#!/usr/bin/env python
+# Copyright (C) The Arvados Authors. All rights reserved.
+#
+# SPDX-License-Identifier: Apache-2.0
+
+import logging
+
+logger = logging.getLogger('run-command')
+log_handler = logging.StreamHandler()
+log_handler.setFormatter(logging.Formatter("run-command: %(message)s"))
+logger.addHandler(log_handler)
+logger.setLevel(logging.INFO)
import arvados
import re
import subprocess
import sys
import shutil
-import subst
+import crunchutil.subst as subst
import time
import arvados.commands.put as put
import signal
+import stat
+import copy
+import traceback
+import pprint
+import multiprocessing
+import crunchutil.robust_put as robust_put
+import crunchutil.vwd as vwd
+import argparse
+import json
+import tempfile
+import errno
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--dry-run', action='store_true')
+parser.add_argument('--script-parameters', type=str, default="{}")
+args = parser.parse_args()
os.umask(0077)
-t = arvados.current_task().tmpdir
-
-api = arvados.api('v1')
+if not args.dry_run:
+ api = arvados.api('v1')
+ t = arvados.current_task().tmpdir
+ os.chdir(arvados.current_task().tmpdir)
+ os.mkdir("tmpdir")
+ os.mkdir("output")
-os.chdir(arvados.current_task().tmpdir)
-os.mkdir("tmpdir")
-os.mkdir("output")
+ os.chdir("output")
-os.chdir("output")
+ outdir = os.getcwd()
-taskp = None
-jobp = arvados.current_job()['script_parameters']
-if len(arvados.current_task()['parameters']) > 0:
- p = arvados.current_task()['parameters']
-
-links = []
-
-def sub_link(v):
- r = os.path.basename(v)
- os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
- links.append(r)
- return r
+ taskp = None
+ jobp = arvados.current_job()['script_parameters']
+ if len(arvados.current_task()['parameters']) > 0:
+ taskp = arvados.current_task()['parameters']
+else:
+ outdir = "/tmp"
+ jobp = json.loads(args.script_parameters)
+ os.environ['JOB_UUID'] = 'zzzzz-8i9sb-1234567890abcde'
+ os.environ['TASK_UUID'] = 'zzzzz-ot0gb-1234567890abcde'
+ os.environ['CRUNCH_SRC'] = '/tmp/crunch-src'
+ if 'TASK_KEEPMOUNT' not in os.environ:
+ os.environ['TASK_KEEPMOUNT'] = '/keep'
def sub_tmpdir(v):
return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
+def sub_outdir(v):
+ return outdir
+
def sub_cores(v):
- return os.environ['CRUNCH_NODE_SLOTS']
+ return str(multiprocessing.cpu_count())
def sub_jobid(v):
return os.environ['JOB_UUID']
def sub_taskid(v):
return os.environ['TASK_UUID']
-subst.default_subs["link "] = sub_link
+def sub_jobsrc(v):
+ return os.environ['CRUNCH_SRC']
+
subst.default_subs["task.tmpdir"] = sub_tmpdir
+subst.default_subs["task.outdir"] = sub_outdir
+subst.default_subs["job.srcdir"] = sub_jobsrc
subst.default_subs["node.cores"] = sub_cores
-subst.default_subs["job.id"] = sub_jobid
-subst.default_subs["task.id"] = sub_taskid
-
-rcode = 1
-
-def machine_progress(bytes_written, bytes_expected):
- return "run-command: wrote {} total {}\n".format(
- bytes_written, -1 if (bytes_expected is None) else bytes_expected)
+subst.default_subs["job.uuid"] = sub_jobid
+subst.default_subs["task.uuid"] = sub_taskid
class SigHandler(object):
def __init__(self):
self.sig = None
- def send_signal(self, sp, signum):
- sp.send_signal(signum)
+ def send_signal(self, subprocesses, signum):
+ for sp in subprocesses:
+ sp.send_signal(signum)
self.sig = signum
-if "foreach" in jobp:
- if arvados.current_task()['sequence'] == 0:
- var = jobp["foreach"]["var"]
- values = jobp["foreach"]["values"]
- fn = subst.do_substitution(jobp, values)
- mode = os.stat(fn)
- prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
- if mode != None:
- if stat.S_ISDIR(mode):
- items = ["$(dir %s/%s)" % (prefix, l) for l in os.listdir(fn)]
- else stat.S_ISREG(mode):
- with open(fn) as f:
- items = [line for line in f]
-
- print("run-command: parallelizing on %s with items %s" % (var, items))
-
+# http://rightfootin.blogspot.com/2006/09/more-on-python-flatten.html
+def flatten(l, ltypes=(list, tuple)):
+ ltype = type(l)
+ l = list(l)
+ i = 0
+ while i < len(l):
+ while isinstance(l[i], ltypes):
+ if not l[i]:
+ l.pop(i)
+ i -= 1
+ break
+ else:
+ l[i:i + 1] = l[i]
+ i += 1
+ return ltype(l)
+
+def add_to_group(gr, match):
+ m = match.groups()
+ if m not in gr:
+ gr[m] = []
+ gr[m].append(match.group(0))
+
+class EvaluationError(Exception):
+ pass
+
+# Return the name of variable ('var') that will take on each value in 'items'
+# when performing an inner substitution
+def var_items(p, c, key):
+ if key not in c:
+ raise EvaluationError("'%s' was expected in 'p' but is missing" % key)
+
+ if "var" in c:
+ if not isinstance(c["var"], basestring):
+ raise EvaluationError("Value of 'var' must be a string")
+ # Var specifies the variable name for inner parameter substitution
+ return (c["var"], get_items(p, c[key]))
+ else:
+ # The component function ('key') value is a list, so return the list
+ # directly with no parameter selected.
+ if isinstance(c[key], list):
+ return (None, get_items(p, c[key]))
+ elif isinstance(c[key], basestring):
+ # check if c[key] is a string that looks like a parameter
+ m = re.match("^\$\((.*)\)$", c[key])
+ if m and m.group(1) in p:
+ return (m.group(1), get_items(p, c[key]))
+ else:
+ # backwards compatible, foreach specifies bare parameter name to use
+ return (c[key], get_items(p, p[c[key]]))
+ else:
+ raise EvaluationError("Value of '%s' must be a string or list" % key)
+
+# "p" is the parameter scope, "c" is the item to be expanded.
+# If "c" is a dict, apply function expansion.
+# If "c" is a list, recursively expand each item and return a new list.
+# If "c" is a string, apply parameter substitution
+def expand_item(p, c):
+ if isinstance(c, dict):
+ if "foreach" in c and "command" in c:
+ # Expand a command template for each item in the specified user
+ # parameter
+ var, items = var_items(p, c, "foreach")
+ if var is None:
+ raise EvaluationError("Must specify 'var' in foreach")
+ r = []
for i in items:
- params = copy.copy(jobp)
+ params = copy.copy(p)
params[var] = i
- arvados.api().job_tasks().create(body={
- 'job_uuid': arvados.current_job()['uuid'],
- 'created_by_job_task_uuid': arvados.current_task()['uuid'],
- 'sequence': 1,
- 'parameters': params
- }
- ).execute()
- sys.exit(0)
+ r.append(expand_item(params, c["command"]))
+ return r
+ elif "list" in c and "index" in c and "command" in c:
+ # extract a single item from a list
+ var, items = var_items(p, c, "list")
+ if var is None:
+ raise EvaluationError("Must specify 'var' in list")
+ params = copy.copy(p)
+ params[var] = items[int(c["index"])]
+ return expand_item(params, c["command"])
+ elif "regex" in c:
+ pattern = re.compile(c["regex"])
+ if "filter" in c:
+ # filter list so that it only includes items that match a
+ # regular expression
+ _, items = var_items(p, c, "filter")
+ return [i for i in items if pattern.match(i)]
+ elif "group" in c:
+ # generate a list of lists, where items are grouped on common
+ # subexpression match
+ _, items = var_items(p, c, "group")
+ groups = {}
+ for i in items:
+ match = pattern.match(i)
+ if match:
+ add_to_group(groups, match)
+ return [groups[k] for k in groups]
+ elif "extract" in c:
+ # generate a list of lists, where items are split by
+ # subexpression match
+ _, items = var_items(p, c, "extract")
+ r = []
+ for i in items:
+ match = pattern.match(i)
+ if match:
+ r.append(list(match.groups()))
+ return r
+ elif "batch" in c and "size" in c:
+ # generate a list of lists, where items are split into a batch size
+ _, items = var_items(p, c, "batch")
+ sz = int(c["size"])
+ r = []
+ for j in xrange(0, len(items), sz):
+ r.append(items[j:j+sz])
+ return r
+ raise EvaluationError("Missing valid list context function")
+ elif isinstance(c, list):
+ return [expand_item(p, arg) for arg in c]
+ elif isinstance(c, basestring):
+ m = re.match("^\$\((.*)\)$", c)
+ if m and m.group(1) in p:
+ return expand_item(p, p[m.group(1)])
else:
- sys.exit(1)
-else:
- p = jobp
+ return subst.do_substitution(p, c)
+ else:
+ raise EvaluationError("expand_item() unexpected parameter type %s" % type(c))
+
+# Evaluate in a list context
+# "p" is the parameter scope, "value" will be evaluated
+# if "value" is a list after expansion, return that
+# if "value" is a path to a directory, return a list consisting of each entry in the directory
+# if "value" is a path to a file, return a list consisting of each line of the file
+def get_items(p, value):
+ value = expand_item(p, value)
+ if isinstance(value, list):
+ return value
+ elif isinstance(value, basestring):
+ mode = os.stat(value).st_mode
+ prefix = value[len(os.environ['TASK_KEEPMOUNT'])+1:]
+ if mode is not None:
+ if stat.S_ISDIR(mode):
+ items = [os.path.join(value, l) for l in os.listdir(value)]
+ elif stat.S_ISREG(mode):
+ with open(value) as f:
+ items = [line.rstrip("\r\n") for line in f]
+ return items
+ raise EvaluationError("get_items did not yield a list")
+
+stdoutname = None
+stdoutfile = None
+stdinname = None
+stdinfile = None
+
+# Construct the cross product of all values of each variable listed in fvars
+def recursive_foreach(params, fvars):
+ var = fvars[0]
+ fvars = fvars[1:]
+ items = get_items(params, params[var])
+ logger.info("parallelizing on %s with items %s" % (var, items))
+ if items is not None:
+ for i in items:
+ params = copy.copy(params)
+ params[var] = i
+ if len(fvars) > 0:
+ recursive_foreach(params, fvars)
+ else:
+ if not args.dry_run:
+ arvados.api().job_tasks().create(body={
+ 'job_uuid': arvados.current_job()['uuid'],
+ 'created_by_job_task_uuid': arvados.current_task()['uuid'],
+ 'sequence': 1,
+ 'parameters': params
+ }).execute()
+ else:
+ if isinstance(params["command"][0], list):
+ for c in params["command"]:
+ logger.info(flatten(expand_item(params, c)))
+ else:
+ logger.info(flatten(expand_item(params, params["command"])))
+ else:
+ logger.error("parameter %s with value %s in task.foreach yielded no items" % (var, params[var]))
+ sys.exit(1)
+
+try:
+ if "task.foreach" in jobp:
+ if args.dry_run or arvados.current_task()['sequence'] == 0:
+ # This is the first task to start the other tasks and exit
+ fvars = jobp["task.foreach"]
+ if isinstance(fvars, basestring):
+ fvars = [fvars]
+ if not isinstance(fvars, list) or len(fvars) == 0:
+ logger.error("value of task.foreach must be a string or non-empty list")
+ sys.exit(1)
+ recursive_foreach(jobp, jobp["task.foreach"])
+ if not args.dry_run:
+ if "task.vwd" in jobp:
+ # Set output of the first task to the base vwd collection so it
+ # will be merged with output fragments from the other tasks by
+ # crunch.
+ arvados.current_task().set_output(subst.do_substitution(jobp, jobp["task.vwd"]))
+ else:
+ arvados.current_task().set_output(None)
+ sys.exit(0)
+ else:
+ # This is the only task so taskp/jobp are the same
+ taskp = jobp
+except Exception as e:
+ logger.exception("caught exception")
+ logger.error("job parameters were:")
+ logger.error(pprint.pformat(jobp))
+ sys.exit(1)
try:
+ if not args.dry_run:
+ if "task.vwd" in taskp:
+ # Populate output directory with symlinks to files in collection
+ vwd.checkout(subst.do_substitution(taskp, taskp["task.vwd"]), outdir)
+
+ if "task.cwd" in taskp:
+ os.chdir(subst.do_substitution(taskp, taskp["task.cwd"]))
+
cmd = []
- for c in p["command"]:
- cmd.append(subst.do_substitution(p, c))
+ if isinstance(taskp["command"][0], list):
+ for c in taskp["command"]:
+ cmd.append(flatten(expand_item(taskp, c)))
+ else:
+ cmd.append(flatten(expand_item(taskp, taskp["command"])))
+
+ if "task.stdin" in taskp:
+ stdinname = subst.do_substitution(taskp, taskp["task.stdin"])
+ if not args.dry_run:
+ stdinfile = open(stdinname, "rb")
+
+ if "task.stdout" in taskp:
+ stdoutname = subst.do_substitution(taskp, taskp["task.stdout"])
+ if not args.dry_run:
+ stdoutfile = open(stdoutname, "wb")
+
+ if "task.env" in taskp:
+ env = copy.copy(os.environ)
+ for k,v in taskp["task.env"].items():
+ env[k] = subst.do_substitution(taskp, v)
+ else:
+ env = None
- stdoutname = None
- stdoutfile = None
- if "stdout" in p:
- stdoutname = subst.do_substitution(p, p["stdout"])
- stdoutfile = open(stdoutname, "wb")
+ logger.info("{}{}{}".format(' | '.join([' '.join(c) for c in cmd]), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
- print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+ if args.dry_run:
+ sys.exit(0)
+except subst.SubstitutionError as e:
+ logger.error(str(e))
+ logger.error("task parameters were:")
+ logger.error(pprint.pformat(taskp))
+ sys.exit(1)
+except Exception as e:
+ logger.exception("caught exception")
+ logger.error("task parameters were:")
+ logger.error(pprint.pformat(taskp))
+ sys.exit(1)
- sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
- sig = SigHandler()
+# rcode holds the return codes produced by each subprocess
+rcode = {}
+try:
+ subprocesses = []
+ close_streams = []
+ if stdinfile:
+ close_streams.append(stdinfile)
+ next_stdin = stdinfile
+
+ for i in xrange(len(cmd)):
+ if i == len(cmd)-1:
+ # this is the last command in the pipeline, so its stdout should go to stdoutfile
+ next_stdout = stdoutfile
+ else:
+ # this is an intermediate command in the pipeline, so its stdout should go to a pipe
+ next_stdout = subprocess.PIPE
+
+ sp = subprocess.Popen(cmd[i], shell=False, stdin=next_stdin, stdout=next_stdout, env=env)
+
+ # Need to close the FDs on our side so that subcommands will get SIGPIPE if the
+ # consuming process ends prematurely.
+ if sp.stdout:
+ close_streams.append(sp.stdout)
- # forward signals to the process.
- signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(sp, signum))
- signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(sp, signum))
- signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(sp, signum))
+ # Send this processes's stdout to to the next process's stdin
+ next_stdin = sp.stdout
- # wait for process to complete.
- rcode = sp.wait()
+ subprocesses.append(sp)
- if sig.sig != None:
- print("run-command: terminating on signal %s" % sig.sig)
+ # File descriptors have been handed off to the subprocesses, so close them here.
+ for s in close_streams:
+ s.close()
+
+ # Set up signal handling
+ sig = SigHandler()
+
+ # Forward terminate signals to the subprocesses.
+ signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(subprocesses, signum))
+ signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(subprocesses, signum))
+ signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(subprocesses, signum))
+
+ active = 1
+ pids = set([s.pid for s in subprocesses])
+ while len(pids) > 0:
+ try:
+ (pid, status) = os.wait()
+ except OSError as e:
+ if e.errno == errno.EINTR:
+ pass
+ else:
+ raise
+ else:
+ pids.discard(pid)
+ if not taskp.get("task.ignore_rcode"):
+ rcode[pid] = (status >> 8)
+ else:
+ rcode[pid] = 0
+
+ if sig.sig is not None:
+ logger.critical("terminating on signal %s" % sig.sig)
sys.exit(2)
else:
- print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
+ for i in xrange(len(cmd)):
+ r = rcode[subprocesses[i].pid]
+ logger.info("%s completed with exit code %i (%s)" % (cmd[i][0], r, "success" if r == 0 else "failed"))
except Exception as e:
- print("run-command: caught exception: {}".format(e))
+ logger.exception("caught exception")
# restore default signal handlers.
signal.signal(signal.SIGINT, signal.SIG_DFL)
signal.signal(signal.SIGTERM, signal.SIG_DFL)
signal.signal(signal.SIGQUIT, signal.SIG_DFL)
-for l in links:
- os.unlink(l)
-
-print("run-command: the following output files will be saved to keep:")
-
-subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
-
-print("run-command: start writing output to keep")
-
-done = False
-resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
-reporter = put.progress_writer(machine_progress)
-bytes_expected = put.expected_bytes_for(".")
-while not done:
- try:
- out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected)
- out.do_queued_work()
- out.write_directory_tree(".", max_manifest_depth=0)
- outuuid = out.finish()
- api.job_tasks().update(uuid=arvados.current_task()['uuid'],
- body={
- 'output':outuuid,
- 'success': (rcode == 0),
- 'progress':1.0
- }).execute()
- done = True
- except KeyboardInterrupt:
- print("run-command: terminating on signal 2")
- sys.exit(2)
- except Exception as e:
- print("run-command: caught exception: {}".format(e))
- time.sleep(5)
+logger.info("the following output files will be saved to keep:")
+
+subprocess.call(["find", "-L", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr, cwd=outdir)
+
+logger.info("start writing output to keep")
+
+if "task.vwd" in taskp and "task.foreach" in jobp:
+ for root, dirs, files in os.walk(outdir):
+ for f in files:
+ s = os.lstat(os.path.join(root, f))
+ if stat.S_ISLNK(s.st_mode):
+ os.unlink(os.path.join(root, f))
+
+(outcollection, checkin_error) = vwd.checkin(outdir)
+
+# Success if we ran any subprocess, and they all exited 0.
+success = rcode and all(status == 0 for status in rcode.itervalues()) and not checkin_error
+
+api.job_tasks().update(uuid=arvados.current_task()['uuid'],
+ body={
+ 'output': outcollection.manifest_text(),
+ 'success': success,
+ 'progress':1.0
+ }).execute()
-sys.exit(rcode)
+sys.exit(0 if success else 1)
projects / arvados.git / blobdiff