import sys
import shutil
import subst
+import time
+import arvados.commands.put as put
+import signal
os.umask(0077)
t = arvados.current_task().tmpdir
+api = arvados.api('v1')
+
os.chdir(arvados.current_task().tmpdir)
os.mkdir("tmpdir")
os.mkdir("output")
def sub_tmpdir(v):
return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
+def sub_cores(v):
+ return os.environ['CRUNCH_NODE_SLOTS']
+
subst.default_subs["link "] = sub_link
subst.default_subs["tmpdir"] = sub_tmpdir
+subst.default_subs["node.cores"] = sub_cores
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
+
try:
cmd = []
for c in p["command"]:
print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
- rcode = subprocess.call(cmd, stdout=stdoutfile)
+ sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
+ sig = SigHandler()
- print("run-command: completed with exit code %i" % rcode)
+ # 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))
-except Exception as e:
- print("run-command: caught exception: {}".format(e))
+ # wait for process to complete.
+ rcode = sp.wait()
-finally:
- for l in links:
- os.unlink(l)
+ 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"))
- 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")
-
- out = arvados.CollectionWriter()
- out.write_directory_tree(".", max_manifest_depth=0)
- outuuid = out.finish()
- arvados.api('v1').job_tasks().update(uuid=arvados.current_task()['uuid'],
- body={
- 'output':outuuid,
- 'success': (rcode == 0),
- 'progress':1.0
- }).execute()
+except Exception as e:
+ print("run-command: caught exception: {}".format(e))
-if rcode == 0:
- os.chdir("..")
- shutil.rmtree("tmpdir")
- shutil.rmtree("output")
- print("run-command: success")
-else:
- print("run-command: failed")
+# 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 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
+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)
sys.exit(rcode)