quantRunner

Documentation

Overview

Exposes interfaces and structures required to run PIQUANT in the Kubernetes cluster along with functions to access quantification files, logs, results and summaries of quant jobs.

Example (EstimateNodeCount)

Output:

10
18
18
18
18
19
19
20
20
21
19
17
6

Example (FilesPerNode)

Output:

1619
2690

Index

• func EstimateNodeCount(spectraCount int32, elementCount int32, desiredRunTimeSec int32, ...) int32
• func FilesPerNode(spectraCount int32, nodeCount int32) int32
• func MakePMCFileName(nodeNumber int) string
• type PiquantParams
• type QuantRunner
  • func GetQuantRunner(name string) (QuantRunner, error)

Examples

• Package (EstimateNodeCount)
• Package (FilesPerNode)

Functions

func EstimateNodeCount

func EstimateNodeCount(spectraCount int32, elementCount int32, desiredRunTimeSec int32, coresPerNode int32, maxNodes int32) int32

func FilesPerNode

func FilesPerNode(spectraCount int32, nodeCount int32) int32

func MakePMCFileName

func MakePMCFileName(nodeNumber int) string

MakePMCFileName - generates a name for the PMC list file based on a given node-numer

NOTE: nodes are 0-based whereas pmc filenames are 1-based,
	  so the first node is 0 and will work on pmcs in node00001.pmcs

Types

type PiquantParams

type PiquantParams struct {
	RunTimeEnv        string   `json:"runtimeEnv"`
	JobID             string   `json:"jobId"`
	JobsPath          string   `json:"jobsPath"`
	DatasetPath       string   `json:"datasetPath"`
	DetectorConfig    string   `json:"detectorConfig"`
	Elements          []string `json:"elements"`
	Parameters        string   `json:"parameters"`
	DatasetsBucket    string   `json:"datasetsBucket"`
	ConfigBucket      string   `json:"configBucket"`
	PiquantJobsBucket string   `json:"jobBucket"`
	QuantName         string   `json:"name"`
	PMCListName       string   `json:"pmcListName"`
	Command           string   `json:"command"`
}

PiquantParams - Parameters for running piquant, as generated by PIXLISE API

type QuantRunner

type QuantRunner interface {
	RunPiquant(piquantDockerImage string, params PiquantParams, pmcListNames []string, cfg config.APIConfig, requestorUserId string, log logger.ILogger) error
}

func GetQuantRunner

func GetQuantRunner(name string) (QuantRunner, error)