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