Bug #4903
Updated by Tim Pierce over 9 years ago
Stack trace from job "qr1hi-8i9sb-1fmcoid6lfess9g":https://crvr.se/qr1hi-8i9sb-1fmcoid6lfess9g: <pre> 1/5/2015 5:40:24 PM compute20 1 task-print 0 Traceback (most recent call last): 1/5/2015 5:40:24 PM compute20 1 task-print 0 File "/tmp/crunch-src/crunch_scripts/bwa-index", line 11, in <module> 1/5/2015 5:40:24 PM compute20 1 task-print 0 ref_dir = arvados.util.collection_extract(collection = this_job['script_parameters']['input'], path = 'reference', decompress = False) 1/5/2015 5:40:24 PM compute20 1 task-print 0 File "/usr/local/lib/python2.7/dist-packages/arvados_python_client-0.1-py2.7.egg/arvados/util.py", line 201, in collection_extract 1/5/2015 5:40:24 PM compute20 1 task-print 0 lockfile = open(path + '.lock', 'w') 1/5/2015 5:40:24 PM compute20 1 task-print 0 IOError: [Errno 2] No such file or directory: '/tmp/crunch-job/work/reference.lock' </pre> Possible diagnosis: Crunch jobs are run with @JOB_WORK@ and @TASK_WORK@ environment variables set to temporary working directories. These are made available to jobs as @arvados.current_job().tmpdir@ and @arvados.current_task().tmpdir@ respectively. However, when these jobs run in Docker, the @JOB_WORK@ directory is not guaranteed to exist.