Hi all,
I am trying to set up a Galaxy cluster using the LWR runner. The nodes have
a shared filesystem and in universe.wsgi this parameter is set :
job_working_directory = /mnt/shared
...
clustalw = lwr://http://192.168.33.12:8913
....
this folder has been "chown-ed" to the galaxy user, and also is "a+w",
while it has been verified that can been read / written by ssh-ing to
each node of the cluster. The sticky bit is set.
When I try to run jobs (I used clustalw as example) there seems to be
confusion between where Galaxy puts files and where LWR tries to read
them from. Here are two setups that error out:
1). When in server.ini for LWR the following is set as:
staging_directory = /mnt/shared/000
galaxy error:
galaxy.jobs DEBUG 2013-05-06 10:21:22,320 (128) Working directory for job is: /mnt/shared/000/128
galaxy.jobs.handler DEBUG 2013-05-06 10:21:22,320 dispatching job 128 to lwr runner
galaxy.jobs.handler INFO 2013-05-06 10:21:22,427 (128) Job dispatched
galaxy.datatypes.metadata DEBUG 2013-05-06 10:21:22,875 Cleaning up external metadata files
galaxy.jobs.runners.lwr ERROR 2013-05-06 10:21:22,902 failure running job 128
lwr error (on the cluster node):
File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/app.py", line 81, in setup
manager.setup_job_directory(job_id)
File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/manager.py", line 101, in setup_job_directory
os.mkdir(job_directory)
OSError: [Errno 17] File exists: '/mnt/shared/000/128'
2). When in server.ini for LWR the following is set as:
staging_directory = /mnt/shared
galaxy error:
galaxy.jobs DEBUG 2013-05-06 10:28:46,872 (129) Working directory for job is: /mnt/shared/000/129
galaxy.jobs.handler DEBUG 2013-05-06 10:28:46,872 dispatching job 129 to lwr runner
galaxy.jobs.handler INFO 2013-05-06 10:28:46,967 (129) Job dispatched
192.168.33.1 - - [06/May/2013:10:28:48 -0200] "GET /api/histories/2a56795cad3c7db3 HTTP/1.1" 200 - "http://192.168.33.11:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/537.31 (KHTML, like Gecko) Chrome/26.0.1410.65 Safari/537.31"
galaxy.jobs.runners.lwr DEBUG 2013-05-06 10:28:50,653 run_results {'status': 'status', 'returncode': 0, 'complete': 'true', 'stderr': '', 'stdout': ''}
galaxy.datatypes.metadata DEBUG 2013-05-06 10:28:50,970 Cleaning up external metadata files
galaxy.jobs.runners.lwr ERROR 2013-05-06 10:28:51,050 failure running job 129
lwr error (on the cluster node):
resp.app_iter = FileIterator(result)
File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/framework.py", line 111, in __init__
self.input = open(path, 'rb')
IOError: [Errno 2] No such file or directory: u'/mnt/shared/129/outputs/dataset_170.dat'
The full error stacks are at the end of this email. It might be something very simple that I am missing,
but any feedback would be greatly appreciated. Thanks !
Ntino
--
Konstantinos (Ntino) Krampis, Ph.D.
Asst. Professor, Informatics
J.Craig Venter Institute
kkrampis@jcvi.org
agbiotec@gmail.com
+1-540-200-8277
Web:
http://bit.ly/cloud-research
http://cloudbiolinux.org/
http://twitter.com/agbiotec
---- GALAXY ERROR
galaxy.jobs DEBUG 2013-05-06 10:21:22,320 (128) Working directory for job is: /mnt/shared/000/128
galaxy.jobs.handler DEBUG 2013-05-06 10:21:22,320 dispatching job 128 to lwr runner
galaxy.jobs.handler INFO 2013-05-06 10:21:22,427 (128) Job dispatched
galaxy.datatypes.metadata DEBUG 2013-05-06 10:21:22,875 Cleaning up external metadata files
galaxy.jobs.runners.lwr ERROR 2013-05-06 10:21:22,902 failure running job 128
Traceback (most recent call last):
File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 286, in run_job
file_stager = FileStager(client, command_line, job_wrapper.extra_filenames, input_files, output_files, job_wrapper.tool.tool_dir)
File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 40, in __init__
job_config = client.setup()
File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 212, in setup
return self.__raw_execute_and_parse("setup", { "job_id" : self.job_id })
File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 150, in __raw_execute_and_parse
response = self.__raw_execute(command, args, data)
File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 146, in __raw_execute
response = self.url_open(request, data)
File "/home/vagrant/galaxy-dist/lib/galaxy/jobs/runners/lwr.py", line 134, in url_open
return urllib2.urlopen(request, data)
File "/usr/lib/python2.7/urllib2.py", line 126, in urlopen
return _opener.open(url, data, timeout)
File "/usr/lib/python2.7/urllib2.py", line 406, in open
response = meth(req, response)
File "/usr/lib/python2.7/urllib2.py", line 519, in http_response
'http', request, response, code, msg, hdrs)
File "/usr/lib/python2.7/urllib2.py", line 444, in error
return self._call_chain(*args)
File "/usr/lib/python2.7/urllib2.py", line 378, in _call_chain
result = func(*args)
File "/usr/lib/python2.7/urllib2.py", line 527, in http_error_default
raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error
---- LWR ERROR
Exception happened during processing of request from ('192.168.33.11', 44802)
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib/python2.7/SocketServer.py", line 323, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib/python2.7/SocketServer.py", line 638, in __init__
self.handle()
File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 442, in handle
BaseHTTPRequestHandler.handle(self)
File "/usr/lib/python2.7/BaseHTTPServer.py", line 340, in handle
self.handle_one_request()
File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 437, in handle_one_request
self.wsgi_execute()
File "/usr/local/lib/python2.7/dist-packages/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 287, in wsgi_execute
self.wsgi_start_response)
File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/framework.py", line 35, in __call__
return controller(environ, start_response, **request_args)
File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/framework.py", line 90, in controller_replacement
result = func(**args)
File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/app.py", line 81, in setup
manager.setup_job_directory(job_id)
File "/home/vagrant/jmchilton-lwr-5213f6dce32d/lwr/manager.py", line 101, in setup_job_directory
os.mkdir(job_directory)
OSError: [Errno 17] File exists: '/mnt/shared/000/128'
