Workflows: Structured Representation¶
In order to organize and store the information about workflows, we employ the Exabyte Data Convention, as explained elsewhere in this documentation.
In the expandable section below, the user can find the JSON representation of a workflow with a corresponding example. It contains a series of subworkflows, each of which contains a number of units in turn.
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Used to distinct between different schemas." }, "_id": { "type": "string", "description": "entity identity" }, "description": { "type": "string", "description": "entity description" }, "creator": { "schemaId": "system-entity-reference", "required": [ "_id", "cls" ], "properties": { "_id": { "type": "string", "description": "entity identity" }, "slug": { "type": "string", "description": "entity slug" }, "cls": { "type": "string", "description": "entity class" } }, "description": "Subset of the full information about the user who created the entity.", "title": "entity reference schema" } } }, { "schemaId": "system-bankable", "required": [ "exabyteId", "hash" ], "properties": { "exabyteId": { "type": "string", "description": "Identity of the corresponding bank entity" }, "hash": { "type": "string", "description": "Hash string which is calculated based on the meaningful fields of the entity. Used to identify equal entities." } }, "description": "bankable schema", "title": "bankable schema" } ], "description": "bankable entity schema", "title": "bankable entity schema" }, { "schemaId": "system-defaultable", "properties": { "isDefault": { "default": false, "type": "boolean", "description": "Identifies that entity is defaultable" } }, "description": "defaultable entity schema", "title": "defaultable entity schema" } ], "schemaId": "workflow", "title": "workflow schema", "$schema": "http://json-schema.org/draft-04/schema#", "type": "object", "properties": { "units": { "items": { "schemaId": "workflow-unit", "required": [ "type", "flowchartId" ], "type": "object", "properties": { "status": { "enum": [ "idle", "active", "warning", "error", "finished" ], "type": "string", "description": "Status of the unit." }, "head": { "type": "boolean", "description": "Whether this unit is the first one to be executed." }, "flowchartId": { "type": "string", "description": "Identity of the unit in the workflow. Used to trace the execution flow of the workflow." }, "name": { "type": "string", "description": "name of the unit. e.g. pw_scf" }, "tags": { "schemaId": "system-tags", "properties": { "tags": { "items": { "type": "string" }, "type": "array", "description": "entity tags" } }, "title": "entity tags schema" }, "next": { "type": "string", "description": "Next unit's flowchartId. If empty, the current unit is the last." }, "type": { "type": "string", "description": "type of the unit" }, "enableRender": { "type": "boolean", "description": "Whether Rupy should attempt to use Jinja templating to add context variables into the unit" } }, "title": "workflow unit schema" }, "type": "array", "description": "Contains the Units of the Workflow" }, "isUsingDataset": { "type": "boolean", "description": "Whether to use the dataset tab in the job designer. Mutually exclusive with using the materials tab." }, "subworkflows": { "items": { "anyOf": [ { "schemaId": "workflow-subworkflow", "required": [ "_id", "name", "units", "model", "application", "properties" ], "type": "object", "properties": { "compute": { "schemaId": "job-compute", "required": [ "queue", "nodes", "ppn", "timeLimit" ], "properties": { "errors": { "items": { "required": [ "domain", "reason", "message" ], "type": "object", "properties": { "domain": { "enum": [ "rupy", "alfred", "celim", "webapp" ], "type": "string", "description": "Domain of the error appearance (internal)." }, "message": { "type": "string", "description": "Human-readable error message. e.g. 'File Not Found: /home/demo/data/project1/job-123/job-config.json'" }, "reason": { "type": "string", "description": "Should be a short, unique, machine-readable error code string. e.g. FileNotFound" } } }, "type": "array", "description": "Computation error. Optional. Appears only if something happens on jobs execution." }, "maxCPU": { "type": "integer", "description": "Maximum CPU count per node. This parameter is used to let backend job submission infrastructure know that this job is to be charged for the maximum CPU per node instead of the actual ppn. For premium/fast queues where resources are provisioned on-demand and exclusively per user." }, "cluster": { "required": [ "fqdn", "jid" ], "type": "object", "description": "Cluster where the job is executed. Optional on create. Required on job submission.", "properties": { "jid": { "type": "string", "description": "Job's identity in RMS. e.g. 1234.master-1-staging.exabyte.io" }, "fqdn": { "type": "string", "description": "FQDN of the cluster. e.g. master-1-staging.exabyte.io" } } }, "excludeFilesPattern": { "type": "string", "description": "A Python compatible regex to exclude files from upload. e.g. ^.*.txt& excludes all files with .txt suffix" }, "ppn": { "type": "integer", "description": "number of CPUs used for the job inside the RMS." }, "queue": { "enum": [ "D", "OR", "SR", "OF", "SF" ], "type": "string", "description": "Name of the submission queue inside the Resource Management System (RMS). D: debug, OR: on-demand reuglar, SR: saving reuglar, OF: on-demand fast, SF: saving fast" }, "timeLimit": { "type": "string", "description": "Wallclock time limit for computing a job. Clock format: 'hh:mm:ss'" }, "notify": { "type": "string", "description": "Email notification for the job: n - never, a - job aborted, b - job begins, e - job ends. Last three could be combined." }, "nodes": { "type": "integer", "description": "number of nodes used for the job inside the RMS." }, "email": { "type": "string", "description": "Email address to notify about job execution." }, "arguments": { "type": "object", "description": "Optional arguments specific to using application - VASP, Quantum Espresso, etc. Specified elsewhere" } }, "description": "compute parameters", "title": "compute arguments schema" }, "name": { "type": "string", "description": "Human-readable name of the subworkflow. e.g. Total-energy" }, "isDraft": { "default": false, "type": "boolean", "description": "Defines whether to store the results/properties extracted in this unit to properties collection" }, "application": { "description": "information about the simulation engine/application.", "title": "application schema (base)", "schemaId": "software-application", "required": [ "name" ], "type": "object", "properties": { "build": { "type": "string", "description": "Application build. e.g. VTST" }, "shortName": { "type": "string", "description": "The short name of the application. e.g. qe" }, "version": { "type": "string", "description": "Application version. e.g. 5.3.5" }, "name": { "type": "string", "description": "The name of the application. e.g. espresso" }, "summary": { "type": "string", "description": "Application's short description." } } }, "units": { "items": { "schemaId": "workflow-unit", "required": [ "type", "flowchartId" ], "type": "object", "properties": { "status": { "enum": [ "idle", "active", "warning", "error", "finished" ], "type": "string", "description": "Status of the unit." }, "head": { "type": "boolean", "description": "Whether this unit is the first one to be executed." }, "flowchartId": { "type": "string", "description": "Identity of the unit in the workflow. Used to trace the execution flow of the workflow." }, "name": { "type": "string", "description": "name of the unit. e.g. pw_scf" }, "tags": { "schemaId": "system-tags", "properties": { "tags": { "items": { "type": "string" }, "type": "array", "description": "entity tags" } }, "title": "entity tags schema" }, "next": { "type": "string", "description": "Next unit's flowchartId. If empty, the current unit is the last." }, "type": { "type": "string", "description": "type of the unit" }, "enableRender": { "type": "boolean", "description": "Whether Rupy should attempt to use Jinja templating to add context variables into the unit" } }, "title": "workflow unit schema" }, "type": "array", "description": "Contains the Units of the subworkflow" }, "model": { "schemaId": "model", "required": [ "type", "subtype", "method" ], "properties": { "subtype": { "type": "string", "description": "general subtype of the model, eg. `lda`" }, "type": { "type": "string", "description": "general type of the model, eg. `dft`" }, "method": { "schemaId": "method", "required": [ "type", "subtype" ], "properties": { "subtype": { "type": "string", "description": "general subtype of this method, eg. `ultra-soft`" }, "type": { "type": "string", "description": "general type of this method, eg. `pseudopotential`" }, "precision": { "type": "object", "description": "Object showing the actual possible precision based on theory and implementation" }, "data": { "type": "object", "description": "additional data specific to method, eg. array of pseudopotentials" } }, "title": "method schema (base)" } }, "description": "Model used inside the subworkflow", "title": "model schema (base)" }, "_id": { "type": "string", "description": "subworkflow identity" }, "properties": { "items": { "type": "string", "description": "property names, eg. `band_gaps`, `band_structure`" }, "type": "array", "description": "Array of characteristic properties calculated by this subworkflow" } }, "title": "subworkflow schema" } ] }, "type": "array", "description": "Array of subworkflows. Subworkflow can be an instance of workflow to allow for nesting" }, "properties": { "items": { "type": "string", "description": "property names, eg. `band_gaps`, `band_structure`" }, "type": "array", "description": "Array of characteristic properties calculated by this workflow (TODO: add enums)" }, "workflows": { "items": { "type": "object" }, "type": "array", "description": "Array of workflows with the same schema as the current one." } } } |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 | { "exabyteId": "qKtTzu9utCo6ac4n7", "hash": "f4fd707d2e47c15f8d786cf159040954", "name": "workflow", "creator": { "_id": "HtxACY2wX4b2hS8Rv", "slug": "exadmin", "cls": "User" }, "tags": [ "workflow" ], "slug": "workflow", "units": [ { "type": "subworkflow", "_id": "LCthJ6E2QabYCZqf4", "flowchartId": "05c362dc27ff1bb98d16fd60" } ], "createdAt": "2018-11-19 06:41:46.877Z", "owner": { "_id": "HtxACY2wX4b2hS8Rv", "slug": "exabyte", "cls": "Account" }, "schemaVersion": "0.2.0", "_id": "FPjAaKfuYAL7tiHbm", "subworkflows": [ { "name": "Band Structure", "application": { "shortName": "qe", "version": "5.1.1", "name": "espresso", "summary": "Quantum Espresso" }, "units": [ { "status": "idle", "head": true, "flowchartId": "pw-scf", "name": "pw_scf", "tags": [ "test-tags" ], "type": "execution" } ], "model": { "subtype": "gga", "type": "dft", "method": { "subtype": "us", "data": { "dataset": { "files": [ { "valenceElectrons": 4, "name": "pseudopotential file", "electronicConfiguration": "s2p2", "generationDate": "05Jan2001", "textHeading": "PAW_PBE Si 05Jan2001\n 4.00000000000000\nparameters from PSCTR are:\n VRHFIN =Si: s2p2\n LEXCH = PE\n EATOM = 103.0669 eV, 7.5752 Ry\n \n TITEL = PAW_PBE Si 05Jan2001\n LULTRA = F use ultrasoft PP ?\n IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no\n RPACOR = 1.500 partial core radius\n POMASS = 28.085; ZVAL = 4.000 mass and valenz\n RCORE = 1.900 outmost cutoff radius\n RWIGS = 2.480; RWIGS = 1.312 wigner-seitz radius (au A)\n ENMAX = 245.345; ENMIN = 184.009 eV\n ICORE = 2 local potential\n LCOR = T correct aug charges\n LPAW = T paw PP\n EAUG = 322.069\n DEXC = 0.000\n RMAX = 1.950 core radius for proj-oper\n RAUG = 1.300 factor for augmentation sphere\n RDEP = 1.993 radius for radial grids\n RDEPT = 1.837 core radius for aug-charge\n \n Atomic configuration\n 6 entries n l j E occ.\n 1 0 0.50 -1785.8828 2.0000\n 2 0 0.50 -139.4969 2.0000\n 2 1 1.50 -95.5546 6.0000\n 3 0 0.50 -10.8127 2.0000\n 3 1 0.50 -4.0811 2.0000\n 3 2 1.50 -4.0817 0.0000\n Description\n l E TYP RCUT TYP RCUT\n 0 -10.8127223 23 1.900\n 0 -7.6451159 23 1.900\n 1 -4.0811372 23 1.900\n 1 2.4879257 23 1.900\n 2 -4.0817478 7 1.900\n Error from kinetic energy argument (eV)\n", "title": "Si paw pbe vasp 5.2", "apps": [ "vasp" ], "element": "Si", "source": "vasp", "radii": { "units": "angstrom", "cutoff": 1.9, "wignerSeitz": 1.312, "name": "radii", "partialCore": 1.5 }, "mass": 28.085, "energyCutoff": { "units": "eV", "max": 245.345, "name": "energy cutoff", "min": 184.009 }, "path": "/export/share/pseudo/ag/gga/pbe/gbrv/1.4/us/ag_pbe_gbrv_1.4.upf", "type": "paw", "exchangeCorrelation": { "approximation": "gga", "functional": "pbe" } } ], "elements": [ "Si", "Ge", "As" ], "name": "my set", "format": "upf", "apps": [ "espresso" ], "source": "gbrv", "version": "1.5", "type": "us", "exchangeCorrelation": { "approximation": "gga", "functional": "pbe" } } }, "type": "pseudopotential" } }, "_id": "LCthJ6E2QabYCZqf4", "properties": [ "band_structure" ] } ], "properties": [ "band_structure" ], "isDefault": true } |
There are a few notable points to emphasize from the example above.
Nested data¶
We use top-level workflow as a "container", and separate the details of each individual section of calculation inside a subworkflow.
Templating¶
We allow for using templates inside the input to individual units. In this way, we can decouple material-specific information from the workflow-specific one. More explanation can be found inside the units documentation page.
Properties¶
The "Properties" section serves as an aggregator of all the properties that are extracted at the workflow or subworkflow levels. The "results" key serves the same purpose, but for the case of units.