Open Microscopy Environment

Posted: **Fri Jan 27, 2012 6:09 pm**

Hi,

I'd like to submit jobs into queue using PBS for my python code.
Normally, I first starts an IPython interpreter session by (bin/omero shell) and run my code within the session by

Code: Select all: In [1]: execfile('mycode.py')

But I need to be online to complete my job this way.

When I tried

Code: Select all: $ python mycode.py

then, I cannot import omero.

So, is there anyway to run my code without starting the IPython session (bin/omero shell)?

I tried something like

Code: Select all: $bin/omero shell mycode.py

but it does not work.

Thanks in advance,
BK

Posted: **Fri Jan 27, 2012 8:05 pm**

Hi BK,

Probably your best bet is to pass a session key to your script via qsub. First, login locally:

Code: Select all: $ bin/omero login USER@HOST Previous session expired for USER on HOST:4064 Password: Created session d89d42c5-b50e-4294-8b2b-ebf1b4778fd8 (USER@HOST:4064). Idle timeout: 10.0 min. Current group: GROUP

Then submit with a qsub variable list:

Code: Select all: OMERO_SESSION=d89d42c5-b50e-4294-8b2b-ebf1b4778fd8 qsub -v OMERO_SESSION ...

In your script, then, you can reference $OMERO_SESSION.

Alternatively, you can stage-in the active sessions file:

Code: Select all: $ bin/omero sessions file /Users/YOU/omero/sessions/HOST/USER/d89d42c5-b50e-4294-8b2b-ebf1b4778fd8 $ cat `bin/omero sessions file` omero.sess=d89d42c5-b50e-4294-8b2b-ebf1b4778fd8 omero.user=USER omero.host=HOST

But that may only be practical if you are already staging files in or out: http://www.clusterresources.com/torquedocs/6.3filestaging.shtml

Cheers,
~Josh

Posted: **Fri Jan 27, 2012 9:31 pm**

Thanks Josh,

Actually, it could be simply resolved by adding the OMERO_DIST/lib/python folder into the python path such as

Code: Select all: import sys Path = '/OMERO_DIST/lib/python/' sys.path.append(Path)

but when I submit multiple jobs, each of which connects to the server with the same account and retrieve data from the same table,
I got the following error.

Traceback (most recent call last):
File "test__pattern_1.py", line 108, in <module>
data, message = contentDB.retrieveDB(conn, 'slf33')
File "/xxx/lib/python/contentDB.py", line 690, in retrieveDB
values = table.read(chunk_col[col], chunk_row[row][0], chunk_row[row][-1]+1)
File "/xxx/lib/python/omero_Tables_ice.py", line 699, in read
return _M_omero.grid.Table._op_read.invoke(self, ((colNumbers, start, stop), _ctx))
Ice.UnknownLocalException: exception ::Ice::UnknownLocalException
{
unknown = TcpTransceiver.cpp:158: Ice::ConnectionLostException:
connection lost: recv() returned zero
}

Do you have any idea with this error message?

BK

Posted: **Sat Jan 28, 2012 9:02 am**

That looks like the session is being closed at some point. Could you show us your code? One option is to run in the controlling terminal (where you run qsub): bin/omero sessions keepalive

Code: Select all: $ bin/omero sessions keepalive Using session d342b8d5-adca-4f29-acd4-bb5c860f79e8 (USER@HOST:4064). Idle timeout: 10.0 min. Current group: GROUP Running keep alive every 60 seconds Press enter to cancel.

but this will depend on why the session is being closed.

Cheers,
~Josh

Open Microscopy Environment

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