crunch_scripts/run-command

   1 #!/usr/bin/env python
   2
   3 import arvados
   4 import re
   5 import os
   6 import subprocess
   7 import sys
   8 import shutil
   9 import subst
  10 import time
  11 import arvados.commands.put as put
  12 import signal
  13
  14 os.umask(0077)
  15
  16 t = arvados.current_task().tmpdir
  17
  18 api = arvados.api('v1')
  19
  20 os.chdir(arvados.current_task().tmpdir)
  21 os.mkdir("tmpdir")
  22 os.mkdir("output")
  23
  24 os.chdir("output")
  25
  26 if len(arvados.current_task()['parameters']) > 0:
  27     p = arvados.current_task()['parameters']
  28 else:
  29     p = arvados.current_job()['script_parameters']
  30
  31 links = []
  32
  33 def sub_link(v):
  34     r = os.path.basename(v)
  35     os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
  36     links.append(r)
  37     return r
  38
  39 def sub_tmpdir(v):
  40     return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
  41
  42 def sub_cores(v):
  43      return os.environ['CRUNCH_NODE_SLOTS']
  44
  45 subst.default_subs["link "] = sub_link
  46 subst.default_subs["tmpdir"] = sub_tmpdir
  47 subst.default_subs["node.cores"] = sub_cores
  48
  49 rcode = 1
  50
  51 def machine_progress(bytes_written, bytes_expected):
  52     return "run-command: {} written {} total\n".format(
  53         bytes_written, -1 if (bytes_expected is None) else bytes_expected)
  54
  55 def send_signal(sp, signum, sig):
  56     sp.send_signal(signum)
  57     sig.append(signum)
  58
  59 try:
  60     cmd = []
  61     for c in p["command"]:
  62         cmd.append(subst.do_substitution(p, c))
  63
  64     stdoutname = None
  65     stdoutfile = None
  66     if "stdout" in p:
  67         stdoutname = subst.do_substitution(p, p["stdout"])
  68         stdoutfile = open(stdoutname, "wb")
  69
  70     print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
  71
  72     sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
  73     sig = []
  74
  75     # forward signals to the process.
  76     signal.signal(signal.SIGINT, lambda signum, frame: send_signal(sp, signum, sig))
  77     signal.signal(signal.SIGTERM, lambda signum, frame: send_signal(sp, signum, sig))
  78     signal.signal(signal.SIGQUIT, lambda signum, frame: send_signal(sp, signum, sig))
  79
  80     # wait for process to complete.
  81     rcode = sp.wait()
  82
  83     if len(sig) > 0:
  84         print("run-command: terminating on signal %s" % sig[0])
  85         sys.exit(rcode)
  86     else:
  87         print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
  88
  89 except Exception as e:
  90     print("run-command: caught exception: {}".format(e))
  91
  92 finally:
  93     # restore default signal handlers.
  94     signal.signal(signal.SIGINT, signal.SIG_DFL)
  95     signal.signal(signal.SIGTERM, signal.SIG_DFL)
  96     signal.signal(signal.SIGQUIT, signal.SIG_DFL)
  97
  98     for l in links:
  99         os.unlink(l)
 100
 101     print("run-command: the follow output files will be saved to keep:")
 102
 103     subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
 104
 105     print("run-command: start writing output to keep")
 106
 107     done = False
 108     resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
 109     reporter = put.progress_writer(machine_progress)
 110     bytes_expected = put.expected_bytes_for(".")
 111     while not done:
 112         try:
 113             out = put.ArvPutCollectionWriter(resume_cache, reporter, bytes_expected)
 114             out.do_queued_work()
 115             out.write_directory_tree(".", max_manifest_depth=0)
 116             outuuid = out.finish()
 117             api.job_tasks().update(uuid=arvados.current_task()['uuid'],
 118                                                  body={
 119                                                      'output':outuuid,
 120                                                      'success': (rcode == 0),
 121                                                      'progress':1.0
 122                                                  }).execute()
 123             done = True
 124         except KeyboardInterrupt:
 125             print("run-command: terminating on signal SIGINT")
 126             done = True
 127         except Exception as e:
 128             print("run-command: caught exception: {}".format(e))
 129             time.sleep(5)
 130
 131 sys.exit(rcode)