MBM and Maget test - executors don't register with server

[ghost]

Running:

pydpiper_testing/test_MBM_and_MAGeT.py test-data/

and has been waiting for an hour at this stage, which I presume is wrong:

Warning: Not masking your images from atlas masks after LSQ6 alignment ... probably not what you want (this can have negative effects on your registration and statistics) [/usr/local/lib/python3.6/dist-packages/pydpiper-2.0.13-py3.6.egg/EGG-INFO/scripts/MBM.py:315]

Total number of stages in the pipeline: 1858 Number of stages already processed: 0 Daemon is running at: 172.17.0.3:39423 The pipeline's uri is: PYRO:obj_2a7e1beb261d4c34a2fb47b949b311a2@172.17.0.3:39423 .0.localhost

Submitted 20 executors (clients) to the queue. Waiting for them to register with the server... .........................................................................................................................................................................................................................................................................................

Any suggestions as to what might be the issue?

--

Pydpiper was downloaded with

git clone https://github.com/Mouse-Imaging-Centre/pydpiper.git

It is run on a container based on:

nistmni/minc-toolkit:1.9.16

torque was built and installed from github latest.

[gdevenyi]

Containers cannot communicate outside the cluster. If you want to do cluster work, you will need to install pydpiper in the base system.

[gdevenyi]

If you wish to run locally you can do so by editing the sample.cfg, as per: https://github.com/Mouse-Imaging-Centre/pydpiper/blob/master/pydpiper_testing/test_MBM_and_MAGeT.py#L6

[ghost]

Could you just be a bit more explicit of what exactly to change to run locally? I've been through every line of that file and none seem appropriate. I tried setting num_execs to 0 and 1 just in case that was taken into consideration elsewhere, but it was not.

[gdevenyi]

The configuration file is a 1-1 mapping to --help options:

  --local               Don't submit anything to any specified queueing system
                        but instead run as a server/executor

[ghost]

Thank you.

[ghost]

Sorry to repoen this - I just want to check that after:

`Total number of stages in the pipeline: 1858 Number of stages already processed: 0 Daemon is running at: 172.17.0.5:45343 The pipeline's uri is: PYRO:obj_e25c6374de0f4b98b47a4efb6f016015@172.17.0.5:45343 . Submitted 20 executors (clients) to the queue. Waiting for them to register with the server...

Client registered (Eh!): PYRO:obj_b4166e290fe54fc6b1da884756df5088@172.17.0.5:37335 Client registered (Eh!): PYRO:obj_016fab94f6ad4714ab7baad9f228018a@172.17.0.5:40189 Client registered (Eh!): PYRO:obj_cd57c767ba6345d5b20304cfce9a1cd8@172.17.0.5:39919 Client registered (Eh!): PYRO:obj_06da3e3683d244f5901c38bd8dfe3a90@172.17.0.5:41167 Client registered (Eh!): PYRO:obj_2e79b935840c4dd9aab18d1437938a43@172.17.0.5:35385 Client registered (Eh!): PYRO:obj_ef6e82df4f38438e9cfd348394bb67fc@172.17.0.5:45387 Client registered (Eh!): PYRO:obj_ef57c2d3e800494186ba75e0fd09f534@172.17.0.5:41887 Client registered (Eh!): PYRO:obj_4828b335c0434fd4b4ed5be9dd02e3d3@172.17.0.5:43061 Client registered (Eh!): PYRO:obj_adf01ed35dcd4bb98059203366d4691f@172.17.0.5:42801 Client registered (Eh!): PYRO:obj_16a5caf850b847edbd4b22140b0d3b45@172.17.0.5:43197 Client registered (Eh!): PYRO:obj_7243652fd26b42769f81e4629587025f@172.17.0.5:33261 Client registered (Eh!): PYRO:obj_b6bddfdb32c544a4986351ee6fbb9410@172.17.0.5:36257 Client registered (Eh!): PYRO:obj_eadc3d74627d40678097b868f5b1cef7@172.17.0.5:37051 Client registered (Eh!): PYRO:obj_a5c96edfe67f4c8b9bea87257c5e728c@172.17.0.5:46655 Client registered (Eh!): PYRO:obj_98eddcd99a5f4c1388ab2dc39d72a67a@172.17.0.5:35869 Client registered (Eh!): PYRO:obj_0ae1e159dd004bcaa8cdbc68e1182e63@172.17.0.5:33371 Client registered (Eh!): PYRO:obj_0a94ed3c2ad04eff96ed0b943ff5597e@172.17.0.5:40705 Client registered (Eh!): PYRO:obj_69845758feb34cefbe617adbd84e8edf@172.17.0.5:41949 Client registered (Eh!): PYRO:obj_fe7551b1cacf4e06b5c3b2c09986b795@172.17.0.5:45435 Client registered (Eh!): PYRO:obj_1f4d4c6e475646c8a486f49a5003a1b1@172.17.0.5:45999.......`

I should expect no further output until the process is finished, in approx 24 hours?

[gdevenyi]

You can follow progress at pipeline.log

The server itself doesn't output much of anything while its running except for submitting new executors and reporting they registered.

[ghost]

Thanks Gabriel.