Bug #7496
closed
[SDKs] picard run-command fails with Broken Pipe socket.error on tb05z
Description
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr Traceback (most recent call last):
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/tmp/crunch-job/src/crunch_scripts/run-command", line 438, in <module>
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr 'progress':1.0
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/tmp/crunch-job-work/.arvados.venv/local/lib/python2.7/site-packages/oauth2client/util.py", line 142, in positional_wrapper
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr return wrapped(*args, **kwargs)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/tmp/crunch-job-work/.arvados.venv/local/lib/python2.7/site-packages/googleapiclient/http.py", line 722, in execute
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr body=self.body, headers=self.headers)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/tmp/crunch-job-work/.arvados.venv/local/lib/python2.7/site-packages/arvados/api.py", line 33, in intercept_http_request
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr return self.orig_http_request(uri, **kwargs)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/tmp/crunch-job-work/.arvados.venv/local/lib/python2.7/site-packages/httplib2/_init__.py", line 1609, in request
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr (response, content) = self._request(conn, authority, uri, request_uri, method, body, headers, redirections, cachekey)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/tmp/crunch-job-work/.arvados.venv/local/lib/python2.7/site-packages/httplib2/__init__.py", line 1351, in request
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr (response, content) = self._conn_request(conn, request_uri, method, body, headers)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/tmp/crunch-job-work/.arvados.venv/local/lib/python2.7/site-packages/httplib2/_init__.py", line 1273, in _conn_request
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr conn.request(method, request_uri, body, headers)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/usr/lib/python2.7/httplib.py", line 962, in request
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr self._send_request(method, url, body, headers)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/usr/lib/python2.7/httplib.py", line 996, in _send_request
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr self.endheaders(body)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/usr/lib/python2.7/httplib.py", line 958, in endheaders
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr self._send_output(message_body)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/usr/lib/python2.7/httplib.py", line 818, in _send_output
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr self.send(msg)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/usr/lib/python2.7/httplib.py", line 794, in send
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr self.sock.sendall(data)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/usr/lib/python2.7/ssl.py", line 229, in sendall
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr v = self.send(data[count:])
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr File "/usr/lib/python2.7/ssl.py", line 198, in send
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr v = self._sslobj.write(data)
2015-10-09_08:05:06 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr socket.error: [Errno 32] Broken pipe
2015-10-09_08:05:16 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr crunchstat: notice: stats not available: stat memory.stat, statgroup memory, cid 44457f5761a77fc7c39935cde648821adcdb40c2007d50f769592c10f25423f5, parent docker, root /sys/fs/cgroup
2015-10-09_08:05:16 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr crunchstat: notice: stats not available: stat cpuacct.stat, statgroup cpuacct, cid 44457f5761a77fc7c39935cde648821adcdb40c2007d50f769592c10f25423f5, parent docker, root /sys/fs/cgroup
2015-10-09_08:05:16 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr crunchstat: notice: stats not available: stat blkio.io_service_bytes, statgroup blkio, cid 44457f5761a77fc7c39935cde648821adcdb40c2007d50f769592c10f25423f5, parent docker, root /sys/fs/cgroup
2015-10-09_08:05:16 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr crunchstat: notice: stats not available: stat cgroup.procs, statgroup cpuacct, cid 44457f5761a77fc7c39935cde648821adcdb40c2007d50f769592c10f25423f5, parent docker, root /sys/fs/cgroup
2015-10-09_08:05:24 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 stderr srun: error: compute1: task 0: Exited with exit code 1
2015-10-09_08:05:24 tb05z-8i9sb-ptlj63ffq4uvk2q 17963 0 child 1698 on compute1.1 exit 1 success=false
Related issues
Updated by Brett Smith over 8 years ago
- Subject changed from Broken pipe on tb05z to [SDKs] picard run-command fails with Broken Pipe socket.error on tb05z
#7587 has become the umbrella bug for this issue.
Updated by Brett Smith over 8 years ago
- Status changed from New to Feedback
A fix for #7587 is merged, so this is expected to be resolved as long as the job runs with an arvados_sdk_version with the fix.
Updated by Brett Smith over 8 years ago
Bryan, have you seen this at all recently? If not, is it OK to resolve it?
Updated by Bryan Cosca over 8 years ago
- Status changed from Feedback to Resolved
Nope I haven't seen this.