Breadcrumbs in computations

ehomer · November 5, 2021, 9:19pm

I am running Gibbs workflows in atomate and I am suprised that there are not automatic breadcrumbs to tie completed gibbs_tasks entries back to specific tasks or workflows. Or perhaps there are and I have failed to understand or make use of possible options. Or maybe there are reasons that there is no connection. Can you let me know how I misunderstood, or how I can leave breadcrumbs to tie results with specific tasks?

mattmcdermott · November 6, 2021, 1:50am

Hi @ehomer, I think you are correct in that there are no keys in any of the gibbs_tasks entries that refer back to the specific deformation tasks. It appears there’s actually a TODO comment in the code about that:

github.com

hackingmaterials/atomate/blob/43a347a0cfd7586526c22b00f11f0b18b8747d0a/atomate/vasp/firetasks/parse_outputs.py#L699

    
      
              import traceback
          
          
    logger.warning("Quasi-harmonic analysis failed!")
              gibbs_dict["success"] = False
              gibbs_dict["traceback"] = traceback.format_exc()
              gibbs_dict["metadata"].update({"task_label_tag": tag})
              gibbs_dict["created_at"] = datetime.utcnow()
          
          
gibbs_dict = jsanitize(gibbs_dict)
          
          
# TODO: @matk86: add a list of task_ids that were used to construct the analysis to DB?
          # -computron
          if not db_file:
              dump_file = "gibbs.json"
              logger.info(f"Dumping the analysis summary to {dump_file}")
              with open(dump_file, "w") as f:
                  f.write(json.dumps(gibbs_dict, default=DATETIME_HANDLER))
          else:
              coll = mmdb.db["gibbs_tasks"]
              coll.insert_one(gibbs_dict)

I replied to your comment on the GitHub issue I created a couple years back – it seems like the Gibbs workflow in particular hasn’t seen much love in the past few years. If you are able to make a pull request it would be much appreciated