I cannot get the interface to complete and make files

[cchaswell]

What happened?
I downloaded halfpipe:latest last week and have not been able to get the interface to complete. It runs, but then sits for 12+ hours and I finally have to end it.

Is there an error message?
No. It does not do anything but hang. No err.txt gets created. No execgraph file or submit_slurm is created either.

What is the exact command that you used to run Halfpipe?
Please copy it here in full.

Which settings did you use?
This is what the log.txt shows.
[2021-04-26 21:12:01,0434] [halfpipe ] [INFO ] Halfpipe version 1.0.0b6+40.g8199f57
[2021-04-26 21:12:01,0438] [halfpipe ] [IMPORTANT] Option "--verbose" was not specified. Will not print detailed logs to the terminal.
��Detailed logs information will only be available in the "log.txt" file in the working directory.
[2021-04-26 21:12:01,0439] [halfpipe ] [INFO ] Stage: spec-ui
[2021-04-26 21:30:54,0201] [halfpipe ] [INFO ] Stage: workflow
[2021-04-26 21:30:54,0202] [halfpipe ] [INFO ] config.nipype.omp_nthreads=2 (from --use-cluster)
[2021-04-26 21:30:58,0058] [halfpipe ] [INFO ] Loading spec file /ext/mnt/BIACnfs/duhsnas-pri.dhe.duke.edu/morey_biac/Lab/Duke_data/spec.json
[2021-04-26 21:30:58,0099] [halfpipe ] [INFO ] Initializing file database
[2021-04-26 21:30:58,0671] [halfpipe ] [INFO ] Initializing new workflow d38ff754
[2021-04-26 21:50:07,0027] [nipype.workflow ] [IMPORTANT]
� Running fMRIPREP version 20.2.1+halfpipe.2:
� * BIDS dataset path: /ext/mnt/BIACnfs/duhsnas-pri.dhe.duke.edu/morey_biac/Lab/Duke_data/rawdata.
� * Participant list: ['1258', '12947', '12966', '13116', '13265', '13297', '13313', '13354', '1341', '13585', '13831', '13864', '13877', '14010', '14157', '14254', '15125', '1515', '15464', '15586', '15780', '15786', '15871', '15933', '16206', '16691', '16736', '16769', '16778', '16812', '16834', '16907', '16959', '17320', '17574', '17581', '17596', '17615', '17649', '17666', '17672', '1786', '18298', '18377', '18405', '18409', '18464', '18493', '18515', '1853', '18540', '18595', '18603', '18615', '18652', '18678', '18689', '18754', '18792', '18826', '18836', '18867', '18898', '18912', '18925', '19027', '19038', '19079', '19118', '19130', '19137', '19171', '19181', '19200', '19205', '19229', '19232', '19262', '19271', '19276', '19290', '19296', '19315', '19316', '19320', '19337', '19427', '19454', '19471', '19472', '1948', '19560', '19676', '20286', '20296', '20487', '20494', '20501', '20521', '20552', '20565', '20587', '20597', '20624', '20656', '20693', '20761', '20795', '20835', '20876', '20925', '20957', '21010', '21012', '21024', '21036', '21089', '21120', '21155', '21218', '21225', '21246', '21263', '21313', '21331', '21368', '21414', '21423', '21496', '21522', '21547', '21587', '21604', '21617', '21629', '21632', '2166', '21671', '21694', '21792', '21816', '21930', '22061', '22216', '22285', '22374', '22384', '22392', '22520', '22527', '22549', '22651', '22665', '2317', '2622', '2768', '29316', '29355', '29388', '29748', '29759', '29906', '29915', '3008', '3020', '30223', '3369', '3379', '3707', '3881', '38928', '38932', '38983', '39132', '3920', '39298', '39323', '39358', '39372', '39410', '39475', '39517', '39523', '39527', '39534', '39627', '39656', '39695', '39697', '39715', '39787', '39867', '39871', '4083', '4246', '4537', '4564', '4601', '5216', '5353', '5434', '5534', '5601', '5617', '5647', '5785', '5818', '5997', '6049', '6251', '6359', '6841', '6934', '6982', '7072', '7245', '7332', '7514', '7676', '7822', '8253', '8354', '8469', '8507', '8593', '8600', '8734', '9576', '9655', '9751', '9985', '9989'].
� * Run identifier: 20210426-211158_faaef73f-1f15-4c9d-8dc6-d87277174843.
�� * Output spaces: MNI152NLin2009cAsym:res-2.
[2021-04-26 22:09:15,0239] [nipype.workflow ] [INFO ] fMRIPrep workflow graph with 73080 nodes built successfully.
[2021-04-26 23:19:51,0371] [halfpipe ] [INFO ] Finished workflow d38ff754
[2021-04-26 23:22:17,0066] [halfpipe ] [INFO ] Initializing new execgraph d38ff754
[2021-04-27 02:07:33,0076] [nipype.workflow ] [INFO ] Workflow nipype settings: ['check', 'execution', 'logging', 'monitoring']

[HippocampusGirl]

Hi Courtney,
That sounds problematic. To help me diagnose the problem, could you re-run with the option --watchdog at the end of the command? A few hours should be sufficient. Then, please send me the resulting log files.

[cchaswell]

I started from the beginning and it doesn't run very long now. It ends with this message:

I might test with another data set just to see if there is an issue with this data. There are 234 functionals and 232 anatomicals so I thought maybe there was an issue with that. I assume that the program will only run the 232 subjects that match.

This is the log file, but err and workflow weren't created.
log.txt

[HippocampusGirl]

I think I know what the performance issue is, and plan to upload a bug fix soon

[HippocampusGirl]

I have uploaded some performance improvements to the latest tag, but some others are pending at nipy/nipype#3331

[HippocampusGirl]

Works for me now on latest. Please re-open if you continue having issues :-)