should contain everythin needed to launch an mpi call.
In practice, it is copied from :py:data:`~pylada.default_comm` and
modified for the purpose of a particular call (e.g. could use fewer
than all available procs)
:type comm: :py:class:`~pylada.process.mpi.Communicator`
:param dict formatter:
Dictionary with which to format the communicator. If ``comm`` is
present, then it will be updated with ``comm``'s input.
:param dict env:
Dictionary containing the environment variables in which to do call.
:param stdout:
File object to which to hook-up the standard output. See Popen_.
:param stderr:
File object to which to hook-up the standard error. See Popen_.
:param str outdir:
Path to the working directory.
.. _Popen:: http://docs.python.org/library/subprocess.html#popen-constructor
"""
from shlex import split as shlex_split
from subprocess import Popen
from pylada import machine_dependent_call_modifier
from pylada.misc import local_path
# At this point formatter is {"program": vasp}
# and cmdl is "mpirun -n {n} {placement} {program}"
# Set in formatter: 'placement': '', 'ppn': 8, 'n': 8
# make sure that the formatter contains stuff from the communicator, eg the
# number of processes.
if comm is not None and formatter is not None:
formatter.update(comm)
# Set in formatter: 'placement': '-machinefile /home.../pylada_commtempfile'
# Stuff that will depend on the supercomputer.
machine_dependent_call_modifier(formatter, comm, env)
# if a formatter exists, then use it on the cmdl string.
if formatter is not None:
cmdl = cmdl.format(**formatter)
# otherwise, if comm is not None, use that.
elif comm is not None:
cmdl = cmdl.format(**comm)
# Split command from string to list
cmdl = shlex_split(cmdl)
# makes sure the directory exists:
local_path(outdir).ensure(dir=True)
# Finally, start the process.
popen = Popen(cmdl,
stdout=stdout,
stderr=stderr,
stdin=stdin,
cwd=outdir,
env=env)
popen.wait()
#if testValidProgram: popen.wait()
return popen
