X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/74fb942ca46cf6f039b961b572f9c0f160a24b93..bd1f0b637be6c97374b31ed5c442ff88d25e626e:/crunch_scripts/run-command diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command index 840b4b6248..c624e3cadf 100755 --- a/crunch_scripts/run-command +++ b/crunch_scripts/run-command @@ -1,18 +1,25 @@ #!/usr/bin/env python +import logging +logging.basicConfig(level=logging.INFO, format="run-command: %(message)s") + 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 import stat import copy import traceback +import pprint +import multiprocessing +import crunchutil.robust_put as robust_put +import crunchutil.vwd as vwd os.umask(0077) @@ -26,24 +33,23 @@ os.mkdir("output") os.chdir("output") +outdir = os.getcwd() + taskp = None jobp = arvados.current_job()['script_parameters'] if len(arvados.current_task()['parameters']) > 0: - p = arvados.current_task()['parameters'] + taskp = arvados.current_task()['parameters'] links = [] -def sub_link(v): - r = os.path.basename(v) - os.symlink(os.path.join(os.environ['TASK_KEEPMOUNT'], v) , r) - links.append(r) - return r - def sub_tmpdir(v): return os.path.join(arvados.current_task().tmpdir, 'tmpdir') +def sub_outdir(v): + return outdir + def sub_cores(v): - return os.environ['CRUNCH_NODE_SLOTS'] + return str(multiprocessing.cpu_count()) def sub_jobid(v): return os.environ['JOB_UUID'] @@ -51,17 +57,15 @@ def sub_jobid(v): def sub_taskid(v): return os.environ['TASK_UUID'] -subst.default_subs["link "] = sub_link +def sub_jobsrc(v): + return os.environ['CRUNCH_SRC'] + subst.default_subs["task.tmpdir"] = sub_tmpdir +subst.default_subs["task.outdir"] = sub_outdir +subst.default_subs["job.srcdir"] = sub_jobsrc subst.default_subs["node.cores"] = sub_cores -subst.default_subs["job.id"] = sub_jobid -subst.default_subs["task.id"] = sub_taskid - -rcode = 1 - -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) +subst.default_subs["job.uuid"] = sub_jobid +subst.default_subs["task.uuid"] = sub_taskid class SigHandler(object): def __init__(self): @@ -84,7 +88,7 @@ def expand_item(p, c): return r elif isinstance(c, list): return expand_list(p, c) - elif isinstance(c, str): + elif isinstance(c, str) or isinstance(c, unicode): return [subst.do_substitution(p, c)] return [] @@ -99,9 +103,9 @@ 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 = ["$(dir %s/%s)" % (prefix, l) for l in os.listdir(fn)] + items = ["$(dir %s/%s/)" % (prefix, l) for l in os.listdir(fn)] elif stat.S_ISREG(mode): with open(fn) as f: items = [line for line in f] @@ -109,42 +113,68 @@ def get_items(p, value): else: return None -if "task.foreach" in jobp: - if arvados.current_task()['sequence'] == 0: - var = jobp["task.foreach"] - items = get_items(jobp, jobp[var]) - if items != None: - print("run-command: parallelizing on %s with items %s" % (var, items)) - - for i in items: - params = copy.copy(jobp) - params[var] = i - arvados.api().job_tasks().create(body={ - 'job_uuid': arvados.current_job()['uuid'], - 'created_by_job_task_uuid': arvados.current_task()['uuid'], - 'sequence': 1, - 'parameters': params - } - ).execute() - arvados.current_task().set_output(None) - sys.exit(0) - else: - sys.exit(1) -else: - p = jobp +stdoutname = None +stdoutfile = None +stdinname = None +stdinfile = None +rcode = 1 try: - cmd = expand_list(p, p["command"]) + if "task.foreach" in jobp: + 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 is not None: + for i in items: + params = copy.copy(jobp) + params[var] = i + arvados.api().job_tasks().create(body={ + 'job_uuid': arvados.current_job()['uuid'], + 'created_by_job_task_uuid': arvados.current_task()['uuid'], + 'sequence': 1, + 'parameters': params + } + ).execute() + 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 - stdoutname = None - stdoutfile = None - if "save.stdout" in p: - stdoutname = subst.do_substitution(p, p["save.stdout"]) + 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 "task.stdin" in taskp: + stdinname = subst.do_substitution(taskp, taskp["task.stdin"]) + stdinfile = open(stdinname, "rb") + + if "task.stdout" in taskp: + stdoutname = subst.do_substitution(taskp, taskp["task.stdout"]) stdoutfile = open(stdoutname, "wb") - print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else "")) + logging.info("{}{}{}".format(' '.join(cmd), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else "")) - sp = subprocess.Popen(cmd, shell=False, stdout=stdoutfile) +except Exception as e: + logging.exception("caught exception") + logging.error("task parameters was:") + logging.error(pprint.pformat(taskp)) + sys.exit(1) + +try: + sp = subprocess.Popen(cmd, shell=False, stdin=stdinfile, stdout=stdoutfile) sig = SigHandler() # forward signals to the process. @@ -155,15 +185,14 @@ try: # wait for process to complete. rcode = sp.wait() - if sig.sig != None: - print("run-command: terminating on signal %s" % sig.sig) + if sig.sig is not None: + logging.critical("terminating on signal %s" % sig.sig) sys.exit(2) else: - print("run-command: completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed")) + logging.info("completed with exit code %i (%s)" % (rcode, "success" if rcode == 0 else "failed")) except Exception as e: - print("run-command: caught exception:") - traceback.print_exc(file=sys.stdout) + logging.exception("caught exception") # restore default signal handlers. signal.signal(signal.SIGINT, signal.SIG_DFL) @@ -173,35 +202,27 @@ signal.signal(signal.SIGQUIT, signal.SIG_DFL) for l in links: os.unlink(l) -print("run-command: the following output files will be saved to keep:") - -subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"]) - -print("run-command: 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: - print("run-command: terminating on signal 2") - sys.exit(2) - except Exception as e: - print("run-command: caught exception:") - traceback.print_exc(file=sys.stdout) - time.sleep(5) +logging.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") + +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) + +api.job_tasks().update(uuid=arvados.current_task()['uuid'], + body={ + 'output': outcollection, + 'success': (rcode == 0), + 'progress':1.0 + }).execute() sys.exit(rcode)