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Source code for cwltool.job
import datetime
import functools
import itertools
import logging
import math
import os
import re
import shutil
import signal
import stat
import subprocess # nosec
import sys
import tempfile
import threading
import time
import uuid
from abc import ABCMeta, abstractmethod
from threading import Timer
from typing import (
IO,
Callable,
Dict,
Iterable,
List,
Mapping,
Match,
MutableMapping,
MutableSequence,
Optional,
TextIO,
Tuple,
Union,
cast,
)
import psutil
import shellescape
from prov.model import PROV
from schema_salad.sourceline import SourceLine
from schema_salad.utils import json_dump, json_dumps
from typing_extensions import TYPE_CHECKING
from . import env_to_stdout, run_job
from .builder import Builder
from .context import RuntimeContext
from .cuda import cuda_check
from .errors import UnsupportedRequirement, WorkflowException
from .loghandler import _logger
from .pathmapper import MapperEnt, PathMapper
from .process import stage_files
from .secrets import SecretStore
from .utils import (
CWLObjectType,
CWLOutputType,
DirectoryType,
HasReqsHints,
OutputCallbackType,
bytes2str_in_dicts,
create_tmp_dir,
ensure_non_writable,
ensure_writable,
processes_to_kill,
)
if TYPE_CHECKING:
from .provenance_profile 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 = """#!/bin/bash
python3 "run_job.py" "job.json"
"""
[docs]def relink_initialworkdir(
pathmapper: PathMapper,
host_outdir: str,
container_outdir: str,
inplace_update: bool = False,
) -> None:
for _, vol in pathmapper.items_exclude_children():
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 therefore 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):
try:
os.remove(host_outdir_tgt)
except PermissionError:
pass
elif os.path.isdir(host_outdir_tgt) and not vol.resolved.startswith("_:"):
shutil.rmtree(host_outdir_tgt)
if not vol.resolved.startswith("_:"):
try:
os.symlink(vol.resolved, host_outdir_tgt)
except FileExistsError:
pass
def neverquote(string: str, pos: int = 0, endpos: int = 0) -> Optional[Match[str]]:
return None
CollectOutputsType = Union[Callable[[str, int], CWLObjectType], functools.partial]
class JobBase(HasReqsHints, metaclass=ABCMeta):
def __init__(
self,
builder: Builder,
joborder: CWLObjectType,
make_path_mapper: Callable[..., PathMapper],
requirements: List[CWLObjectType],
hints: List[CWLObjectType],
name: str,
) -> None:
"""Initialize the job object."""
super().__init__()
self.builder = builder
self.joborder = joborder
self.stdin = None # type: Optional[str]
self.stderr = None # type: Optional[str]
self.stdout = None # type: Optional[str]
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[str]
self.pathmapper = PathMapper([], "", "")
self.make_path_mapper = make_path_mapper
self.generatemapper = None # type: Optional[PathMapper]
# set in CommandLineTool.job(i)
self.collect_outputs = cast(CollectOutputsType, None)
self.output_callback = None # type: Optional[OutputCallbackType]
self.outdir = ""
self.tmpdir = ""
self.environment = {} # type: MutableMapping[str, str]
self.generatefiles = {
"class": "Directory",
"listing": [],
"basename": "",
} # type: DirectoryType
self.stagedir = None # type: Optional[str]
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
self.mpi_procs = None # type: Optional[int]
def __repr__(self): # type: () -> str
"""Represent this Job object."""
return "CommandLineJob(%s)" % self.name
@abstractmethod
def run(
self,
runtimeContext: RuntimeContext,
tmpdir_lock: Optional[threading.Lock] = None,
) -> None:
pass
def _setup(self, runtimeContext: RuntimeContext) -> None:
cuda_req, _ = self.builder.get_requirement(
"http://commonwl.org/cwltool#CUDARequirement"
)
if cuda_req:
count = cuda_check(
cuda_req, math.ceil(self.builder.resources["cudaDeviceCount"])
)
if count == 0:
raise WorkflowException("Could not satisfy CUDARequirement")
if not os.path.exists(self.outdir):
os.makedirs(self.outdir)
def is_streamable(file: str) -> bool:
if not runtimeContext.streaming_allowed:
return False
for inp in self.joborder.values():
if isinstance(inp, dict) and inp.get("location", None) == file:
return inp.get("streamable", False)
return False
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:
if not (
is_streamable(knownfile) and stat.S_ISFIFO(os.stat(p[0]).st_mode)
):
raise WorkflowException(
"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(
self.generatefiles["listing"],
self.builder.outdir,
runtimeContext,
False,
)
if _logger.isEnabledFor(logging.DEBUG):
_logger.debug(
"[job %s] initial work dir %s",
self.name,
json_dumps(
{
p: self.generatemapper.mapper(p)
for p in self.generatemapper.files()
},
indent=4,
),
)
self.base_path_logs = runtimeContext.set_log_dir(
self.outdir, runtimeContext.log_dir, self.name
)
def _execute(
self,
runtime: List[str],
env: MutableMapping[str, str],
runtimeContext: RuntimeContext,
monitor_function=None, # type: Optional[Callable[[subprocess.Popen[str]], None]]
) -> None:
"""Execute the tool, either directly or via script.
Note: we are now at the point where self.environment is
ignored. The caller is responsible for correctly splitting that
into the runtime and env arguments.
`runtime` is the list of arguments to put at the start of the
command (e.g. docker run).
`env` is the environment to be set for running the resulting
command line.
"""
scr = self.get_requirement("ShellCommandRequirement")[0]
shouldquote = needs_shell_quoting_re.search
if scr is not None:
shouldquote = neverquote
# If mpi_procs (is not None and > 0) then prepend the
# appropriate MPI job launch command and flags before the
# execution.
if self.mpi_procs:
menv = runtimeContext.mpi_config
mpi_runtime = [
menv.runner,
menv.nproc_flag,
str(self.mpi_procs),
] + menv.extra_flags
runtime = mpi_runtime + runtime
menv.pass_through_env_vars(env)
menv.set_env_vars(env)
_logger.info(
"[job %s] %s$ %s%s%s%s",
self.name,
self.outdir,
" \\\n ".join(
[
shellescape.quote(str(arg)) if shouldquote(str(arg)) else str(arg)
for arg in (runtime + self.command_line)
]
),
" < %s" % self.stdin if self.stdin else "",
" > %s" % os.path.join(self.base_path_logs, self.stdout)
if self.stdout
else "",
" 2> %s" % os.path.join(self.base_path_logs, 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: CWLObjectType
try:
stdin_path = None
if self.stdin is not None:
rmap = self.pathmapper.reversemap(self.stdin)
if rmap is None:
raise WorkflowException(f"{self.stdin} missing from pathmapper")
else:
stdin_path = rmap[1]
def stderr_stdout_log_path(
base_path_logs: str, stderr_or_stdout: Optional[str]
) -> Optional[str]:
if stderr_or_stdout is not None:
abserr = os.path.join(base_path_logs, stderr_or_stdout)
dnerr = os.path.dirname(abserr)
if dnerr and not os.path.exists(dnerr):
os.makedirs(dnerr)
return abserr
return None
stderr_path = stderr_stdout_log_path(self.base_path_logs, self.stderr)
stdout_path = stderr_stdout_log_path(self.base_path_logs, self.stdout)
commands = [str(x) for x in runtime + self.command_line]
if runtimeContext.secret_store is not None:
commands = cast(
List[str],
runtimeContext.secret_store.retrieve(cast(CWLOutputType, commands)),
)
env = cast(
MutableMapping[str, str],
runtimeContext.secret_store.retrieve(cast(CWLOutputType, env)),
)
job_script_contents = None # type: Optional[str]
builder: Optional[Builder] = getattr(self, "builder", None)
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,
make_job_dir=lambda: runtimeContext.create_outdir(),
job_script_contents=job_script_contents,
timelimit=self.timelimit,
name=self.name,
monitor_function=monitor_function,
default_stdout=runtimeContext.default_stdout,
default_stderr=runtimeContext.default_stderr,
)
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 processStatus != "success":
if rcode < 0:
_logger.warning(
"[job %s] was terminated by signal: %s",
self.name,
signal.Signals(-rcode).name,
)
else:
_logger.warning("[job %s] exited with status: %d", self.name, rcode)
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(
"'listing' in self.generatefiles but no "
"generatemapper was setup."
)
runtimeContext.log_dir_handler(
self.outdir, self.base_path_logs, stdout_path, stderr_path
)
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("'%s' not found: %s", runtime[0], str(e))
else:
_logger.error("'%s' not found: %s", self.command_line[0], str(e))
else:
_logger.exception("Exception while running job")
processStatus = "permanentFail"
except WorkflowException as err:
_logger.error("[job %s] Job error:\n%s", self.name, str(err))
processStatus = "permanentFail"
except Exception:
_logger.exception("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("[job %s] completed %s", self.name, processStatus)
else:
_logger.info("[job %s] completed %s", self.name, processStatus)
if _logger.isEnabledFor(logging.DEBUG):
_logger.debug(
"[job %s] outputs %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"
)
if self.output_callback:
with runtimeContext.workflow_eval_lock:
self.output_callback(outputs, processStatus)
if self.stagedir is not None and os.path.exists(self.stagedir):
_logger.debug(
"[job %s] Removing input staging directory %s",
self.name,
self.stagedir,
)
shutil.rmtree(self.stagedir, True)
if runtimeContext.rm_tmpdir:
_logger.debug(
"[job %s] Removing temporary directory %s", self.name, self.tmpdir
)
shutil.rmtree(self.tmpdir, True)
@abstractmethod
def _required_env(self) -> Dict[str, str]:
"""Variables required by the CWL spec (HOME, TMPDIR, etc).
Note that with containers, the paths will (likely) be those from
inside.
"""
def _preserve_environment_on_containers_warning(
self, varname: Optional[Iterable[str]] = None
) -> None:
"""When running in a container, issue a warning."""
# By default, don't do anything; ContainerCommandLineJob below
# will issue a warning.
def prepare_environment(
self, runtimeContext: RuntimeContext, envVarReq: Mapping[str, str]
) -> None:
"""Set up environment variables.
Here we prepare the environment for the job, based on any
preserved variables and `EnvVarRequirement`. Later, changes due
to `MPIRequirement`, `Secrets`, or `SoftwareRequirement` are
applied (in that order).
"""
# Start empty
env: Dict[str, str] = {}
# Preserve any env vars
if runtimeContext.preserve_entire_environment:
self._preserve_environment_on_containers_warning()
env.update(os.environ)
elif runtimeContext.preserve_environment:
self._preserve_environment_on_containers_warning(
runtimeContext.preserve_environment
)
for key in runtimeContext.preserve_environment:
try:
env[key] = os.environ[key]
except KeyError:
_logger.warning(
f"Attempting to preserve environment variable '{key}' which is not present"
)
# Set required env vars
env.update(self._required_env())
# Apply EnvVarRequirement
env.update(envVarReq)
# Set on ourselves
self.environment = env
def process_monitor(self, sproc): # type: (subprocess.Popen[str]) -> None
monitor = psutil.Process(sproc.pid)
# Value must be list rather than integer to utilise pass-by-reference in python
memory_usage = [None] # type: MutableSequence[Optional[int]]
def get_tree_mem_usage(memory_usage: MutableSequence[Optional[int]]) -> None:
children = monitor.children()
try:
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
except psutil.NoSuchProcess:
mem_tm.cancel()
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(
"[job %s] Max memory used: %iMiB",
self.name,
round(memory_usage[0] / (2**20)),
)
else:
_logger.debug(
"Could not collect memory usage, job ended before monitoring began."
)
class CommandLineJob(JobBase):
def run(
self,
runtimeContext: RuntimeContext,
tmpdir_lock: Optional[threading.Lock] = None,
) -> 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)
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([], self.environment, runtimeContext, monitor_function)
def _required_env(self) -> Dict[str, str]:
env = {}
env["HOME"] = self.outdir
env["TMPDIR"] = self.tmpdir
env["PATH"] = os.environ["PATH"]
if "SYSTEMROOT" in os.environ:
env["SYSTEMROOT"] = os.environ["SYSTEMROOT"]
return env
CONTROL_CODE_RE = r"\x1b\[[0-9;]*[a-zA-Z]"
class ContainerCommandLineJob(JobBase, metaclass=ABCMeta):
"""Commandline job using containers."""
CONTAINER_TMPDIR: str = "/tmp" # nosec
@abstractmethod
def get_from_requirements(
self,
r: CWLObjectType,
pull_image: bool,
force_pull: bool,
tmp_outdir_prefix: str,
) -> Optional[str]:
pass
@abstractmethod
def create_runtime(
self,
env: MutableMapping[str, str],
runtime_context: RuntimeContext,
) -> Tuple[List[str], Optional[str]]:
"""Return the list of commands to run the selected container engine."""
@staticmethod
@abstractmethod
def append_volume(
runtime: List[str], source: str, target: str, writable: bool = False
) -> None:
"""Add binding arguments to the runtime list."""
@abstractmethod
def add_file_or_directory_volume(
self, runtime: List[str], volume: MapperEnt, host_outdir_tgt: Optional[str]
) -> None:
"""Append volume a file/dir mapping to the runtime option list."""
@abstractmethod
def add_writable_file_volume(
self,
runtime: List[str],
volume: MapperEnt,
host_outdir_tgt: Optional[str],
tmpdir_prefix: str,
) -> None:
"""Append a writable file mapping to the runtime option list."""
@abstractmethod
def add_writable_directory_volume(
self,
runtime: List[str],
volume: MapperEnt,
host_outdir_tgt: Optional[str],
tmpdir_prefix: str,
) -> None:
"""Append a writable directory mapping to the runtime option list."""
def _preserve_environment_on_containers_warning(
self, varnames: Optional[Iterable[str]] = None
) -> None:
"""When running in a container, issue a warning."""
if varnames is None:
flags = "--preserve-entire-environment"
else:
flags = "--preserve-environment={" + ", ".join(varnames) + "}"
_logger.warning(
f"You have specified `{flags}` while running a container which will override variables set in the container. This may break the container, be non-portable, and/or affect reproducibility."
)
def create_file_and_add_volume(
self,
runtime: List[str],
volume: MapperEnt,
host_outdir_tgt: Optional[str],
secret_store: Optional[SecretStore],
tmpdir_prefix: str,
) -> str:
"""Create the file and add a mapping."""
if not host_outdir_tgt:
new_file = os.path.join(
create_tmp_dir(tmpdir_prefix),
os.path.basename(volume.target),
)
writable = True if volume.type == "CreateWritableFile" else False
contents = volume.resolved
if secret_store:
contents = cast(str, secret_store.retrieve(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, "w") as file_literal:
file_literal.write(contents)
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: PathMapper,
runtime: List[str],
tmpdir_prefix: str,
secret_store: Optional[SecretStore] = None,
any_path_okay: bool = False,
) -> 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[str]
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: RuntimeContext,
tmpdir_lock: Optional[threading.Lock] = None,
) -> None:
debug = runtimeContext.debug
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
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(str(cmd))
try:
subprocess.check_call(cmd, stdout=sys.stderr) # nosec
except OSError:
raise SourceLine(
docker_req, None, WorkflowException, debug
).makeError(
f"Either Docker container {img_id} is not available with "
f"user space docker implementation {user_space_docker_cmd} "
f" or {user_space_docker_cmd} is missing or broken."
)
else:
raise SourceLine(docker_req, None, WorkflowException, debug).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,
runtimeContext.force_docker_pull,
runtimeContext.tmp_outdir_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("%s error", container, exc_info=True)
if docker_is_req:
raise UnsupportedRequirement(
"{} is required to run this tool: {}".format(
container, str(err)
)
) from 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)
# Copy as don't want to modify our env
env = dict(os.environ)
(runtime, cidfile) = self.create_runtime(env, runtimeContext)
runtime.append(str(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: str,
tmpdir_prefix: str,
cleanup_cidfile: bool,
process, # type: subprocess.Popen[str]
) -> 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 # type: Optional[str]
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.warning(
"Ignored error cleaning up Docker cidfile: %s", exc
)
return
try:
with open(cidfile) as cidhandle:
cid = cidhandle.readline().strip()
except (OSError):
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)
stats_file_name = stats_file.name
try:
with open(stats_file_name, mode="w") as stats_file_handle:
stats_proc = subprocess.Popen( # nosec
["docker", "stats", "--no-trunc", "--format", "{{.MemPerc}}", cid],
stdout=stats_file_handle,
stderr=subprocess.DEVNULL,
)
process.wait()
stats_proc.kill()
except OSError as exc:
_logger.warning("Ignored error with docker stats: %s", exc)
return
max_mem_percent = 0 # type: float
mem_percent = 0 # type: float
with open(stats_file_name) as stats:
while True:
line = stats.readline()
if not line:
break
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(
"[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: List[str],
stdin_path: Optional[str],
stdout_path: Optional[str],
stderr_path: Optional[str],
env: Mapping[str, str],
cwd: str,
make_job_dir: Callable[[], str],
job_script_contents: Optional[str] = None,
timelimit: Optional[int] = None,
name: Optional[str] = None,
monitor_function=None, # type: Optional[Callable[[subprocess.Popen[str]], None]]
default_stdout=None, # type: Optional[Union[IO[bytes], TextIO]]
default_stderr=None, # type: Optional[Union[IO[bytes], TextIO]]
) -> int:
if job_script_contents is None and not FORCE_SHELLED_POPEN:
stdin = subprocess.PIPE # type: Union[IO[bytes], int]
if stdin_path is not None:
stdin = open(stdin_path, "rb")
stdout = (
default_stdout if default_stdout is not None else sys.stderr
) # type: Union[IO[bytes], TextIO]
if stdout_path is not None:
stdout = open(stdout_path, "wb")
stderr = (
default_stderr if default_stderr is not None else sys.stderr
) # type: Union[IO[bytes], TextIO]
if stderr_path is not None:
stderr = open(stderr_path, "wb")
sproc = subprocess.Popen(
commands,
shell=False, # nosec
close_fds=True,
stdin=stdin,
stdout=stdout,
stderr=stderr,
env=env,
cwd=cwd,
universal_newlines=True,
)
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(
"[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, IO) and hasattr(stdin, "close"):
stdin.close()
if stdout is not sys.stderr and hasattr(stdout, "close"):
stdout.close()
if stderr is not sys.stderr and hasattr(stderr, "close"):
stderr.close()
return rcode
else:
if job_script_contents is None:
job_script_contents = SHELL_COMMAND_TEMPLATE
job_description = {
"commands": commands,
"cwd": cwd,
"env": env,
"stdout_path": stdout_path,
"stderr_path": stderr_path,
"stdin_path": stdin_path,
}
job_dir = make_job_dir()
try:
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)
job_script = os.path.join(job_dir, "run_job.bash")
with open(job_script, "w") as _:
_.write(job_script_contents)
job_run = os.path.join(job_dir, "run_job.py")
shutil.copyfile(run_job.__file__, job_run)
env_getter = os.path.join(job_dir, "env_to_stdout.py")
shutil.copyfile(env_to_stdout.__file__, env_getter)
sproc = subprocess.Popen( # nosec
["bash", job_script],
shell=False, # nosec
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,
universal_newlines=True,
)
processes_to_kill.append(sproc)
if sproc.stdin is not None:
sproc.stdin.close()
rcode = sproc.wait()
return rcode
finally:
shutil.rmtree(job_dir)