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
Updated by Brett Smith over 10 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 10 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 10 years ago
Bryan, have you seen this at all recently? If not, is it OK to resolve it?
Updated by Bryan Cosca over 10 years ago
- Status changed from Feedback to Resolved
Nope I haven't seen this.