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task.go
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task.go
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package core
import (
"errors"
"fmt"
"github.com/MG-RAST/AWE/lib/conf"
"github.com/MG-RAST/AWE/lib/logger"
"os/exec"
"strings"
"time"
)
const (
TASK_STAT_INIT = "init"
TASK_STAT_QUEUED = "queued"
TASK_STAT_INPROGRESS = "in-progress"
TASK_STAT_PENDING = "pending"
TASK_STAT_SUSPEND = "suspend"
TASK_STAT_COMPLETED = "completed"
TASK_STAT_SKIPPED = "user_skipped"
TASK_STAT_FAIL_SKIP = "skipped"
TASK_STAT_PASSED = "passed"
)
type Task struct {
Id string `bson:"taskid" json:"taskid"`
Info *Info `bson:"info" json:"-"`
Inputs []*IO `bson:"inputs" json:"inputs"`
Outputs []*IO `bson:"outputs" json:"outputs"`
Predata []*IO `bson:"predata" json:"predata"`
Cmd *Command `bson:"cmd" json:"cmd"`
App *App `bson:"app" json:"app"`
AppVariablesArray []*AppVariable // not in App as workunit does not need AppVariables and I want to pass App
Partition *PartInfo `bson:"partinfo" json:"-"`
DependsOn []string `bson:"dependsOn" json:"dependsOn"`
TotalWork int `bson:"totalwork" json:"totalwork"`
MaxWorkSize int `bson:"maxworksize" json:"maxworksize"`
RemainWork int `bson:"remainwork" json:"remainwork"`
WorkStatus []string `bson:"workstatus" json:"-"`
State string `bson:"state" json:"state"`
Skip int `bson:"skip" json:"-"`
CreatedDate time.Time `bson:"createdDate" json:"createddate"`
StartedDate time.Time `bson:"startedDate" json:"starteddate"`
CompletedDate time.Time `bson:"completedDate" json:"completeddate"`
ComputeTime int `bson:"computetime" json:"computetime"`
UserAttr map[string]string `bson:"userattr" json:"userattr"`
ClientGroups string `bson:"clientgroups" json:"clientgroups"`
}
// Deprecated JobDep struct uses deprecated TaskDep struct which uses the deprecated IOmap. Maintained for backwards compatibility.
// Jobs that cannot be parsed into the Job struct, but can be parsed into the JobDep struct will be translated to the new Job struct.
// (=deprecated=)
type TaskDep struct {
Id string `bson:"taskid" json:"taskid"`
Info *Info `bson:"info" json:"-"`
Inputs IOmap `bson:"inputs" json:"inputs"`
Outputs IOmap `bson:"outputs" json:"outputs"`
Predata IOmap `bson:"predata" json:"predata"`
Cmd *Command `bson:"cmd" json:"cmd"`
App *App `bson:"app" json:"app"`
AppVariablesArray []*AppVariable // not in App as workunit does not need AppVariables and I want to pass App
Partition *PartInfo `bson:"partinfo" json:"-"`
DependsOn []string `bson:"dependsOn" json:"dependsOn"`
TotalWork int `bson:"totalwork" json:"totalwork"`
MaxWorkSize int `bson:"maxworksize" json:"maxworksize"`
RemainWork int `bson:"remainwork" json:"remainwork"`
WorkStatus []string `bson:"workstatus" json:"-"`
State string `bson:"state" json:"state"`
Skip int `bson:"skip" json:"-"`
CreatedDate time.Time `bson:"createdDate" json:"createddate"`
StartedDate time.Time `bson:"startedDate" json:"starteddate"`
CompletedDate time.Time `bson:"completedDate" json:"completeddate"`
ComputeTime int `bson:"computetime" json:"computetime"`
UserAttr map[string]string `bson:"userattr" json:"userattr"`
ClientGroups string `bson:"clientgroups" json:"clientgroups"`
}
func NewTask(job *Job, rank int) *Task {
return &Task{
Id: fmt.Sprintf("%s_%d", job.Id, rank),
Info: job.Info,
Inputs: []*IO{},
Outputs: []*IO{},
Predata: []*IO{},
Cmd: &Command{},
Partition: nil,
DependsOn: []string{},
TotalWork: 1,
RemainWork: 1,
WorkStatus: []string{},
State: TASK_STAT_INIT,
Skip: 0,
}
}
// fill some info (lacked in input json) for a task
func (task *Task) InitTask(job *Job) (err error) {
//validate taskid
if len(task.Id) == 0 {
return errors.New("invalid taskid:" + task.Id)
}
parts := strings.Split(task.Id, "_")
if len(parts) == 1 {
// is not standard taskid, convert it
task.Id = fmt.Sprintf("%s_%s", job.Id, task.Id)
for j := 0; j < len(task.DependsOn); j++ {
depend := task.DependsOn[j]
task.DependsOn[j] = fmt.Sprintf("%s_%s", job.Id, depend)
}
}
task.Info = job.Info
if task.ClientGroups != "" {
task.Info.ClientGroups = task.ClientGroups
}
if task.TotalWork <= 0 {
task.setTotalWork(1)
}
task.WorkStatus = make([]string, task.TotalWork)
task.RemainWork = task.TotalWork
// set node / host / url for files
for _, io := range task.Inputs {
if io.Node == "" {
io.Node = "-"
}
if _, err = io.DataUrl(); err != nil {
return err
}
logger.Debug(2, "inittask input: host="+io.Host+", node="+io.Node+", url="+io.Url)
}
for _, io := range task.Outputs {
if io.Node == "" {
io.Node = "-"
}
if _, err = io.DataUrl(); err != nil {
return err
}
logger.Debug(2, "inittask output: host="+io.Host+", node="+io.Node+", url="+io.Url)
}
for _, io := range task.Predata {
if io.Node == "" {
io.Node = "-"
}
if _, err = io.DataUrl(); err != nil {
return err
}
// predata IO can not be empty
if (io.Url == "") && (io.Node == "-") {
return errors.New("Invalid IO, required fields url or host / node missing")
}
logger.Debug(2, "inittask predata: host="+io.Host+", node="+io.Node+", url="+io.Url)
}
if len(task.Cmd.Environ.Private) > 0 {
task.Cmd.HasPrivateEnv = true
}
task.setTokenForIO()
task.State = TASK_STAT_INIT
return
}
func (task *Task) UpdateState(newState string) string {
task.State = newState
return task.State
}
func (task *Task) CreateIndex() (err error) {
for _, io := range task.Inputs {
if len(io.ShockIndex) > 0 {
idxinfo, err := io.GetIndexInfo()
if err != nil {
errMsg := "could not retrieve index info from input shock node, taskid=" + task.Id
logger.Error("error: " + errMsg)
return errors.New(errMsg)
}
if _, ok := idxinfo[io.ShockIndex]; !ok {
if err := ShockPutIndex(io.Host, io.Node, io.ShockIndex, task.Info.DataToken); err != nil {
errMsg := "failed to create index on shock node for taskid=" + task.Id
logger.Error("error: " + errMsg)
return errors.New(errMsg)
}
}
}
}
return
}
//get part size based on partition/index info
//if fail to get index info, task.TotalWork fall back to 1 and return nil
func (task *Task) InitPartIndex() (err error) {
if task.TotalWork == 1 && task.MaxWorkSize == 0 {
return
}
var input_io *IO
if task.Partition == nil {
if len(task.Inputs) == 1 {
for _, io := range task.Inputs {
input_io = io
task.Partition = new(PartInfo)
task.Partition.Input = io.FileName
task.Partition.MaxPartSizeMB = task.MaxWorkSize
break
}
} else {
task.setTotalWork(1)
logger.Error("warning: lacking parition info while multiple inputs are specified, taskid=" + task.Id)
return
}
} else {
if task.MaxWorkSize > 0 {
task.Partition.MaxPartSizeMB = task.MaxWorkSize
}
if task.Partition.MaxPartSizeMB == 0 && task.TotalWork <= 1 {
task.setTotalWork(1)
return
}
found := false
for _, io := range task.Inputs {
if io.FileName == task.Partition.Input {
found = true
input_io = io
}
}
if !found {
task.setTotalWork(1)
logger.Error("warning: invalid partition info, taskid=" + task.Id)
return
}
}
var totalunits int
idxinfo, err := input_io.GetIndexInfo()
if err != nil {
task.setTotalWork(1)
logger.Error("warning: invalid file info, taskid=" + task.Id)
return nil
}
idxtype := conf.DEFAULT_INDEX
if _, ok := idxinfo[idxtype]; !ok { //if index not available, create index
if err := ShockPutIndex(input_io.Host, input_io.Node, idxtype, task.Info.DataToken); err != nil {
task.setTotalWork(1)
logger.Error("warning: fail to create index on shock for taskid=" + task.Id)
return nil
}
totalunits, err = input_io.TotalUnits(idxtype) //get index info again
if err != nil {
task.setTotalWork(1)
logger.Error("warning: fail to get index units, taskid=" + task.Id + ":" + err.Error())
return nil
}
} else { //index existing, use it directly
totalunits = int(idxinfo[idxtype].TotalUnits)
}
//adjust total work based on needs
if task.Partition.MaxPartSizeMB > 0 { // fixed max part size
//this implementation for chunkrecord indexer only
chunkmb := int(conf.DEFAULT_CHUNK_SIZE / 1048576)
var totalwork int
if totalunits*chunkmb%task.Partition.MaxPartSizeMB == 0 {
totalwork = totalunits * chunkmb / task.Partition.MaxPartSizeMB
} else {
totalwork = totalunits*chunkmb/task.Partition.MaxPartSizeMB + 1
}
if totalwork < task.TotalWork { //use bigger splits (specified by size or totalwork)
totalwork = task.TotalWork
}
task.setTotalWork(totalwork)
}
if totalunits < task.TotalWork {
task.setTotalWork(totalunits)
}
task.Partition.Index = idxtype
task.Partition.TotalIndex = totalunits
return
}
func (task *Task) setTotalWork(num int) {
task.TotalWork = num
task.RemainWork = num
task.WorkStatus = make([]string, num)
}
func (task *Task) setTokenForIO() {
if !task.Info.Auth || task.Info.DataToken == "" {
return
}
for _, io := range task.Inputs {
io.DataToken = task.Info.DataToken
}
for _, io := range task.Outputs {
io.DataToken = task.Info.DataToken
}
}
func (task *Task) ParseWorkunit() (wus []*Workunit, err error) {
//if a task contains only one workunit, assign rank 0
if task.TotalWork == 1 {
workunit := NewWorkunit(task, 0)
wus = append(wus, workunit)
return
}
// if a task contains N (N>1) workunits, assign rank 1..N
for i := 1; i <= task.TotalWork; i++ {
workunit := NewWorkunit(task, i)
wus = append(wus, workunit)
}
return
}
func (task *Task) Skippable() bool {
// For a task to be skippable, it should meet
// the following requirements (this may change
// in the future):
// 1.- It should have exactly one input file
// and one output file (This way, we can connect tasks
// Ti-1 and Ti+1 transparently)
// 2.- It should be a simple pipeline task. That is,
// it should just have at most one "parent" Ti-1 ---> Ti
return (len(task.Inputs) == 1) &&
(len(task.Outputs) == 1) &&
(len(task.DependsOn) <= 1)
}
func (task *Task) DeleteOutput() {
if task.State == TASK_STAT_COMPLETED ||
task.State == TASK_STAT_SKIPPED ||
task.State == TASK_STAT_FAIL_SKIP {
for _, io := range task.Outputs {
if io.Delete {
if nodeid, err := io.DeleteNode(); err != nil {
logger.Error(fmt.Sprintf("warning: fail to delete shock node %s: %s", nodeid, err.Error()))
}
}
}
}
}
func (task *Task) DeleteInput() {
if task.State == TASK_STAT_COMPLETED ||
task.State == TASK_STAT_SKIPPED ||
task.State == TASK_STAT_FAIL_SKIP {
for _, io := range task.Inputs {
if io.Delete {
if nodeid, err := io.DeleteNode(); err != nil {
logger.Error(fmt.Sprintf("warning: fail to delete shock node %s: %s", nodeid, err.Error()))
}
}
}
}
}
//creat index (=deprecated=)
func createIndex(host string, nodeid string, indexname string) (err error) {
argv := []string{}
argv = append(argv, "-X")
argv = append(argv, "PUT")
target_url := fmt.Sprintf("%s/node/%s?index=%s", host, nodeid, indexname)
argv = append(argv, target_url)
cmd := exec.Command("curl", argv...)
err = cmd.Run()
if err != nil {
return
}
return
}