X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/c5be0c3abd926adc54e0c1de65e8dfdd25a84ea1..78317dade4e29b06f1f83b16603cc8ef5c42c434:/crunch_scripts/run-command diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command index 7d77248674..48c8b5821d 100755 --- a/crunch_scripts/run-command +++ b/crunch_scripts/run-command @@ -1,12 +1,20 @@ #!/usr/bin/env python +import logging + +logger = logging.getLogger('run-command') +log_handler = logging.StreamHandler() +log_handler.setFormatter(logging.Formatter("run-command: %(message)s")) +logger.addHandler(log_handler) +logger.setLevel(logging.INFO) + import arvados import re import os import subprocess import sys import shutil -import subst +import crunchutil.subst as subst import time import arvados.commands.put as put import signal @@ -15,10 +23,10 @@ import copy import traceback import pprint import multiprocessing -import logging +import crunchutil.robust_put as robust_put +import crunchutil.vwd as vwd os.umask(0077) -logging.basicConfig(format="run-command: %(message)s") t = arvados.current_task().tmpdir @@ -39,12 +47,6 @@ if len(arvados.current_task()['parameters']) > 0: links = [] -def sub_link(v): - r = os.path.join(outdir, os.path.basename(v)) - os.symlink(v, r) - links.append(r) - return r - def sub_tmpdir(v): return os.path.join(arvados.current_task().tmpdir, 'tmpdir') @@ -63,7 +65,6 @@ def sub_taskid(v): def sub_jobsrc(v): return os.environ['CRUNCH_SRC'] -subst.default_subs["link "] = sub_link subst.default_subs["task.tmpdir"] = sub_tmpdir subst.default_subs["task.outdir"] = sub_outdir subst.default_subs["job.srcdir"] = sub_jobsrc @@ -71,10 +72,6 @@ subst.default_subs["node.cores"] = sub_cores subst.default_subs["job.uuid"] = sub_jobid subst.default_subs["task.uuid"] = sub_taskid -def machine_progress(bytes_written, bytes_expected): - return "run-command: wrote {} total {}\n".format( - bytes_written, -1 if (bytes_expected is None) else bytes_expected) - class SigHandler(object): def __init__(self): self.sig = None @@ -111,7 +108,7 @@ def get_items(p, value): fn = subst.do_substitution(p, value) mode = os.stat(fn).st_mode prefix = fn[len(os.environ['TASK_KEEPMOUNT'])+1:] - if mode != None: + if mode is not None: if stat.S_ISDIR(mode): items = ["$(dir %s/%s/)" % (prefix, l) for l in os.listdir(fn)] elif stat.S_ISREG(mode): @@ -123,6 +120,8 @@ def get_items(p, value): stdoutname = None stdoutfile = None +stdinname = None +stdinfile = None rcode = 1 try: @@ -130,8 +129,8 @@ try: if arvados.current_task()['sequence'] == 0: var = jobp["task.foreach"] items = get_items(jobp, jobp[var]) - logging.info("parallelizing on %s with items %s" % (var, items)) - if items != None: + logger.info("parallelizing on %s with items %s" % (var, items)) + if items is not None: for i in items: params = copy.copy(jobp) params[var] = i @@ -142,29 +141,49 @@ try: 'parameters': params } ).execute() - arvados.current_task().set_output(None) + if "task.vwd" in jobp: + # Base vwd collection will be merged with output fragments from + # the other tasks by crunch. + arvados.current_task().set_output(subst.do_substitution(jobp, jobp["task.vwd"])) + else: + arvados.current_task().set_output(None) sys.exit(0) else: sys.exit(1) else: taskp = jobp + if "task.vwd" in taskp: + # Populate output directory with symlinks to files in collection + vwd.checkout(subst.do_substitution(taskp, taskp["task.vwd"]), outdir) + + if "task.cwd" in taskp: + os.chdir(subst.do_substitution(taskp, taskp["task.cwd"])) + cmd = expand_list(taskp, taskp["command"]) - if "save.stdout" in taskp: - stdoutname = subst.do_substitution(taskp, taskp["save.stdout"]) - stdoutfile = open(stdoutname, "wb") + if "task.stdin" in taskp: + stdinname = subst.do_substitution(taskp, taskp["task.stdin"]) + stdinfile = open(stdinname, "rb") - logging.info("{}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else "")) + if "task.stdout" in taskp: + stdoutname = subst.do_substitution(taskp, taskp["task.stdout"]) + stdoutfile = open(stdoutname, "wb") + logger.info("{}{}{}".format(' '.join(cmd), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else "")) +except subst.SubstitutionError as e: + logger.error(str(e)) + logger.error("task parameters was:") + logger.error(pprint.pformat(taskp)) + sys.exit(1) except Exception as e: - logging.exception("caught exception") - logging.error("task parameters was:") - logging.error(pprint.pformat(taskp)) + logger.exception("caught exception") + logger.error("task parameters was:") + logger.error(pprint.pformat(taskp)) sys.exit(1) try: - sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile) + sp = subprocess.Popen(cmd, shell=False, stdin=stdinfile, stdout=stdoutfile) sig = SigHandler() # forward signals to the process. @@ -175,14 +194,14 @@ try: # wait for process to complete. rcode = sp.wait() - if sig.sig != None: - logging.critical("terminating on signal %s" % sig.sig) + if sig.sig is not None: + logger.critical("terminating on signal %s" % sig.sig) sys.exit(2) else: - logging.info("completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed")) + logger.info("completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed")) except Exception as e: - logging.exception("caught exception") + logger.exception("caught exception") # restore default signal handlers. signal.signal(signal.SIGINT, signal.SIG_DFL) @@ -192,34 +211,27 @@ signal.signal(signal.SIGQUIT, signal.SIG_DFL) for l in links: os.unlink(l) -logging.info("the following output files will be saved to keep:") +logger.info("the following output files will be saved to keep:") subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr) -logging.info("start writing output to keep") - -done = False -resume_cache = put.ResumeCache(os.path.join(arvados.current_task().tmpdir, "upload-output-checkpoint")) -reporter = put.progress_writer(machine_progress) -bytes_expected = put.expected_bytes_for(".") -while not done: - try: - out = put.ArvPutCollectionWriter.from_cache(resume_cache, reporter, bytes_expected) - out.do_queued_work() - out.write_directory_tree(".", max_manifest_depth=0) - outuuid = out.finish() - api.job_tasks().update(uuid=arvados.current_task()['uuid'], - body={ - 'output':outuuid, - 'success': (rcode == 0), - 'progress':1.0 - }).execute() - done = True - except KeyboardInterrupt: - logging.critical("terminating on signal 2") - sys.exit(2) - except Exception as e: - logging.exception("caught exception:") - time.sleep(5) +logger.info("start writing output to keep") + +if "task.vwd" in taskp: + if "task.foreach" in jobp: + # This is a subtask, so don't merge with the original collection, that will happen at the end + outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=False).manifest_text() + else: + # Just a single task, so do merge with the original collection + outcollection = vwd.checkin(subst.do_substitution(taskp, taskp["task.vwd"]), outdir, merge=True).manifest_text() +else: + outcollection = robust_put.upload(outdir, logger) + +api.job_tasks().update(uuid=arvados.current_task()['uuid'], + body={ + 'output': outcollection, + 'success': (rcode == 0), + 'progress':1.0 + }).execute() sys.exit(rcode)