Warning
This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.
Source code for cwltool.job
from __future__ import absolute_import
import datetime
import functools
import itertools
import logging
import threading
import os
import re
import shutil
import stat
import sys
import tempfile
import time
import uuid
from abc import ABCMeta, abstractmethod
from io import IOBase, open # pylint: disable=redefined-builtin
from threading import Timer
from typing import (IO, Any, AnyStr, Callable, Dict, Iterable, List, Tuple,
MutableMapping, MutableSequence, Optional, Union, cast)
import psutil
import shellescape
from prov.model import PROV
from schema_salad.sourceline import SourceLine
from six import PY2, with_metaclass
from future.utils import raise_from
from typing_extensions import (TYPE_CHECKING, # pylint: disable=unused-import
Text)
from .builder import Builder, HasReqsHints # pylint: disable=unused-import
from .context import RuntimeContext # pylint: disable=unused-import
from .context import getdefault
from .errors import WorkflowException
from .expression import JSON
from .loghandler import _logger
from .pathmapper import (MapperEnt, PathMapper, # pylint: disable=unused-import
ensure_writable, ensure_non_writable)
from .process import UnsupportedRequirement, stage_files
from .secrets import SecretStore # pylint: disable=unused-import
from .utils import (DEFAULT_TMP_PREFIX, Directory, bytes2str_in_dicts,
copytree_with_merge, json_dump, json_dumps, onWindows,
processes_to_kill, subprocess)
if TYPE_CHECKING:
from .provenance import ProvenanceProfile # pylint: disable=unused-import
needs_shell_quoting_re = re.compile(r"""(^$|[\s|&;()<>\'"$@])""")
FORCE_SHELLED_POPEN = os.getenv("CWLTOOL_FORCE_SHELL_POPEN", "0") == "1"
SHELL_COMMAND_TEMPLATE = u"""#!/bin/bash
python "run_job.py" "job.json"
"""
PYTHON_RUN_SCRIPT = u"""
import json
import os
import sys
if os.name == 'posix':
try:
import subprocess32 as subprocess # type: ignore
except Exception:
import subprocess
else:
import subprocess # type: ignore
with open(sys.argv[1], "r") as f:
popen_description = json.load(f)
commands = popen_description["commands"]
cwd = popen_description["cwd"]
env = popen_description["env"]
env["PATH"] = os.environ.get("PATH")
stdin_path = popen_description["stdin_path"]
stdout_path = popen_description["stdout_path"]
stderr_path = popen_description["stderr_path"]
if stdin_path is not None:
stdin = open(stdin_path, "rb")
else:
stdin = subprocess.PIPE
if stdout_path is not None:
stdout = open(stdout_path, "wb")
else:
stdout = sys.stderr
if stderr_path is not None:
stderr = open(stderr_path, "wb")
else:
stderr = sys.stderr
if os.name == 'nt':
close_fds = False
for key, value in env.items():
env[key] = str(value)
else:
close_fds = True
sp = subprocess.Popen(commands,
shell=False,
close_fds=close_fds,
stdin=stdin,
stdout=stdout,
stderr=stderr,
env=env,
cwd=cwd)
if sp.stdin:
sp.stdin.close()
rcode = sp.wait()
if stdin is not subprocess.PIPE:
stdin.close()
if stdout is not sys.stderr:
stdout.close()
if stderr is not sys.stderr:
stderr.close()
sys.exit(rcode)
"""
def deref_links(outputs): # type: (Any) -> None
if isinstance(outputs, MutableMapping):
if outputs.get("class") == "File":
st = os.lstat(outputs["path"])
if stat.S_ISLNK(st.st_mode):
outputs["basename"] = os.path.basename(outputs["path"])
outputs["path"] = os.readlink(outputs["path"])
else:
for v in outputs.values():
deref_links(v)
if isinstance(outputs, MutableSequence):
for output in outputs:
deref_links(output)
[docs]def relink_initialworkdir(pathmapper, # type: PathMapper
host_outdir, # type: Text
container_outdir, # type: Text
inplace_update=False # type: bool
): # type: (...) -> None
for _, vol in pathmapper.items():
if not vol.staged:
continue
if (vol.type in ("File", "Directory") or (
inplace_update and vol.type in
("WritableFile", "WritableDirectory"))):
if not vol.target.startswith(container_outdir):
# this is an input file written outside of the working
# directory, so therefor ineligable for being an output file.
# Thus, none of our business
continue
host_outdir_tgt = os.path.join(
host_outdir, vol.target[len(container_outdir) + 1:])
if os.path.islink(host_outdir_tgt) \
or os.path.isfile(host_outdir_tgt):
os.remove(host_outdir_tgt)
elif os.path.isdir(host_outdir_tgt) \
and not vol.resolved.startswith("_:"):
shutil.rmtree(host_outdir_tgt)
if onWindows():
# If this becomes a big issue for someone then we could
# refactor the code to process output from a running container
# and avoid all the extra IO below
if vol.type in ("File", "WritableFile"):
shutil.copy(vol.resolved, host_outdir_tgt)
elif vol.type in ("Directory", "WritableDirectory"):
copytree_with_merge(vol.resolved, host_outdir_tgt)
elif not vol.resolved.startswith("_:"):
os.symlink(vol.resolved, host_outdir_tgt)
class JobBase(with_metaclass(ABCMeta, HasReqsHints)):
def __init__(self,
builder, # type: Builder
joborder, # type: JSON
make_path_mapper, # type: Callable[..., PathMapper]
requirements, # type: List[Dict[Text, Text]]
hints, # type: List[Dict[Text, Text]]
name, # type: Text
): # type: (...) -> None
"""Initialize the job object."""
self.builder = builder
self.joborder = joborder
self.stdin = None # type: Optional[Text]
self.stderr = None # type: Optional[Text]
self.stdout = None # type: Optional[Text]
self.successCodes = [] # type: Iterable[int]
self.temporaryFailCodes = [] # type: Iterable[int]
self.permanentFailCodes = [] # type: Iterable[int]
self.requirements = requirements
self.hints = hints
self.name = name
self.command_line = [] # type: List[Text]
self.pathmapper = PathMapper([], u"", u"")
self.make_path_mapper = make_path_mapper
self.generatemapper = None # type: Optional[PathMapper]
# set in CommandLineTool.job(i)
self.collect_outputs = cast(Callable[[Text, int], MutableMapping[Text, Any]],
None) # type: Union[Callable[[Text, int], MutableMapping[Text, Any]], functools.partial[MutableMapping[Text, Any]]]
self.output_callback = cast(Callable[[Any, Any], Any], None)
self.outdir = u""
self.tmpdir = u""
self.environment = {} # type: MutableMapping[Text, Text]
self.generatefiles = {"class": "Directory", "listing": [], "basename": ""} # type: Directory
self.stagedir = None # type: Optional[Text]
self.inplace_update = False
self.prov_obj = None # type: Optional[ProvenanceProfile]
self.parent_wf = None # type: Optional[ProvenanceProfile]
self.timelimit = None # type: Optional[int]
self.networkaccess = False # type: bool
def __repr__(self): # type: () -> str
"""Represent this Job object."""
return "CommandLineJob(%s)" % self.name
@abstractmethod
def run(self,
runtimeContext, # type: RuntimeContext
tmpdir_lock=None # type: Optional[threading.Lock]
): # type: (...) -> None
pass
def _setup(self, runtimeContext): # type: (RuntimeContext) -> None
if not os.path.exists(self.outdir):
os.makedirs(self.outdir)
for knownfile in self.pathmapper.files():
p = self.pathmapper.mapper(knownfile)
if p.type == "File" and not os.path.isfile(p[0]) and p.staged:
raise WorkflowException(
u"Input file %s (at %s) not found or is not a regular "
"file." % (knownfile, self.pathmapper.mapper(knownfile)[0]))
if 'listing' in self.generatefiles:
runtimeContext = runtimeContext.copy()
runtimeContext.outdir = self.outdir
self.generatemapper = self.make_path_mapper(
cast(List[Any], self.generatefiles["listing"]),
self.builder.outdir, runtimeContext, False)
if _logger.isEnabledFor(logging.DEBUG):
_logger.debug(
u"[job %s] initial work dir %s", self.name,
json_dumps({p: self.generatemapper.mapper(p)
for p in self.generatemapper.files()}, indent=4))
def _execute(self,
runtime, # type: List[Text]
env, # type: MutableMapping[Text, Text]
runtimeContext, # type: RuntimeContext
monitor_function=None, # type: Optional[Callable[[subprocess.Popen], None]]
): # type: (...) -> None
scr, _ = self.get_requirement("ShellCommandRequirement")
shouldquote = needs_shell_quoting_re.search # type: Callable[[Any], Any]
if scr is not None:
shouldquote = lambda x: False
_logger.info(u"[job %s] %s$ %s%s%s%s",
self.name,
self.outdir,
" \\\n ".join([shellescape.quote(Text(arg)) if shouldquote(Text(arg)) else Text(arg) for arg in
(runtime + self.command_line)]),
u' < %s' % self.stdin if self.stdin else '',
u' > %s' % os.path.join(self.outdir, self.stdout) if self.stdout else '',
u' 2> %s' % os.path.join(self.outdir, self.stderr) if self.stderr else '')
if self.joborder is not None and runtimeContext.research_obj is not None:
job_order = self.joborder
if runtimeContext.process_run_id is not None \
and runtimeContext.prov_obj is not None and isinstance(job_order, (list, dict)):
runtimeContext.prov_obj.used_artefacts(
job_order, runtimeContext.process_run_id, str(self.name))
else:
_logger.warning("research_obj set but one of process_run_id "
"or prov_obj is missing from runtimeContext: "
"{}". format(runtimeContext))
outputs = {} # type: MutableMapping[Text,Any]
try:
stdin_path = None
if self.stdin is not None:
rmap = self.pathmapper.reversemap(self.stdin)
if rmap is None:
raise WorkflowException(
"{} missing from pathmapper".format(self.stdin))
else:
stdin_path = rmap[1]
stderr_path = None
if self.stderr is not None:
abserr = os.path.join(self.outdir, self.stderr)
dnerr = os.path.dirname(abserr)
if dnerr and not os.path.exists(dnerr):
os.makedirs(dnerr)
stderr_path = abserr
stdout_path = None
if self.stdout is not None:
absout = os.path.join(self.outdir, self.stdout)
dnout = os.path.dirname(absout)
if dnout and not os.path.exists(dnout):
os.makedirs(dnout)
stdout_path = absout
commands = [Text(x) for x in runtime + self.command_line]
if runtimeContext.secret_store is not None:
commands = runtimeContext.secret_store.retrieve(commands)
env = runtimeContext.secret_store.retrieve(env)
job_script_contents = None # type: Optional[Text]
builder = getattr(self, "builder", None) # type: Builder
if builder is not None:
job_script_contents = builder.build_job_script(commands)
rcode = _job_popen(
commands,
stdin_path=stdin_path,
stdout_path=stdout_path,
stderr_path=stderr_path,
env=env,
cwd=self.outdir,
job_dir=tempfile.mkdtemp(prefix=getdefault(runtimeContext.tmp_outdir_prefix, DEFAULT_TMP_PREFIX)),
job_script_contents=job_script_contents,
timelimit=self.timelimit,
name=self.name,
monitor_function=monitor_function
)
if rcode in self.successCodes:
processStatus = "success"
elif rcode in self.temporaryFailCodes:
processStatus = "temporaryFail"
elif rcode in self.permanentFailCodes:
processStatus = "permanentFail"
elif rcode == 0:
processStatus = "success"
else:
processStatus = "permanentFail"
if 'listing' in self.generatefiles:
if self.generatemapper:
relink_initialworkdir(
self.generatemapper, self.outdir, self.builder.outdir,
inplace_update=self.inplace_update)
else:
raise ValueError("'lsiting' in self.generatefiles but no "
"generatemapper was setup.")
outputs = self.collect_outputs(self.outdir, rcode)
outputs = bytes2str_in_dicts(outputs) # type: ignore
except OSError as e:
if e.errno == 2:
if runtime:
_logger.error(u"'%s' not found: %s", runtime[0], Text(e))
else:
_logger.error(u"'%s' not found: %s", self.command_line[0], Text(e))
else:
_logger.exception(u"Exception while running job")
processStatus = "permanentFail"
except WorkflowException as err:
_logger.error(u"[job %s] Job error:\n%s", self.name, Text(err))
processStatus = "permanentFail"
except Exception as e:
_logger.exception(u"Exception while running job")
processStatus = "permanentFail"
if runtimeContext.research_obj is not None \
and self.prov_obj is not None \
and runtimeContext.process_run_id is not None:
# creating entities for the outputs produced by each step (in the provenance document)
self.prov_obj.record_process_end(str(self.name), runtimeContext.process_run_id,
outputs, datetime.datetime.now())
if processStatus != "success":
_logger.warning(u"[job %s] completed %s", self.name, processStatus)
else:
_logger.info(u"[job %s] completed %s", self.name, processStatus)
if _logger.isEnabledFor(logging.DEBUG):
_logger.debug(u"[job %s] %s", self.name,
json_dumps(outputs, indent=4))
if self.generatemapper is not None and runtimeContext.secret_store is not None:
# Delete any runtime-generated files containing secrets.
for _, p in self.generatemapper.items():
if p.type == "CreateFile":
if runtimeContext.secret_store.has_secret(p.resolved):
host_outdir = self.outdir
container_outdir = self.builder.outdir
host_outdir_tgt = p.target
if p.target.startswith(container_outdir + "/"):
host_outdir_tgt = os.path.join(
host_outdir, p.target[len(container_outdir) + 1:])
os.remove(host_outdir_tgt)
if runtimeContext.workflow_eval_lock is None:
raise WorkflowException("runtimeContext.workflow_eval_lock must not be None")
with runtimeContext.workflow_eval_lock:
self.output_callback(outputs, processStatus)
if self.stagedir is not None and os.path.exists(self.stagedir):
_logger.debug(u"[job %s] Removing input staging directory %s", self.name, self.stagedir)
shutil.rmtree(self.stagedir, True)
if runtimeContext.rm_tmpdir:
_logger.debug(u"[job %s] Removing temporary directory %s", self.name, self.tmpdir)
shutil.rmtree(self.tmpdir, True)
def process_monitor(self, sproc): # type: (subprocess.Popen) -> None
monitor = psutil.Process(sproc.pid)
memory_usage = [None] # Value must be list rather than integer to utilise pass-by-reference in python
def get_tree_mem_usage(memory_usage): # type: (List[int]) -> None
children = monitor.children()
rss = monitor.memory_info().rss
while len(children):
rss += sum([process.memory_info().rss for process in children])
children = list(itertools.chain(*[process.children() for process in children]))
if memory_usage[0] is None or rss > memory_usage[0]:
memory_usage[0] = rss
mem_tm = Timer(interval=1, function=get_tree_mem_usage, args=(memory_usage,))
mem_tm.daemon = True
mem_tm.start()
sproc.wait()
mem_tm.cancel()
if memory_usage[0] is not None:
_logger.info(u"[job %s] Max memory used: %iMiB", self.name,
round(memory_usage[0] / (2 ** 20)))
else:
_logger.debug(u"Could not collect memory usage, job ended before monitoring began.")
class CommandLineJob(JobBase):
def run(self,
runtimeContext, # type: RuntimeContext
tmpdir_lock=None # type: Optional[threading.Lock]
): # type: (...) -> None
if tmpdir_lock:
with tmpdir_lock:
if not os.path.exists(self.tmpdir):
os.makedirs(self.tmpdir)
else:
if not os.path.exists(self.tmpdir):
os.makedirs(self.tmpdir)
self._setup(runtimeContext)
env = self.environment
vars_to_preserve = runtimeContext.preserve_environment
if runtimeContext.preserve_entire_environment is not False:
vars_to_preserve = os.environ
if vars_to_preserve:
for key, value in os.environ.items():
if key in vars_to_preserve and key not in env:
# On Windows, subprocess env can't handle unicode.
env[key] = str(value) if onWindows() else value
env["HOME"] = str(self.outdir) if onWindows() else self.outdir
env["TMPDIR"] = str(self.tmpdir) if onWindows() else self.tmpdir
if "PATH" not in env:
env["PATH"] = str(os.environ["PATH"]) if onWindows() else os.environ["PATH"]
if "SYSTEMROOT" not in env and "SYSTEMROOT" in os.environ:
env["SYSTEMROOT"] = str(os.environ["SYSTEMROOT"]) if onWindows() \
else os.environ["SYSTEMROOT"]
stage_files(self.pathmapper, ignore_writable=True, symlink=True,
secret_store=runtimeContext.secret_store)
if self.generatemapper is not None:
stage_files(self.generatemapper, ignore_writable=self.inplace_update,
symlink=True, secret_store=runtimeContext.secret_store)
relink_initialworkdir(
self.generatemapper, self.outdir, self.builder.outdir,
inplace_update=self.inplace_update)
monitor_function = functools.partial(self.process_monitor)
self._execute([], env, runtimeContext, monitor_function)
CONTROL_CODE_RE = r'\x1b\[[0-9;]*[a-zA-Z]'
class ContainerCommandLineJob(with_metaclass(ABCMeta, JobBase)):
"""Commandline job using containers."""
@abstractmethod
def get_from_requirements(self,
r, # type: Dict[Text, Text]
pull_image, # type: bool
force_pull=False, # type: bool
tmp_outdir_prefix=DEFAULT_TMP_PREFIX # type: Text
): # type: (...) -> Optional[Text]
pass
@abstractmethod
def create_runtime(self,
env, # type: MutableMapping[Text, Text]
runtime_context # type: RuntimeContext
): # type: (...) -> Tuple[List[Text], Optional[Text]]
"""Return the list of commands to run the selected container engine."""
pass
@staticmethod
@abstractmethod
def append_volume(runtime, source, target, writable=False):
# type: (List[Text], Text, Text, bool) -> None
"""Add binding arguments to the runtime list."""
pass
@abstractmethod
def add_file_or_directory_volume(self,
runtime, # type: List[Text]
volume, # type: MapperEnt
host_outdir_tgt # type: Optional[Text]
): # type: (...) -> None
"""Append volume a file/dir mapping to the runtime option list."""
pass
@abstractmethod
def add_writable_file_volume(self,
runtime, # type: List[Text]
volume, # type: MapperEnt
host_outdir_tgt, # type: Optional[Text]
tmpdir_prefix # type: Text
): # type: (...) -> None
"""Append a writable file mapping to the runtime option list."""
pass
@abstractmethod
def add_writable_directory_volume(self,
runtime, # type: List[Text]
volume, # type: MapperEnt
host_outdir_tgt, # type: Optional[Text]
tmpdir_prefix # type: Text
): # type: (...) -> None
"""Append a writable directory mapping to the runtime option list."""
pass
def create_file_and_add_volume(self,
runtime, # type: List[Text]
volume, # type: MapperEnt
host_outdir_tgt, # type: Optional[Text]
secret_store, # type: Optional[SecretStore]
tmpdir_prefix # type: Text
): # type: (...) -> Text
"""Create the file and add a mapping."""
if not host_outdir_tgt:
tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
new_file = os.path.join(
tempfile.mkdtemp(prefix=tmp_prefix, dir=tmp_dir),
os.path.basename(volume.target))
writable = True if volume.type == "CreateWritableFile" else False
if secret_store:
contents = secret_store.retrieve(volume.resolved)
else:
contents = volume.resolved
dirname = os.path.dirname(host_outdir_tgt or new_file)
if not os.path.exists(dirname):
os.makedirs(dirname)
with open(host_outdir_tgt or new_file, "wb") as file_literal:
file_literal.write(contents.encode("utf-8"))
if not host_outdir_tgt:
self.append_volume(runtime, new_file, volume.target,
writable=writable)
if writable:
ensure_writable(host_outdir_tgt or new_file)
else:
ensure_non_writable(host_outdir_tgt or new_file)
return host_outdir_tgt or new_file
def add_volumes(self,
pathmapper, # type: PathMapper
runtime, # type: List[Text]
tmpdir_prefix, # type: Text
secret_store=None, # type: Optional[SecretStore]
any_path_okay=False # type: bool
): # type: (...) -> None
"""Append volume mappings to the runtime option list."""
container_outdir = self.builder.outdir
for key, vol in (itm for itm in pathmapper.items() if itm[1].staged):
host_outdir_tgt = None # type: Optional[Text]
if vol.target.startswith(container_outdir + "/"):
host_outdir_tgt = os.path.join(
self.outdir, vol.target[len(container_outdir) + 1:])
if not host_outdir_tgt and not any_path_okay:
raise WorkflowException(
"No mandatory DockerRequirement, yet path is outside "
"the designated output directory, also know as "
"$(runtime.outdir): {}".format(vol))
if vol.type in ("File", "Directory"):
self.add_file_or_directory_volume(
runtime, vol, host_outdir_tgt)
elif vol.type == "WritableFile":
self.add_writable_file_volume(
runtime, vol, host_outdir_tgt, tmpdir_prefix)
elif vol.type == "WritableDirectory":
self.add_writable_directory_volume(
runtime, vol, host_outdir_tgt, tmpdir_prefix)
elif vol.type in ["CreateFile", "CreateWritableFile"]:
new_path = self.create_file_and_add_volume(
runtime, vol, host_outdir_tgt, secret_store, tmpdir_prefix)
pathmapper.update(
key, new_path, vol.target, vol.type, vol.staged)
def run(self,
runtimeContext, # type: RuntimeContext
tmpdir_lock=None # type: Optional[threading.Lock]
): # type: (...) -> None
if tmpdir_lock:
with tmpdir_lock:
if not os.path.exists(self.tmpdir):
os.makedirs(self.tmpdir)
else:
if not os.path.exists(self.tmpdir):
os.makedirs(self.tmpdir)
(docker_req, docker_is_req) = self.get_requirement("DockerRequirement")
self.prov_obj = runtimeContext.prov_obj
img_id = None
env = cast(MutableMapping[Text, Text], os.environ)
user_space_docker_cmd = runtimeContext.user_space_docker_cmd
if docker_req is not None and user_space_docker_cmd:
# For user-space docker implementations, a local image name or ID
# takes precedence over a network pull
if 'dockerImageId' in docker_req:
img_id = str(docker_req["dockerImageId"])
elif 'dockerPull' in docker_req:
img_id = str(docker_req["dockerPull"])
cmd = [user_space_docker_cmd, "pull", img_id]
_logger.info(Text(cmd))
try:
subprocess.check_call(cmd, stdout=sys.stderr)
except OSError:
raise WorkflowException(SourceLine(docker_req).makeError(
"Either Docker container {} is not available with "
"user space docker implementation {} or {} is missing "
"or broken.".format(img_id, user_space_docker_cmd,
user_space_docker_cmd)))
else:
raise WorkflowException(SourceLine(docker_req).makeError(
"Docker image must be specified as 'dockerImageId' or "
"'dockerPull' when using user space implementations of "
"Docker"))
else:
try:
if docker_req is not None and runtimeContext.use_container:
img_id = str(
self.get_from_requirements(
docker_req, runtimeContext.pull_image,
getdefault(runtimeContext.force_docker_pull, False),
getdefault(runtimeContext.tmp_outdir_prefix, DEFAULT_TMP_PREFIX)))
if img_id is None:
if self.builder.find_default_container:
default_container = self.builder.find_default_container()
if default_container:
img_id = str(default_container)
if docker_req is not None and img_id is None and runtimeContext.use_container:
raise Exception("Docker image not available")
if self.prov_obj is not None and img_id is not None \
and runtimeContext.process_run_id is not None:
container_agent = self.prov_obj.document.agent(
uuid.uuid4().urn,
{"prov:type": PROV["SoftwareAgent"],
"cwlprov:image": img_id,
"prov:label": "Container execution of image %s" % img_id})
# FIXME: img_id is not a sha256 id, it might just be "debian:8"
# img_entity = document.entity("nih:sha-256;%s" % img_id,
# {"prov:label": "Container image %s" % img_id} )
# The image is the plan for this activity-agent association
# document.wasAssociatedWith(process_run_ID, container_agent, img_entity)
self.prov_obj.document.wasAssociatedWith(
runtimeContext.process_run_id, container_agent)
except Exception as err:
container = "Singularity" if runtimeContext.singularity else "Docker"
_logger.debug(u"%s error", container, exc_info=True)
if docker_is_req:
raise_from(UnsupportedRequirement(
"%s is required to run this tool: %s" % (container, Text(err))), err)
else:
raise WorkflowException(
"{0} is not available for this tool, try "
"--no-container to disable {0}, or install "
"a user space Docker replacement like uDocker with "
"--user-space-docker-cmd.: {1}".format(container, err))
self._setup(runtimeContext)
(runtime, cidfile) = self.create_runtime(env, runtimeContext)
runtime.append(Text(img_id))
monitor_function = None
if cidfile:
monitor_function = functools.partial(
self.docker_monitor, cidfile, runtimeContext.tmpdir_prefix,
not bool(runtimeContext.cidfile_dir))
elif runtimeContext.user_space_docker_cmd:
monitor_function = functools.partial(self.process_monitor)
self._execute(runtime, env, runtimeContext, monitor_function)
def docker_monitor(self, cidfile, tmpdir_prefix, cleanup_cidfile, process):
# type: (Text, Text, bool, subprocess.Popen) -> None
"""Record memory usage of the running Docker container."""
# Todo: consider switching to `docker create` / `docker start`
# instead of `docker run` as `docker create` outputs the container ID
# to stdout, but the container is frozen, thus allowing us to start the
# monitoring process without dealing with the cidfile or too-fast
# container execution
cid = None
while cid is None:
time.sleep(1)
if process.returncode is not None:
if cleanup_cidfile:
try:
os.remove(cidfile)
except OSError as exc:
_logger.warn("Ignored error cleaning up Docker cidfile: %s", exc)
return
try:
with open(cidfile) as cidhandle:
cid = cidhandle.readline().strip()
except (OSError, IOError):
cid = None
max_mem = psutil.virtual_memory().total
tmp_dir, tmp_prefix = os.path.split(tmpdir_prefix)
stats_file = tempfile.NamedTemporaryFile(prefix=tmp_prefix, dir=tmp_dir)
try:
with open(stats_file.name, mode="w") as stats_file_handle:
stats_proc = subprocess.Popen(
['docker', 'stats', '--no-trunc', '--format', '{{.MemPerc}}',
cid], stdout=stats_file_handle, stderr=subprocess.DEVNULL)
process.wait()
stats_proc.kill()
except OSError as exc:
_logger.warn("Ignored error with docker stats: %s", exc)
return
max_mem_percent = 0
with open(stats_file.name, mode="r") as stats:
for line in stats:
try:
mem_percent = float(re.sub(
CONTROL_CODE_RE, '', line).replace('%', ''))
if mem_percent > max_mem_percent:
max_mem_percent = mem_percent
except ValueError:
break
_logger.info(u"[job %s] Max memory used: %iMiB", self.name,
int((max_mem_percent / 100 * max_mem) / (2 ** 20)))
if cleanup_cidfile:
os.remove(cidfile)
def _job_popen(commands, # type: List[Text]
stdin_path, # type: Optional[Text]
stdout_path, # type: Optional[Text]
stderr_path, # type: Optional[Text]
env, # type: MutableMapping[AnyStr, AnyStr]
cwd, # type: Text
job_dir, # type: Text
job_script_contents=None, # type: Optional[Text]
timelimit=None, # type: Optional[int]
name=None, # type: Optional[Text]
monitor_function=None # type: Optional[Callable[[subprocess.Popen], None]]
): # type: (...) -> int
if job_script_contents is None and not FORCE_SHELLED_POPEN:
stdin = subprocess.PIPE # type: Union[IO[Any], int]
if stdin_path is not None:
stdin = open(stdin_path, "rb")
stdout = sys.stderr # type: IO[Any]
if stdout_path is not None:
stdout = open(stdout_path, "wb")
stderr = sys.stderr # type: IO[Any]
if stderr_path is not None:
stderr = open(stderr_path, "wb")
sproc = subprocess.Popen(commands,
shell=False,
close_fds=not onWindows(),
stdin=stdin,
stdout=stdout,
stderr=stderr,
env=env,
cwd=cwd)
processes_to_kill.append(sproc)
if sproc.stdin is not None:
sproc.stdin.close()
tm = None
if timelimit is not None and timelimit > 0:
def terminate(): # type: () -> None
try:
_logger.warning(
u"[job %s] exceeded time limit of %d seconds and will"
"be terminated", name, timelimit)
sproc.terminate()
except OSError:
pass
tm = Timer(timelimit, terminate)
tm.daemon = True
tm.start()
if monitor_function:
monitor_function(sproc)
rcode = sproc.wait()
if tm is not None:
tm.cancel()
if isinstance(stdin, IOBase):
stdin.close()
if stdout is not sys.stderr:
stdout.close()
if stderr is not sys.stderr:
stderr.close()
return rcode
else:
if job_script_contents is None:
job_script_contents = SHELL_COMMAND_TEMPLATE
env_copy = {}
key = None # type: Any
for key in env:
env_copy[key] = env[key]
job_description = {
u"commands": commands,
u"cwd": cwd,
u"env": env_copy,
u"stdout_path": stdout_path,
u"stderr_path": stderr_path,
u"stdin_path": stdin_path}
if PY2:
with open(os.path.join(job_dir, "job.json"), mode="wb") as job_file:
json_dump(job_description, job_file, ensure_ascii=False)
else:
with open(os.path.join(job_dir, "job.json"), mode="w",
encoding='utf-8') as job_file:
json_dump(job_description, job_file, ensure_ascii=False)
try:
job_script = os.path.join(job_dir, "run_job.bash")
with open(job_script, "wb") as _:
_.write(job_script_contents.encode('utf-8'))
job_run = os.path.join(job_dir, "run_job.py")
with open(job_run, "wb") as _:
_.write(PYTHON_RUN_SCRIPT.encode('utf-8'))
sproc = subprocess.Popen(
["bash", job_script.encode("utf-8")],
shell=False,
cwd=job_dir,
# The nested script will output the paths to the correct files if they need
# to be captured. Else just write everything to stderr (same as above).
stdout=sys.stderr,
stderr=sys.stderr,
stdin=subprocess.PIPE,
)
processes_to_kill.append(sproc)
if sproc.stdin is not None:
sproc.stdin.close()
rcode = sproc.wait()
return rcode
finally:
shutil.rmtree(job_dir)