Open phetogoportia opened 1 year ago
@Athanaseus
I am trying to calibrate uGMRT data with caracal; however, it fails with an error instead:
# MSUtils.flag_stats - 2022-10-15 20:18:51,926 INFO - Computing correlation flag stats data... # MSUtils.flag_stats - 2022-10-15 20:18:51,926 INFO - Correlation Names: ['RR', 'LL'] # MSUtils.flag_stats - 2022-10-15 20:18:58,439 INFO - Output json file: /stimela_mount/output/3c105-cal-flag-flagging-summary-0.json. # MSUtils.flag_stats - 2022-10-15 20:18:58,443 INFO - Plotting flag stats data. # MSUtils.flag_stats - 2022-10-15 20:18:58,473 INFO - Output plots: /stimela_mount/output/3c105-cal-flag-flagging-summary-plots-0.html. # Traceback (most recent call last): # File "/stimela_mount/code/run.py", line 35, in <module> # flag_stats.plot_statistics(**args) # File "/usr/local/lib/python3.6/dist-packages/MSUtils/flag_stats.py", line 423, in plot_statistics # _plot_flag_stats(**flag_data, outfile=htmlfile) # File "/usr/local/lib/python3.6/dist-packages/MSUtils/flag_stats.py", line 417, in _plot_flag_stats # row(plot_list[1], plot_list[0]))) # File "/usr/local/lib/python3.6/dist-packages/bokeh/io/saving.py", line 86, in save # _save_helper(obj, filename, resources, title, template, theme) # File "/usr/local/lib/python3.6/dist-packages/bokeh/io/saving.py", line 148, in _save_helper # html = file_html(obj, resources, title=title, template=template, theme=theme) # File "/usr/local/lib/python3.6/dist-packages/bokeh/embed/standalone.py", line 304, in file_html # (docs_json, render_items) = standalone_docs_json_and_render_items(models_seq, suppress_callback_warning=suppress_callback_warning) # File "/usr/local/lib/python3.6/dist-packages/bokeh/embed/util.py", line 294, in standalone_docs_json_and_render_items # docs_json[docid] = doc.to_json() # File "/usr/local/lib/python3.6/dist-packages/bokeh/document/document.py", line 902, in to_json # doc_json = self.to_json_string() # File "/usr/local/lib/python3.6/dist-packages/bokeh/document/document.py", line 959, in to_json_string # return serialize_json(json, indent=indent) # File "/usr/local/lib/python3.6/dist-packages/bokeh/core/json_encoder.py", line 166, in serialize_json # return json.dumps(obj, cls=BokehJSONEncoder, allow_nan=False, indent=indent, separators=separators, sort_keys=True, **kwargs) # File "/usr/lib/python3.6/json/__init__.py", line 238, in dumps # **kw).encode(obj) # File "/usr/lib/python3.6/json/encoder.py", line 199, in encode # chunks = self.iterencode(o, _one_shot=True) # File "/usr/lib/python3.6/json/encoder.py", line 257, in iterencode # return _iterencode(o, 0) # ValueError: Out of range float values are not JSON compliant 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: cd /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 && singularity run --workdir /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 --containall returns error code 1 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: job failed at 2022-10-15 20:18:58.768665 after 0:00:41.322741 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: Traceback (most recent call last): 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: File "/home/phetogo/venv/cara/lib/python3.8/site-packages/stimela/recipe.py", line 713, in run 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: job.run_job() 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: File "/home/phetogo/venv/cara/lib/python3.8/site-packages/stimela/recipe.py", line 425, in run_job 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: self.job.run(output_wrangler=self.apply_output_wranglers) 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: File "/home/phetogo/venv/cara/lib/python3.8/site-packages/stimela/singularity.py", line 123, in run 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: utils.xrun(f"cd {self.execdir} && singularity run --workdir {self.execdir} --containall", 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: File "/home/phetogo/venv/cara/lib/python3.8/site-packages/stimela/utils/xrun_poll.py", line 227, in xrun 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: raise StimelaCabRuntimeError("{} returns error code {}".format(command_name, status)) 2022-10-15 20:18:58 CARACal.Stimela.flag-summary-ms0 ERROR: stimela.utils.StimelaCabRuntimeError: cd /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 && singularity run --workdir /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 --containall returns error code 1 2022-10-15 20:18:58 CARACal.Stimela.flag INFO: Completed jobs : ['save-3C105_flag_before-ms0', 'flag-autocorr-ms0', 'flag-spw-ms0', 'flag-manual-ms0-0', 'flag-manual-ms0-1', 'flag-manual-ms0-2', 'flag-manual-ms0-3', 'flag-rfi-ms0'] 2022-10-15 20:18:58 CARACal.Stimela.flag INFO: Remaining jobs : [] 2022-10-15 20:18:58 CARACal.Stimela.flag INFO: Saving pipeline information in .last_flag.json 2022-10-15 20:18:58 CARACal ERROR: Job 'flag-summary-ms0:: Flagging summary ms=3c105-cal.ms' failed: cd /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 && singularity run --workdir /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 --containall returns error code 1 [PipelineException] 2022-10-15 20:18:58 CARACal INFO: More information can be found in the logfile at output-3c/logs-20221015-195321/log-caracal.txt 2022-10-15 20:18:58 CARACal INFO: You are running version 1.0.6-24-g63019ef0 2022-10-15 20:18:58 CARACal ERROR: Traceback (most recent call last): 2022-10-15 20:18:58 CARACal ERROR: File "/home/phetogo/Software/caracal/caracal/main.py", line 187, in __run 2022-10-15 20:18:58 CARACal ERROR: pipeline.run_workers() 2022-10-15 20:18:58 CARACal ERROR: File "/home/phetogo/Software/caracal/caracal/workers/worker_administrator.py", line 441, in run_workers 2022-10-15 20:18:58 CARACal ERROR: worker.worker(self, recipe, config) 2022-10-15 20:18:58 CARACal ERROR: File "/home/phetogo/Software/caracal/caracal/workers/flag_worker.py", line 551, in worker 2022-10-15 20:18:58 CARACal ERROR: recipe.run() 2022-10-15 20:18:58 CARACal ERROR: File "/home/phetogo/venv/cara/lib/python3.8/site-packages/stimela/recipe.py", line 764, in run 2022-10-15 20:18:58 CARACal ERROR: raise PipelineException(exc, self.completed, job, self.remaining) from None 2022-10-15 20:18:58 CARACal ERROR: stimela.exceptions.PipelineException: Job 'flag-summary-ms0:: Flagging summary ms=3c105-cal.ms' failed: cd /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 && singularity run --workdir /home/phetogo/new_project/3C105/ugmrt/.stimela_workdir-16658570665552719 --containall returns error code 1 2022-10-15 20:18:58 CARACal INFO: exiting with error code 1
Duplicate of #1422
@Athanaseus
I am trying to calibrate uGMRT data with caracal; however, it fails with an error instead: