Data storage

AiiDA archive format

An AiiDA archive file is a file usually ending with extension .aiida, typically compressed in .zip or .tar.gz format, with the following content:

  • metadata.json file containing information on the version of AiiDA as well as the database schema.

  • data.json file containing the nodes and their links.

  • nodes/ directory containing the repository files corresponding to the nodes.

metadata.json

This file contains important information, and it is necessary for the correct interpretation of data.json. Apart from the data schema, the AiiDA and archive versions are also mentioned. This is used to avoid any incompatibilities among different versions of AiiDA. It should be noted that the schema described in metadata.json is related to the data itself - abstracted schema focused on the extracted information - and not how the data is stored in the database (database schema). This makes the import/export mechanism transparent to the database system used, backend selected and how the data is organised in the database (database schema).

Let’s have a look at the contents of metadata.json:

{
  "export_version": "0.7",
  "aiida_version": "1.0.0",
  "export_parameters": {
    "graph_traversal_rules": {
      "input_calc_forward": false,
      "input_calc_backward": true,
      "create_forward": true,
      "create_backward": true,
      "return_forward": true,
      "return_backward": false,
      "input_work_forward": false,
      "input_work_backward": true,
      "call_calc_forward": true,
      "call_calc_backward": false,
      "call_work_forward": true,
      "call_work_backward": false
    },
    "entities_starting_set": {
      "Node": ["1024e35e-166b-4104-95f6-c1706df4ce15"]
    },
    "include_comments": true,
    "include_logs": false
  },
  "unique_identifiers": {
    "Computer": "uuid",
    "Group": "uuid",
    "User": "email",
    "Node": "uuid",
    "Log": "uuid",
    "Comment": "uuid"
  },
  "all_fields_info": {
    "Computer": {
      "transport_type": {},
      "hostname": {},
      "description": {},
      "scheduler_type": {},
      "metadata": {},
      "uuid": {},
      "name": {}
    },
    "User": {
      "last_name": {},
      "first_name": {},
      "institution": {},
      "email": {}
    },
    "Node": {
      "ctime": {
        "convert_type": "date"
      },
      "uuid": {},
      "mtime": {
        "convert_type": "date"
      },
      "node_type": {},
      "label": {},
      "user": {
        "related_name": "dbnodes",
        "requires": "User"
      },
      "dbcomputer": {
        "related_name": "dbnodes",
        "requires": "Computer"
      },
      "description": {},
      "process_type": {}
    },
    "Group": {
      "description": {},
      "user": {
        "related_name": "dbgroups",
        "requires": "User"
      },
      "time": {
        "convert_type": "date"
      },
      "type_string": {},
      "uuid": {},
      "label": {}
    },
    "Log": {
      "uuid": {},
      "time": {
        "convert_type": "date"
      },
      "loggername": {},
      "levelname": {},
      "message": {},
      "metadata": {},
      "dbnode": {
        "requires": "Node",
        "related_name": "dblogs"
      }
    },
    "Comment": {
      "uuid": {},
      "ctime": {
        "convert_type": "date"
      },
      "mtime": {
        "convert_type": "date"
      },
      "content": {},
      "dbnode": {
        "related_name": "dbcomments",
        "requires": "Node"
      },
      "user": {
        "related_name": "dbcomments",
        "requires": "User"
      }
    }
  }
}

At the beginning of the file, we see the version of the archive file (under export_version) and the version of the AiiDA code. New archive versions are introduced for several different reasons; this may generally be when:

  • a change occurs in what can or cannot be exported for each entity,

  • the database and/or archive schemes are updated or changed,

  • or standardized exported property values are updated in AiiDA.

注解

For archives of version 0.3 and older it is advisable that you manually try to convince yourself that the migration was completely successful. While all migrations are tested, trying to include reasonable edge-cases, the migrations involed from version 0.3 to 0.4 are intricate and the possibility of a missing edge-case test is quite real. It is worth noting that if you ever have an issue, please report it on GitHub, join the AiiDA mailing list, or use the contact form.

The entities that are exported are mentioned in unique_identifiers with their respective unique identifiers. Knowing the unique IDs is useful for duplicate avoidance (in order to avoid the insertion of the node multiple times).

Then in all_fields_info, the properties of each entity are mentioned. The correlations with other entities are also mentioned. For example, the entity Node is related to a Computer and a User. The corresponding entity names appear nested next to the properties to show this correlation.

注解

If you have migrated an archive file to the newest version, there may be an extra entry in metadata.json. This simply states from which archive version the file was migrated.

注解

If you supply an old archive file that the current AiiDA code does not support, verdi archive import will automatically try to migrate the archive by calling verdi archive migrate.

data.json

A sample of the data.json file follows:

{
  "links_uuid": [
    {
      "output": "1024e35e-166b-4104-95f6-c1706df4ce15",
      "label": "parameters",
      "input": "628ba258-ccc1-47bf-bab7-8aee64b563ea",
      "type": "input_calc"
    }
  ],
  "export_data": {
    "User": {
      "2": {
        "first_name": "AiiDA",
        "last_name": "theossrv2",
        "institution": "EPFL, Lausanne",
        "email": "aiida@theossrv2.epfl.ch"
      }
    },
    "Computer": {
      "1": {
        "name": "theospc14-direct",
        "description": "theospc14 (N. Mounet's PC) with direct scheduler",
        "hostname": "theospc14.epfl.ch",
        "transport_type": "ssh",
        "metadata": {
          "default_mpiprocs_per_machine": 8,
          "workdir": "/scratch/{username}/aiida_run/",
          "append_text": "",
          "prepend_text": "",
          "mpirun_command": ["mpirun", "-np", "{tot_num_mpiprocs}"]
        },
        "scheduler_type": "direct",
        "uuid": "fb7729ff-8254-4bc0-bbec-acbdb573cfe2"
      }
    },
    "Node": {
      "5921143": {
        "uuid": "628ba258-ccc1-47bf-bab7-8aee64b563ea",
        "description": "",
        "dbcomputer": 1,
        "label": "",
        "user": 2,
        "mtime": "2016-08-21T11:55:53.132925",
        "node_type": "data.dict.Dict.",
        "ctime": "2016-08-21T11:55:53.118306",
        "process_type": ""
      },
      "20063": {
        "uuid": "1024e35e-166b-4104-95f6-c1706df4ce15",
        "description": "",
        "dbcomputer": 1,
        "label": "",
        "user": 2,
        "mtime": "2016-02-16T10:33:54.095973",
        "process_type": "aiida.calculations:codtools.ciffilter",
        "node_type": "process.calculation.calcjob.CalcJobNode.",
        "ctime": "2015-10-02T20:08:06.628472"
      }
    },
    "Comment": {
      "1": {
        "uuid": "8c165836-6ae1-4ae8-8cf1-fb111abc483e",
        "ctime": "2016-08-21T11:56:05.501162",
        "mtime": "2016-08-21T11:56:05.501697",
        "content": "vc-relax calculation with cold smearing",
        "dbnode": 20063,
        "user": 2
      }
    }
  },
  "groups_uuid": {},
  "node_attributes": {
    "5921143": {
      "CONTROL": {
        "calculation": "vc-relax",
        "restart_mode": "from_scratch",
        "max_seconds": 83808
      },
      "ELECTRONS": {
        "electron_maxstep": 100,
        "conv_thr": 3.6e-10
      },
      "SYSTEM": {
        "ecutwfc": 90.0,
        "input_dft": "vdw-df2-c09",
        "occupations": "smearing",
        "degauss": 0.02,
        "smearing": "cold",
        "ecutrho": 1080.0
      }
    },
    "20063": {
      "retrieve_list": [
        "aiida.out",
        "aiida.err",
        "_scheduler-stdout.txt",
        "_scheduler-stderr.txt"
      ],
      "last_job_info": {
        "job_state": "DONE",
        "job_id": "13489"
      },
      "scheduler_state": "DONE",
      "parser": "codtools.ciffilter",
      "linkname_retrieved": "retrieved",
      "jobresource_params": {
        "num_machines": 1,
        "num_mpiprocs_per_machine": 1,
        "default_mpiprocs_per_machine": 8
      },
      "remote_workdir": "/scratch/aiida/aiida_run/10/24/e35e-166b-4104-95f6-c1706df4ce15",
      "process_state": "finished",
      "max_wallclock_seconds": 900,
      "retrieve_singlefile_list": [],
      "scheduler_lastchecktime": "2015-10-02T20:30:36.481951+00:00",
      "job_id": "13489",
      "exit_status": 0,
      "process_status": null,
      "process_label": "vc-relax",
      "sealed": true
    }
  },
  "node_extras": {
    "5921143": {},
    "20063": {}
  }
}

At the start of the JSON file shown above, the links among the various AiiDA nodes are stated (links_uuid field). For every link the UUIDs of the connected nodes, as well as the name of the link, are mentioned.

Then follows the data “grouped” into entity types. It is worth noticing the references between the instances of the various entities. For example the DbNode with identifier 5921143 belongs to the user with identifier 2 and was generated by the computer with identifier 1.

The name of the entities is a reference to the base ORM entities. This ensures that the archive files are compatible between different actual database backend/schema implementations (e.g. Django, SQLAlchemy, …).

If any groups are extracted, then they are mentioned in the corresponding field (groups_uuid).

Attributes and extras of the extracted nodes, are described in the final part of the JSON file. The identifier of the corresponding node is used as a key for the attribute or extra.