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