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 import stat
  14 import copy
  15
  16 os.umask(0077)
  17
  18 t = arvados.current_task().tmpdir
  19
  20 api = arvados.api('v1')
  21
  22 os.chdir(arvados.current_task().tmpdir)
  23 os.mkdir("tmpdir")
  24 os.mkdir("output")
  25
  26 os.chdir("output")
  27
  28 taskp = None
  29 jobp = arvados.current_job()['script_parameters']
  30 if len(arvados.current_task()['parameters']) > 0:
  31     p = arvados.current_task()['parameters']
  32
  33 links = []
  34
  35 def sub_link(v):
  36     r = os.path.basename(v)
  37     os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r)
  38     links.append(r)
  39     return r
  40
  41 def sub_tmpdir(v):
  42     return os.path.join(arvados.current_task().tmpdir, 'tmpdir')
  43
  44 def sub_cores(v):
  45      return os.environ['CRUNCH_NODE_SLOTS']
  46
  47 def sub_jobid(v):
  48      return os.environ['JOB_UUID']
  49
  50 def sub_taskid(v):
  51      return os.environ['TASK_UUID']
  52
  53 subst.default_subs["link "] = sub_link
  54 subst.default_subs["task.tmpdir"] = sub_tmpdir
  55 subst.default_subs["node.cores"] = sub_cores
  56 subst.default_subs["job.id"] = sub_jobid
  57 subst.default_subs["task.id"] = sub_taskid
  58
  59 rcode = 1
  60
  61 def machine_progress(bytes_written, bytes_expected):
  62     return "run-command: wrote {} total {}\n".format(
  63         bytes_written, -1 if (bytes_expected is None) else bytes_expected)
  64
  65 class SigHandler(object):
  66     def __init__(self):
  67         self.sig = None
  68
  69     def send_signal(self, sp, signum):
  70         sp.send_signal(signum)
  71         self.sig = signum
  72
  73 def expand_item(p, c):
  74     if isinstance(c, dict):
  75         if "foreach" in c and "command" in c:
  76             var = c["foreach"]
  77             items = get_items(p, p[var])
  78             r = []
  79             for i in items:
  80                 params = copy.copy(p)
  81                 params[var] = i
  82                 r.extend(expand_list(params, c["command"]))
  83             return r
  84     elif isinstance(c, list):
  85         return expand_list(p, c)
  86     elif isinstance(c, str):
  87         return [subst.do_substitution(p, c)]
  88
  89     return []
  90
  91 def expand_list(p, l):
  92     return [exp for arg in l for exp in expand_item(p, arg)]
  93
  94 def get_items(p, value):
  95     if isinstance(value, list):
  96         return expand_list(p, value)
  97
  98     fn = subst.do_substitution(p, value)
  99     mode = os.stat(fn).st_mode
 100     prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:]
 101     if mode != None:
 102         if stat.S_ISDIR(mode):
 103             items = ["$(dir %s/%s)" % (prefix, l) for l in os.listdir(fn)]
 104         elif stat.S_ISREG(mode):
 105             with open(fn) as f:
 106                 items = [line for line in f]
 107         return items
 108     else:
 109         return None
 110
 111 if "task.foreach" in jobp:
 112     if arvados.current_task()['sequence'] == 0:
 113         var = jobp["task.foreach"]
 114         items = get_items(jobp, jobp[var])
 115         if items != None:
 116             print("run-command: parallelizing on %s with items %s" % (var, items))
 117
 118             for i in items:
 119                 params = copy.copy(jobp)
 120                 params[var] = i
 121                 arvados.api().job_tasks().create(body={
 122                     'job_uuid': arvados.current_job()['uuid'],
 123                     'created_by_job_task_uuid': arvados.current_task()['uuid'],
 124                     'sequence': 1,
 125                     'parameters': params
 126                     }
 127                 ).execute()
 128             arvados.current_task().set_output(None)
 129             sys.exit(0)
 130         else:
 131             sys.exit(1)
 132 else:
 133     p = jobp
 134
 135 try:
 136     cmd = expand_list(p, p["command"])
 137
 138     stdoutname = None
 139     stdoutfile = None
 140     if "save.stdout" in p:
 141         stdoutname = subst.do_substitution(p, p["save.stdout"])
 142         stdoutfile = open(stdoutname, "wb")
 143
 144     print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
 145
 146     sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile)
 147     sig = SigHandler()
 148
 149     # forward signals to the process.
 150     signal.signal(signal.SIGINT, lambda signum, frame: sig.send_signal(sp, signum))
 151     signal.signal(signal.SIGTERM, lambda signum, frame: sig.send_signal(sp, signum))
 152     signal.signal(signal.SIGQUIT, lambda signum, frame: sig.send_signal(sp, signum))
 153
 154     # wait for process to complete.
 155     rcode = sp.wait()
 156
 157     if sig.sig != None:
 158         print("run-command: terminating on signal %s" % sig.sig)
 159         sys.exit(2)
 160     else:
 161         print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed"))
 162
 163 except Exception as e:
 164     print("run-command: caught exception: {}".format(e))
 165
 166 # restore default signal handlers.
 167 signal.signal(signal.SIGINT, signal.SIG_DFL)
 168 signal.signal(signal.SIGTERM, signal.SIG_DFL)
 169 signal.signal(signal.SIGQUIT, signal.SIG_DFL)
 170
 171 for l in links:
 172     os.unlink(l)
 173
 174 print("run-command: the following output files will be saved to keep:")
 175
 176 subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
 177
 178 print("run-command: start writing output to keep")
 179
 180 done = False
 181 resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint"))
 182 reporter = put.progress_writer(machine_progress)
 183 bytes_expected = put.expected_bytes_for(".")
 184 while not done:
 185     try:
 186         out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected)
 187         out.do_queued_work()
 188         out.write_directory_tree(".", max_manifest_depth=0)
 189         outuuid = out.finish()
 190         api.job_tasks().update(uuid=arvados.current_task()['uuid'],
 191                                              body={
 192                                                  'output':outuuid,
 193                                                  'success': (rcode == 0),
 194                                                  'progress':1.0
 195                                              }).execute()
 196         done = True
 197     except KeyboardInterrupt:
 198         print("run-command: terminating on signal 2")
 199         sys.exit(2)
 200     except Exception as e:
 201         print("run-command: caught exception: {}".format(e))
 202         time.sleep(5)
 203
 204 sys.exit(rcode)