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: wrote {} total {}\n".format(
  53         bytes_written, -1 if (bytes_expected is None) else bytes_expected)
  54
  55 class SigHandler(object):
  56     def __init__(self):
  57         self.sig = None
  58
  59     def send_signal(self, sp, signum):
  60         sp.send_signal(signum)
  61         self.sig = signum
  62
  63 try:
  64     cmd = []
  65     for c in p["command"]:
  66         cmd.append(subst.do_substitution(p, c))
  67
  68     stdoutname = None
  69     stdoutfile = None
  70     if "stdout" in p:
  71         stdoutname = subst.do_substitution(p, p["stdout"])
  72         stdoutfile = open(stdoutname, "wb")
  73
  74     print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
  75
  76     sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
  77     sig = SigHandler()
  78
  79     # forward signals to the process.
  80     signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(sp, signum))
  81     signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(sp, signum))
  82     signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(sp, signum))
  83
  84     # wait for process to complete.
  85     rcode = sp.wait()
  86
  87     if sig.sig != None:
  88         print("run-command: terminating on signal %s" % sig.sig)
  89         sys.exit(2)
  90     else:
  91         print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
  92
  93 except Exception as e:
  94     print("run-command: caught exception: {}".format(e))
  95
  96 # restore default signal handlers.
  97 signal.signal(signal.SIGINT, signal.SIG_DFL)
  98 signal.signal(signal.SIGTERM, signal.SIG_DFL)
  99 signal.signal(signal.SIGQUIT, signal.SIG_DFL)
 100
 101 for l in links:
 102     os.unlink(l)
 103
 104 print("run-command: the follow output files will be saved to keep:")
 105
 106 subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
 107
 108 print("run-command: start writing output to keep")
 109
 110 done = False
 111 resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
 112 reporter = put.progress_writer(machine_progress)
 113 bytes_expected = put.expected_bytes_for(".")
 114 while not done:
 115     try:
 116         out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected)
 117         out.do_queued_work()
 118         out.write_directory_tree(".", max_manifest_depth=0)
 119         outuuid = out.finish()
 120         api.job_tasks().update(uuid=arvados.current_task()['uuid'],
 121                                              body={
 122                                                  'output':outuuid,
 123                                                  'success': (rcode == 0),
 124                                                  'progress':1.0
 125                                              }).execute()
 126         done = True
 127     except KeyboardInterrupt:
 128         print("run-command: terminating on signal 2")
 129         sys.exit(2)
 130     except Exception as e:
 131         print("run-command: caught exception: {}".format(e))
 132         time.sleep(5)
 133
 134 sys.exit(rcode)