import shutil
import subst
import time
+import arvados.commands.put as put
+import signal
+import stat
+import copy
+import traceback
+import pprint
+import multiprocessing
os.umask(0077)
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']
-else:
- p = arvados.current_job()['script_parameters']
links = []
def sub_link(v):
- r = os.path.basename(v)
- os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
+ r = os.path.join(outdir, os.path.basename(v))
+ os.symlink(v, r)
links.append(r)
return r
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']
+
+def sub_jobsrc(v):
+ return os.environ['CRUNCH_SRC']
subst.default_subs["link "] = sub_link
-subst.default_subs["tmpdir"] = sub_tmpdir
+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.uuid"] = sub_jobid
+subst.default_subs["task.uuid"] = 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)
+
+class SigHandler(object):
+ def __init__(self):
+ self.sig = None
+
+ def send_signal(self, sp, signum):
+ sp.send_signal(signum)
+ self.sig = signum
+
+def expand_item(p, c):
+ if isinstance(c, dict):
+ if "foreach" in c and "command" in c:
+ var = c["foreach"]
+ items = get_items(p, p[var])
+ r = []
+ for i in items:
+ params = copy.copy(p)
+ params[var] = i
+ r.extend(expand_list(params, c["command"]))
+ return r
+ elif isinstance(c, list):
+ return expand_list(p, c)
+ elif isinstance(c, str) or isinstance(c, unicode):
+ return [subst.do_substitution(p, c)]
+
+ return []
+
+def expand_list(p, l):
+ return [exp for arg in l for exp in expand_item(p, arg)]
+
+def get_items(p, value):
+ if isinstance(value, list):
+ return expand_list(p, value)
+
+ fn = subst.do_substitution(p, value)
+ mode = os.stat(fn).st_mode
+ 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)]
+ elif stat.S_ISREG(mode):
+ with open(fn) as f:
+ items = [line for line in f]
+ return items
+ else:
+ return None
+
+stdoutname = None
+stdoutfile = None
+
try:
- cmd = []
- for c in p["command"]:
- cmd.append(subst.do_substitution(p, c))
-
- stdoutname = None
- stdoutfile = None
- if "stdout" in p:
- stdoutname = subst.do_substitution(p, p["stdout"])
+ if "task.foreach" in jobp:
+ if arvados.current_task()['sequence'] == 0:
+ var = jobp["task.foreach"]
+ items = get_items(jobp, jobp[var])
+ print("run-command: parallelizing on %s with items %s" % (var, items))
+ if items != None:
+ for i in items:
+ params = copy.copy(jobp)
+ 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()
+ arvados.current_task().set_output(None)
+ sys.exit(0)
+ else:
+ sys.exit(1)
+ else:
+ p = jobp
+
+ cmd = expand_list(p, p["command"])
+
+ if "save.stdout" in p:
+ stdoutname = subst.do_substitution(p, p["save.stdout"])
stdoutfile = open(stdoutname, "wb")
print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
- rcode = subprocess.call(cmd, stdout=stdoutfile)
+except Exception as e:
+ print("run-command: caught exception:")
+ traceback.print_exc(file=sys.stdout)
+ print("run-command: task parameters was:")
+ pprint.pprint(p)
+ sys.exit(1)
+
+try:
+ sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
+ sig = SigHandler()
+
+ # 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))
+
+ # wait for process to complete.
+ rcode = sp.wait()
- print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
+ if sig.sig != None:
+ print("run-command: 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"))
except Exception as e:
- print("run-command: caught exception: {}".format(e))
-
-finally:
- for l in links:
- os.unlink(l)
-
- print("run-command: the follow 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
- while not done:
- try:
- out = arvados.CollectionWriter()
- 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 Exception as e:
- print("run-command: caught exception: {}".format(e))
- time.sleep(5)
+ print("run-command: caught exception:")
+ traceback.print_exc(file=sys.stdout)
+
+# 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:")
+ traceback.print_exc(file=sys.stdout)
+ time.sleep(5)
sys.exit(rcode)
projects / arvados.git / blobdiff