Warning
This document is for an old release 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
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,
TYPE_CHECKING,
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 . 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 .cwlprov.provenance_profile import (
ProvenanceProfile, # pylint: disable=unused-import
)
CollectOutputsType = Union[
Callable[[str, int], CWLObjectType], functools.partial[CWLObjectType]
]
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
class JobBase(HasReqsHints, metaclass=ABCMeta):
def __init__(
self,
builder: Builder,
joborder: CWLObjectType,
make_path_mapper: Callable[[List[CWLObjectType], str, RuntimeContext, bool], PathMapper],
requirements: List[CWLObjectType],
hints: List[CWLObjectType],
name: str,
) -> None:
"""Initialize the job object."""
super().__init__()
self.builder = builder
self.joborder = joborder
self.stdin: Optional[str] = None
self.stderr: Optional[str] = None
self.stdout: Optional[str] = None
self.successCodes: Iterable[int] = []
self.temporaryFailCodes: Iterable[int] = []
self.permanentFailCodes: Iterable[int] = []
self.requirements = requirements
self.hints = hints
self.name = name
self.command_line: List[str] = []
self.pathmapper = PathMapper([], "", "")
self.make_path_mapper = make_path_mapper
self.generatemapper: Optional[PathMapper] = None
# set in CommandLineTool.job(i)
self.collect_outputs = cast("CollectOutputsType", None)
self.output_callback: Optional[OutputCallbackType] = None
self.outdir = ""
self.tmpdir = ""
self.environment: MutableMapping[str, str] = {}
self.generatefiles: DirectoryType = {
"class": "Directory",
"listing": [],
"basename": "",
}
self.stagedir: Optional[str] = None
self.inplace_update = False
self.prov_obj: Optional[ProvenanceProfile] = None
self.parent_wf: Optional[ProvenanceProfile] = None
self.timelimit: Optional[int] = None
self.networkaccess: bool = False
self.mpi_procs: Optional[int] = None
def __repr__(self) -> 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 cast(bool, 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: Optional[Callable[["subprocess.Popen[str]"], None]] = 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: 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: Optional[str] = None
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 runtimeContext.rm_tmpdir and 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!r} 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: "subprocess.Popen[str]") -> None:
"""Watch a process, logging its max memory usage."""
monitor = psutil.Process(sproc.pid)
# Value must be list rather than integer to utilise pass-by-reference in python
memory_usage: MutableSequence[Optional[int]] = [None]
mem_tm: "Optional[Timer]" = None
def get_tree_mem_usage(memory_usage: MutableSequence[Optional[int]]) -> None:
nonlocal mem_tm
try:
with monitor.oneshot():
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()
except psutil.NoSuchProcess:
if mem_tm is not None:
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"]
for extra in ("SYSTEMROOT", "QEMU_LD_PREFIX"):
if extra in os.environ:
env[extra] = os.environ[extra]
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!r} 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: Optional[str] = None
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"])
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(
f"{container} is required to run this tool: {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)
) from 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),
"podman" if runtimeContext.podman else "docker",
)
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,
docker_exe: str,
process: "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: Optional[str] = None
while cid is None:
time.sleep(1)
# This is needed to avoid a race condition where the job
# was so fast that it already finished when it arrives here
if process.returncode is None:
process.poll()
if process.returncode is not None:
if cleanup_cidfile:
try:
os.remove(cidfile)
except OSError as exc:
_logger.warning("Ignored error cleaning up %s cidfile: %s", docker_exe, 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:
cmds = [docker_exe, "stats"]
if "podman" not in docker_exe:
cmds.append("--no-trunc")
cmds.extend(["--format", "{{.MemPerc}}", cid])
stats_proc = subprocess.Popen( # nosec
cmds,
stdout=stats_file_handle,
stderr=subprocess.DEVNULL,
)
process.wait()
stats_proc.kill()
except OSError as exc:
_logger.warning("Ignored error with %s stats: %s", docker_exe, exc)
return
max_mem_percent: float = 0.0
mem_percent: float = 0.0
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 as exc:
_logger.debug("%s stats parsing error in line %s: %s", docker_exe, line, exc)
_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: Optional[Callable[["subprocess.Popen[str]"], None]] = None,
default_stdout: Optional[Union[IO[bytes], TextIO]] = None,
default_stderr: Optional[Union[IO[bytes], TextIO]] = None,
) -> int:
if job_script_contents is None and not FORCE_SHELLED_POPEN:
stdin: Union[IO[bytes], int] = subprocess.PIPE
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()
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()
return rcode
finally:
shutil.rmtree(job_dir)