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Summary

generate_gantt_chart fails on generating charts based on profiler log file

Actual behavior

Exception occurs:

Traceback (most recent call last): File "./profiler_chart.py", line 2, in generate_gantt_chart('/mnt/connectomics/profiler.log', cores=4) File "/home/siegfriedwagner/.local/lib/python3.6/site-packages/nipype-1.2.0-py3.6.egg/nipype/utils/draw_gantt_chart.py", line 507, in generate_gantt_chart duration = (last_node['finish'] - start_node['start']).total_seconds() TypeError: unsupported operand type(s) for -: 'str' and 'str'

Expected behavior

Graph generates flawlessly

How to replicate the behavior

Run script presented bellow on log from https://gist.github.com/SiegfriedWagner/891bb05bff3cb8224f23915634672a83

Script/Workflow details

from nipype.utils.draw_gantt_chart import generate_gantt_chart generate_gantt_chart('profiler.log', cores=4)

Platform details:

{'commit_hash': 'a0f756d1c',
 'commit_source': 'installation',
 'networkx_version': '2.3',
 'nibabel_version': '2.4.1',
 'nipype_version': '1.2.0',
 'numpy_version': '1.17.0',
 'pkg_path': '/home/siegfriedwagner/.local/lib/python3.6/site-packages/nipype-1.2.0-py3.6.egg/nipype',
 'scipy_version': '1.3.0',
 'sys_executable': '/usr/bin/python',
 'sys_platform': 'linux',
 'sys_version': '3.6.8 (default, Jan 14 2019, 11:02:34) \n'
                '[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]]',
 'traits_version': '5.1.2'}

Execution environment

Choose one

• My python environment outside container

I ran into this issue as well and fixed it for my own purpose. I'll put in a PR with the fix.

With the changes in #3290,

from nipype.utils.draw_gantt_chart import generate_gantt_chart
generate_gantt_chart('profiler.log', cores=4)

with profiler.log from this issue results in a chart like this:

In the PR's comments, the issue of the large values in runtime_threads in the logfile is noted.