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job.go
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// Copyright © 2016-2021 Genome Research Limited
// Author: Sendu Bala <sb10@sanger.ac.uk>.
//
// This file is part of wr.
//
// wr is free software: you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// wr is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with wr. If not, see <http://www.gnu.org/licenses/>.
package jobqueue
// This file contains the job related code.
import (
"context"
"fmt"
"os"
"os/signal"
"path/filepath"
"strings"
"sync/atomic"
"syscall"
"time"
sync "github.com/sasha-s/go-deadlock"
"github.com/VertebrateResequencing/muxfys/v4"
"github.com/VertebrateResequencing/wr/jobqueue/scheduler"
"github.com/VertebrateResequencing/wr/limiter"
"github.com/VertebrateResequencing/wr/queue"
"github.com/gofrs/uuid"
multierror "github.com/hashicorp/go-multierror"
"github.com/ugorji/go/codec"
"github.com/wtsi-ssg/wr/container"
)
// JobState is how we describe the possible job states.
type JobState string
// JobState* constants represent all the possible job states. The fake "new" and
// "deleted" states are for the benefit of the web interface (jstateCount).
// "lost" is also a "fake" state indicating the job was running and we lost
// contact with it; it may be dead. "unknown" is an error case that shouldn't
// happen. "deletable" is a meta state that can be used when filtering jobs to
// mean !(running|complete).
const (
JobStateNew JobState = "new"
JobStateDelayed JobState = "delayed"
JobStateReady JobState = "ready"
JobStateReserved JobState = "reserved"
JobStateRunning JobState = "running"
JobStateLost JobState = "lost"
JobStateBuried JobState = "buried"
JobStateDependent JobState = "dependent"
JobStateComplete JobState = "complete"
JobStateDeleted JobState = "deleted"
JobStateDeletable JobState = "deletable"
JobStateUnknown JobState = "unknown"
)
// jobSchedLimitGroupSeparator is the separator between requirements and limit
// groups in schedular group names.
const jobSchedLimitGroupSeparator = "~"
// jobLimitGroupSeparator is the separator between limit groups in schedular
// group names.
const jobLimitGroupSeparator = ","
// subqueueToJobState converts queue.SubQueue entries to JobStates.
var subqueueToJobState = map[queue.SubQueue]JobState{
queue.SubQueueNew: JobStateNew,
queue.SubQueueDelay: JobStateDelayed,
queue.SubQueueReady: JobStateReady,
queue.SubQueueRun: JobStateRunning,
queue.SubQueueBury: JobStateBuried,
queue.SubQueueDependent: JobStateDependent,
queue.SubQueueRemoved: JobStateComplete,
}
// itemsStateToJobState converts queue.ItemState entries to JobStates.
var itemsStateToJobState = map[queue.ItemState]JobState{
queue.ItemStateDelay: JobStateDelayed,
queue.ItemStateReady: JobStateReady,
queue.ItemStateRun: JobStateReserved,
queue.ItemStateBury: JobStateBuried,
queue.ItemStateDependent: JobStateDependent,
queue.ItemStateRemoved: JobStateComplete,
}
// Job is a struct that represents a command that needs to be run and some
// associated metadata. If you get a Job back from the server (via Reserve() or
// Get*()), you should treat the properties as read-only: changing them will
// have no effect.
type Job struct {
// Cmd is the actual command line that will be run via the shell.
Cmd string
// Cwd determines the command working directory, the directory we cd to
// before running Cmd. When CwdMatters, Cwd is used exactly, otherwise a
// unique sub-directory of Cwd is used as the command working directory.
Cwd string
// CwdMatters should be made true when Cwd contains input files that you
// will refer to using relative (from Cwd) paths in Cmd, and when other Jobs
// have identical Cmds because you have many different directories that
// contain different but identically named input files. Cwd will become part
// of what makes the Job unique.
// When CwdMatters is false (default), Cmd gets run in a unique subfolder of
// Cwd, enabling features like tracking disk space usage and clean up of the
// working directory by simply deleting the whole thing. The TMPDIR
// environment variable is also set to a sister folder of the unique
// subfolder, and this is always cleaned up after the Cmd exits.
CwdMatters bool
// ChangeHome sets the $HOME environment variable to the actual working
// directory before running Cmd, but only when CwdMatters is false.
ChangeHome bool
// RepGroup is a name associated with related Jobs to help group them
// together when reporting on their status etc.
RepGroup string
// ReqGroup is a string that you supply to group together all commands that
// you expect to have similar resource requirements.
ReqGroup string
// Requirements describes the resources this Cmd needs to run, such as RAM,
// Disk and time. These may be determined for you by the system (depending
// on Override) based on past experience of running jobs with the same
// ReqGroup.
Requirements *scheduler.Requirements
// RequirementsOrig is like Requirements, but only has the original RAM,
// Disk and time values set by you, if any.
RequirementsOrig *scheduler.Requirements
// Override determines if your own supplied Requirements get used, or if the
// systems' calculated values get used. 0 means prefer the system values. 1
// means prefer your values if they are higher. 2 means always use your
// values.
Override uint8
// Priority is a number between 0 and 255 inclusive - higher numbered jobs
// will run before lower numbered ones (the default is 0).
Priority uint8
// Retries is the number of times to retry running a Cmd if it fails.
Retries uint8
// NoRetriesOverWalltime is the amount of time that a cmd can run for and
// then fail and still automatically retry. If it runs longer than this
// duration and fails, it will instead be immediately buried.
NoRetriesOverWalltime time.Duration
// LimitGroups are names of limit groups that this job belongs to. If any
// of these groups are defined (elsewhere) to have a limit, then if as many
// other jobs as the limit are currently running, this job will not start
// running. It's a way of not running too many of a type of job at once.
LimitGroups []string
// DepGroups are the dependency groups this job belongs to that other jobs
// can refer to in their Dependencies.
DepGroups []string
// Dependencies describe the jobs that must be complete before this job
// starts.
Dependencies Dependencies
// Behaviours describe what should happen after Cmd is executed, depending
// on its success.
Behaviours Behaviours
// MountConfigs describes remote file systems or object stores that you wish
// to be fuse mounted prior to running the Cmd. Once Cmd exits, the mounts
// will be unmounted (with uploads only occurring if it exits with code 0).
// If you want multiple separate mount points accessed from different local
// directories, you will supply more than one MountConfig in the slice. If
// you want multiple remote locations multiplexed and accessible from a
// single local directory, you will supply a single MountConfig in the
// slice, configured with multiple MountTargets. Relative paths for your
// MountConfig.Mount options will be relative to Cwd (or ActualCwd if
// CwdMatters == false). If a MountConfig.Mount is not specified, it
// defaults to Cwd/mnt if CwdMatters, otherwise ActualCwd itself will be the
// mount point. If a MountConfig.CachBase is not specified, it defaults to
// to Cwd if CwdMatters, otherwise it will be a sister directory of
// ActualCwd.
MountConfigs MountConfigs
// BsubMode set to either Production or Development when Add()ing a job will
// result in the job being assigned a BsubID. Such jobs, when they run, will
// see bsub, bjobs and bkill as symlinks to wr, thus if they call bsub, they
// will actually add jobs to the jobqueue etc. Those jobs will pick up the
// same Requirements.Other as this job, and the same MountConfigs. If
// Requirements.Other["cloud_shared"] is "true", the MountConfigs are not
// reused.
BsubMode string
// MonitorDocker turns on monitoring of a docker container identified by its
// --name or path to its --cidfile, adding its peak RAM and CPU usage to the
// reported RAM and CPU usage of this job.
//
// If the special argument "?" is supplied, monitoring will apply to the
// first new docker container that appears after the Cmd starts to run.
// NB: if multiple jobs that run docker containers start running at the same
// time on the same machine, the reported stats could be wrong for one or
// more of those jobs.
//
// Requires that docker is installed on the machine where the job will run
// (and that the Cmd uses docker to run a container). NB: does not handle
// monitoring of multiple docker containers run by a single Cmd.
MonitorDocker string
// WithDocker will result in CmdLine() returning a `docker run` cmd that
// uses the image specified here to run Cmd by piping Cmd into the
// container's /bin/sh. Cwd will be mounted inside the container and will
// be the working directory in the container. Anything specified by
// ContainerMounts will also be mounted in the container. Any EnvOverride
// environment variable name values will also be set for import in to the
// container. Setting this sets (and overrides) MonitorDocker to this Job's
// Key(), which will also be the container's --name.
WithDocker string
// WithSingularity will result in CmdLine() returning a `singularity shell`
// command that uses the image specified here to run Cmd by piping it in to
// the container. Cwd will be mounted inside the container and will be the
// working directory in the container. Anything specified by ContainerMounts
// will also be mounted in the container. All the job's environment
// variables will be available inside the container.
WithSingularity string
// ContainerMounts is a comma separated list of strings each in the format:
// /outside/container/path[:/inside/container/path] (where inside defaults
// to outside if not provided)). If WithDocker or WithSingularity is also
// specfied, the outside paths will be specified as to be bound to the
// inside paths in the cmd returned by CmdLine().
ContainerMounts string
// The remaining properties are used to record information about what
// happened when Cmd was executed, or otherwise provide its current state.
// It is meaningless to set these yourself.
// the actual working directory used, which would have been created with a
// unique name if CwdMatters = false
ActualCwd string
// peak RAM (MB) used.
PeakRAM int
// peak disk (MB) used.
PeakDisk int64
// true if the Cmd was run and exited.
Exited bool
// if the job ran and exited, its exit code is recorded here, but check
// Exited because when this is not set it could like like exit code 0.
Exitcode int
// true if the job was running but we've lost contact with it
Lost bool
// if the job failed to complete successfully, this will hold one of the
// FailReason* strings. Also set if Lost == true.
FailReason string
// pid of the running or ran process.
Pid int
// host the process is running or did run on.
Host string
// host id the process is running or did run on (cloud specific).
HostID string
// host ip the process is running or did run on (cloud specific).
HostIP string
// time the cmd started running.
StartTime time.Time
// time the cmd stopped running.
EndTime time.Time
// CPU time used.
CPUtime time.Duration
// to read, call job.StdErr() instead; if the job ran, its (truncated)
// STDERR will be here.
StdErrC []byte
// to read, call job.StdOut() instead; if the job ran, its (truncated)
// STDOUT will be here.
StdOutC []byte
// to read, call job.Env() instead, to get the environment variables as a
// []string, where each string is like "key=value".
EnvC []byte
// Since EnvC isn't always populated on job retrieval, this lets job.Env()
// distinguish between no EnvC and merely not requested.
EnvCRetrieved bool
// if set (using output of CompressEnv()), they will be returned in the
// results of job.Env().
EnvOverride []byte
// job's state in the queue: 'delayed', 'ready', 'reserved', 'running',
// 'buried', 'complete' or 'dependent'.
State JobState
// number of times the job had ever entered 'running' state.
Attempts uint32
// remaining number of Release()s allowed before being buried instead.
UntilBuried uint8
// we note which client reserved this job, for validating if that client has
// permission to do other stuff to this Job; the server only ever sets this
// on Reserve(), so clients can't cheat by changing this on their end.
ReservedBy uuid.UUID
// on the server we don't store EnvC with the job, but look it up in db via
// this key.
EnvKey string
// when retrieving jobs with a limit, this tells you how many jobs were
// excluded.
Similar int
// name of the queue the Job was added to.
Queue string
// unique (for this manager session) id of the job submission, present if
// BsubMode was set when the job was added.
BsubID uint64
// delay is the duration we would next spend in the delay queue
DelayTime time.Duration
// we add this internally to match up runners we spawn via the scheduler to
// the Jobs they're allowed to ReserveFiltered().
schedulerGroup string
// we store the MuxFys that we mount during Mount() so we can Unmount() them
// later; this is purely client side.
mountedFS []*muxfys.MuxFys
// killCalled is set for running jobs if Kill() is called on them.
killCalled bool
// incrementedLimitGroups notes that we have incremented limit groups for
// this job, so they should be decremented when the job finishes running.
incrementedLimitGroups []string
sync.RWMutex
}
// CmdLine normally returns Cmd and a no-op function. However, if WithDocker or
// WithSingularity has been set, then:
//
// * Cmd is stored in a tmp file.
// * A new `docker run` or `singularity shell` command is returned that:
// * Pulls the image specified in WithDocker|Singularity if it is missing.
// * Creates a container (with docker, it's name will be our Key()).
// * That will mount Cwd inside the container and use it as the workdir.
// * That will also mount any ContainerMounts.
// * That for docker will tell it to use our explicit EnvOverrides
// (singularity will use all env vars).
// * That will receive a pipe of the Cmd file contents to its shell.
//
// In the case of WithDocker, MonitorDocker will also be set to our Key().
//
// Once you have executed the returned command you should call the returned
// function which will delete the tmp file.
func (j *Job) CmdLine(ctx context.Context) (string, func(), error) {
noop := func() {}
if j.WithDocker != "" || j.WithSingularity != "" {
path, cleanup, err := container.PrepareCmdFile(ctx, j.Cmd)
if err != nil {
return j.Cmd, noop, err
}
var cmd string
if j.WithDocker != "" {
envs, err := j.containerEnv()
if err != nil {
return j.Cmd, cleanup, err
}
cmd = container.DockerRunCmd(j.WithDocker, path, j.Key(), j.containerMounts(), envs)
j.MonitorDocker = j.Key()
} else {
cmd = container.SingularityRunCmd(j.WithSingularity, path, j.containerMounts())
}
return cmd, cleanup, nil
}
return j.Cmd, noop, nil
}
// containerMounts converts ContainerMounts to a slice of the mount values.
func (j *Job) containerMounts() []string {
if j.ContainerMounts == "" {
return nil
}
return strings.Split(j.ContainerMounts, ",")
}
// containerEnv converts EnvOverride to a slice of the envionrment variable
// names that were set.
func (j *Job) containerEnv() ([]string, error) {
overrideEs, err := j.envCurrentOverrides()
if err != nil {
return nil, err
}
names := make([]string, len(overrideEs))
for i, envvar := range overrideEs {
parts := strings.Split(envvar, ":")
names[i] = parts[0]
}
return names, nil
}
// WallTime returns the time the job took to run if it ran to completion, or the
// time taken so far if it is currently running.
func (j *Job) WallTime() time.Duration {
var d time.Duration
if !j.StartTime.IsZero() {
if j.EndTime.IsZero() || j.State == JobStateReserved {
d = time.Since(j.StartTime)
} else {
d = j.EndTime.Sub(j.StartTime)
}
}
return d
}
// Env decompresses and decodes job.EnvC (the output of CompressEnv(), which are
// the environment variables the Job's Cmd should run/ran under). Note that EnvC
// is only populated if you got the Job from GetByCmd(_, _, true) or Reserve().
// If no environment variables were passed in when the job was Add()ed to the
// queue, returns current environment variables instead. In both cases, alters
// the return value to apply any overrides stored in job.EnvOverride.
func (j *Job) Env() ([]string, error) {
overrideEs, err := j.envCurrentOverrides()
if err != nil {
return nil, err
}
if len(j.EnvC) == 0 {
if j.EnvCRetrieved {
env := os.Environ()
if len(overrideEs) > 0 {
env = envOverride(env, overrideEs)
}
return env, err
}
return nil, nil
}
decompressed, err := decompress(j.EnvC)
if err != nil {
return nil, err
}
ch := new(codec.BincHandle)
dec := codec.NewDecoderBytes(decompressed, ch)
es := &envStr{}
err = dec.Decode(es)
if err != nil {
return nil, err
}
env := es.Environ
if len(env) == 0 {
env = os.Environ()
}
if len(overrideEs) > 0 {
env = envOverride(env, overrideEs)
}
return env, err
}
// envCurrentOverrides decompresses and decodes any existing EnvOverride.
func (j *Job) envCurrentOverrides() ([]string, error) {
if len(j.EnvOverride) > 0 {
decompressed, err := decompress(j.EnvOverride)
if err != nil {
return nil, err
}
ch := new(codec.BincHandle)
dec := codec.NewDecoderBytes(decompressed, ch)
overrideEs := &envStr{}
err = dec.Decode(overrideEs)
if err != nil {
return nil, err
}
return overrideEs.Environ, err
}
return nil, nil
}
// EnvAddOverride adds additional overrides to the jobs existing overrides (if
// any). These will then get used to determine the final value of Env(). NB:
// This does not do any updates to a job on the server if called from a client,
// but is suitable for altering a job's environment prior to calling
// Client.Execute().
func (j *Job) EnvAddOverride(env []string) error {
current, err := j.envCurrentOverrides()
if err != nil {
return err
}
j.EnvOverride, err = compressEnv(envOverride(current, env))
return err
}
// Getenv is like os.Getenv(), but for the environment variables stored in the
// the job, including any overrides. Returns blank if Env() would have returned
// an error.
func (j *Job) Getenv(key string) string {
env, err := j.Env()
if err != nil {
return ""
}
for _, envvar := range env {
pair := strings.Split(envvar, "=")
if pair[0] == key {
return pair[1]
}
}
return ""
}
// StdOut returns the decompressed job.StdOutC, which is the head and tail of
// job.Cmd's STDOUT when it ran. If the Cmd hasn't run yet, or if it output
// nothing to STDOUT, you will get an empty string. Note that StdOutC is only
// populated if you got the Job from GetByCmd(_, true), and if the Job's Cmd ran
// but failed.
func (j *Job) StdOut() (string, error) {
if len(j.StdOutC) == 0 {
return "", nil
}
decomp, err := decompress(j.StdOutC)
if err != nil {
return "", err
}
return string(decomp), err
}
// StdErr returns the decompressed job.StdErrC, which is the head and tail of
// job.Cmd's STDERR when it ran. If the Cmd hasn't run yet, or if it output
// nothing to STDERR, you will get an empty string. Note that StdErrC is only
// populated if you got the Job from GetByCmd(_, true), and if the Job's Cmd ran
// but failed.
func (j *Job) StdErr() (string, error) {
if len(j.StdErrC) == 0 {
return "", nil
}
decomp, err := decompress(j.StdErrC)
if err != nil {
return "", err
}
return string(decomp), err
}
// TriggerBehaviours triggers this Job's Behaviours based on if its Cmd got
// executed successfully or not. Should only be called as part of or after
// Execute().
func (j *Job) TriggerBehaviours(success bool) error {
return j.Behaviours.Trigger(success, j)
}
// RemovalRequested tells you if this Job's Behaviours include the 'Remove' one.
func (j *Job) RemovalRequested() bool {
return j.Behaviours.RemovalRequested()
}
// Mount uses the Job's MountConfigs to mount the remote file systems at the
// desired mount points. If a mount point is unspecified, mounts in the sub
// folder Cwd/mnt if CwdMatters (and unspecified CacheBase becomes Cwd),
// otherwise the actual working directory is used as the mount point (and the
// parent of that used for unspecified CacheBase). Relative CacheDir options
// are treated relative to the CacheBase.
//
// If the optional onCwd argument is supplied true, and ActualCwd is not
// defined, then instead of mounting at j.Cwd/mnt, it tries to mount at j.Cwd
// itself. (This will fail if j.Cwd is not empty or already mounted by another
// process.)
//
// Returns any non-shared cache directories, and any directories in (or at) the
// job's actual cwd if anything was mounted there, for the purpose of knowing
// what directories to check and not check for disk usage.
func (j *Job) Mount(onCwd ...bool) ([]string, []string, error) {
cwd := j.Cwd
defaultMount := filepath.Join(j.Cwd, "mnt")
defaultCacheBase := cwd
if j.ActualCwd != "" {
cwd = j.ActualCwd
defaultMount = cwd
defaultCacheBase = filepath.Dir(cwd)
} else if len(onCwd) == 1 && onCwd[0] {
defaultMount = j.Cwd
defaultCacheBase = filepath.Dir(j.Cwd)
}
var uniqueCacheDirs []string
var uniqueMountedDirs []string
for _, mc := range j.MountConfigs {
var rcs []*muxfys.RemoteConfig
for _, mt := range mc.Targets {
accessorConfig, err := muxfys.S3ConfigFromEnvironment(mt.Profile, mt.Path)
if err != nil {
_, erru := j.Unmount()
if erru != nil {
err = fmt.Errorf("%s (and the unmount failed: %s)", err.Error(), erru)
}
return uniqueCacheDirs, uniqueMountedDirs, err
}
accessor, err := muxfys.NewS3Accessor(accessorConfig)
if err != nil {
_, erru := j.Unmount()
if erru != nil {
err = fmt.Errorf("%s (and the unmount failed: %s)", err.Error(), erru)
}
return uniqueCacheDirs, uniqueMountedDirs, err
}
cacheDir := mt.CacheDir
if cacheDir != "" && !filepath.IsAbs(cacheDir) {
cacheDir = filepath.Join(defaultCacheBase, cacheDir)
// *** we should only set this if not writing, or if writing to
// a non-empty dir, which we don't know about at this point...
uniqueCacheDirs = append(uniqueCacheDirs, cacheDir)
} // *** else, the cache is in a unique dir that I don't know about?
rc := &muxfys.RemoteConfig{
Accessor: accessor,
CacheData: mt.Cache,
CacheDir: cacheDir,
Write: mt.Write,
}
rcs = append(rcs, rc)
}
if len(rcs) == 0 {
err := fmt.Errorf("no Targets specified")
_, erru := j.Unmount()
if erru != nil {
err = fmt.Errorf("%s (and the unmount failed: %s)", err.Error(), erru)
}
return uniqueCacheDirs, uniqueMountedDirs, err
}
retries := 10
if mc.Retries > 0 {
retries = mc.Retries
}
mount := mc.Mount
if mount != "" {
if !filepath.IsAbs(mount) {
mount = filepath.Join(cwd, mount)
uniqueMountedDirs = append(uniqueMountedDirs, mount)
}
} else {
mount = defaultMount
uniqueMountedDirs = append(uniqueMountedDirs, mount)
}
cacheBase := mc.CacheBase
if cacheBase != "" {
if !filepath.IsAbs(cacheBase) {
cacheBase = filepath.Join(cwd, cacheBase)
}
} else {
cacheBase = defaultCacheBase
}
cfg := &muxfys.Config{
Mount: mount,
CacheBase: cacheBase,
Retries: retries,
Verbose: mc.Verbose,
}
fs, err := muxfys.New(cfg)
if err != nil {
_, erru := j.Unmount()
if erru != nil {
err = fmt.Errorf("%s (and the unmount failed: %s)", err.Error(), erru)
}
return uniqueCacheDirs, uniqueMountedDirs, err
}
err = fs.Mount(rcs...)
if err != nil {
_, erru := j.Unmount()
if erru != nil {
err = fmt.Errorf("%s (and the unmount failed: %s)", err.Error(), erru)
}
return uniqueCacheDirs, uniqueMountedDirs, err
}
// (we can't use each fs.UnmountOnDeath() function because that tries
// to upload, but if we get killed we don't want that)
j.mountedFS = append(j.mountedFS, fs)
}
// unmount all on death without trying to upload
if len(j.mountedFS) > 0 {
deathSignals := make(chan os.Signal, 2)
signal.Notify(deathSignals, os.Interrupt, syscall.SIGTERM)
go func() {
<-deathSignals
var merr *multierror.Error
for _, fs := range j.mountedFS {
erru := fs.Unmount(true)
if erru != nil {
merr = multierror.Append(merr, erru)
}
}
if len(merr.Errors) > 0 {
panic(merr)
}
}()
}
return uniqueCacheDirs, uniqueMountedDirs, nil
}
// Unmount unmounts any remote filesystems that were previously mounted with
// Mount(), returning a string of any log messages generated during the mount.
// Returns nil error if Mount() had not been called or there were no
// MountConfigs.
//
// Note that for cached writable mounts, created files will only begin to upload
// once Unmount() is called, so this may take some time to return. Supply true
// to disable uploading of files (eg. if you're unmounting following an error).
// If uploading, error could contain the string "failed to upload", which you
// may want to check for. On success, triggers the deletion of any empty
// directories between the mount point(s) and Cwd if not CwdMatters and the
// mount point was (within) ActualCwd.
func (j *Job) Unmount(stopUploads ...bool) (logs string, err error) {
// j.Lock()
// defer j.Unlock()
var doNotUpload bool
if len(stopUploads) == 1 {
doNotUpload = stopUploads[0]
}
var merr *multierror.Error
var allLogs []string
for _, fs := range j.mountedFS {
uerr := fs.Unmount(doNotUpload)
if uerr != nil {
merr = multierror.Append(merr, uerr)
}
theseLogs := fs.Logs()
if len(theseLogs) > 0 {
allLogs = append(allLogs, theseLogs...)
}
}
j.mountedFS = nil
if len(allLogs) > 0 {
logs = strings.TrimSpace(strings.Join(allLogs, ""))
}
err = merr.ErrorOrNil()
if err != nil {
return logs, fmt.Errorf("Unmount failure(s): %s", err.Error())
}
// delete any empty dirs
if j.ActualCwd != "" {
for _, mc := range j.MountConfigs {
if mc.Mount == "" {
err = rmEmptyDirs(j.ActualCwd, j.Cwd)
} else if !filepath.IsAbs(mc.Mount) {
err = rmEmptyDirs(filepath.Join(j.ActualCwd, mc.Mount), j.Cwd)
}
}
}
return logs, err
}
// ToEssense converts a Job to its matching JobEssense, taking less space and
// being required as input for certain methods.
func (j *Job) ToEssense() *JobEssence {
return &JobEssence{JobKey: j.Key()}
}
// noteIncrementedLimitGroups should be used after incrementing limit groups for
// this job. It takes the groups you actually just incremented (as opposed to
// the Job's current LimitGroups), and stores them for decrementing during
// updateAfterExit(). This avoids any issues with the Job's LimitGroups being
// changed between these 2 calls (or between you incrementing and reserving the
// job). The twinned noteIncrementedLimitGroups() and decrementLimitGroups()
// calls ensure we don't decrement groups more times than we incremented them.
func (j *Job) noteIncrementedLimitGroups(groups []string) {
j.Lock()
defer j.Unlock()
j.incrementedLimitGroups = groups
}
// updateAfterExit sets some properties on the job, only if the supplied
// JobEndState indicates the job exited, and if the job wasn't already exited.
// It also calls decrementLimitGroups().
func (j *Job) updateAfterExit(jes *JobEndState, lim *limiter.Limiter) {
j.RLock()
if j.Exited {
j.RUnlock()
return
}
j.RUnlock()
j.decrementLimitGroups(lim)
if jes == nil || !jes.Exited {
return
}
j.Lock()
j.Exited = true
j.Exitcode = jes.Exitcode
j.PeakRAM = jes.PeakRAM
j.PeakDisk = jes.PeakDisk
j.CPUtime = jes.CPUtime
j.EndTime = jes.EndTime
if jes.Cwd != "" {
j.ActualCwd = jes.Cwd
}
j.Unlock()
}
// decrementLimitGroups decrements any limit groups of this job that had been
// passed to noteIncrementedLimitGroups(), and then empties that note to make
// multiple calls to this method safe in terms of decrementing.
func (j *Job) decrementLimitGroups(lim *limiter.Limiter) {
j.Lock()
defer j.Unlock()
if len(j.incrementedLimitGroups) > 0 {
lim.Decrement(j.incrementedLimitGroups)
j.incrementedLimitGroups = []string{}
}
}
// Key calculates a unique key to describe the job.
func (j *Job) Key() string {
concat := fmt.Sprintf("%s.%s", j.Cmd, j.MountConfigs.Key())
if j.CwdMatters {
concat = fmt.Sprintf("%s.%s", j.Cwd, concat)
}
var image string
if j.WithDocker != "" {
image = "docker:" + j.WithDocker
} else if j.WithSingularity != "" {
image = "singularity:" + j.WithSingularity
}
if image != "" {
concat = fmt.Sprintf("%s.%s.%s", concat, image, j.ContainerMounts)
}
return byteKey([]byte(concat))
}
// generateSchedulerGroup returns a stringified form of the given requirements,
// appended with a standard form of the current limit groups of this job. We
// assume that LimitGroups was sorted and deduplicated when it was set on the
// job (this happens in server.createJobs()).
func (j *Job) generateSchedulerGroup(req *scheduler.Requirements) string {
var lgs string
if len(j.LimitGroups) > 0 {
lgs = jobSchedLimitGroupSeparator + strings.Join(j.LimitGroups, jobLimitGroupSeparator)
}
return req.Stringify() + lgs
}
// getSchedulerGroup provides a thread-safe way of getting the schedulerGroup
// property of a Job.
func (j *Job) getSchedulerGroup() string {
j.RLock()
defer j.RUnlock()
return j.schedulerGroup
}
// setSchedulerGroup provides a thread-safe way of setting the schedulerGroup
// property of a Job.
func (j *Job) setSchedulerGroup(newval string) {
j.Lock()
defer j.Unlock()
j.schedulerGroup = newval
}
// ToStatus converts a job to a simplified JStatus, useful for output as JSON.
func (j *Job) ToStatus() (JStatus, error) {
stderr, err := j.StdErr()
if err != nil {
return JStatus{}, err
}
stdout, err := j.StdOut()
if err != nil {
return JStatus{}, err
}
env, err := j.Env()
if err != nil {
return JStatus{}, err
}
var cwdLeaf string
j.RLock()
defer j.RUnlock()
if j.ActualCwd != "" {
cwdLeaf, err = filepath.Rel(j.Cwd, j.ActualCwd)
if err != nil {
return JStatus{}, err
}
cwdLeaf = "/" + cwdLeaf
}
state := j.State
if state == JobStateRunning && j.Lost {
state = JobStateLost
}
ot := make([]string, 0, len(j.Requirements.Other))
for key, val := range j.Requirements.Other {
ot = append(ot, key+":"+val)
}
js := JStatus{
Key: j.Key(),
RepGroup: j.RepGroup,
LimitGroups: j.LimitGroups,
DepGroups: j.DepGroups,
Dependencies: j.Dependencies.Stringify(),
Cmd: j.Cmd,
State: state,
CwdBase: j.Cwd,
Cwd: cwdLeaf,
HomeChanged: j.ChangeHome,
Behaviours: j.Behaviours.String(),
Mounts: j.MountConfigs.String(),
MonitorDocker: j.MonitorDocker,
WithDocker: j.WithDocker,
WithSingularity: j.WithSingularity,
ContainerMounts: j.ContainerMounts,
ExpectedRAM: j.Requirements.RAM,
ExpectedTime: j.Requirements.Time.Seconds(),
RequestedDisk: j.Requirements.Disk,
OtherRequests: ot,
Cores: j.Requirements.Cores,
PeakRAM: j.PeakRAM,
PeakDisk: j.PeakDisk,
Exited: j.Exited,
Exitcode: j.Exitcode,
FailReason: j.FailReason,
Pid: j.Pid,
Host: j.Host,
HostID: j.HostID,
HostIP: j.HostIP,
Walltime: j.WallTime().Seconds(),
CPUtime: j.CPUtime.Seconds(),
Attempts: j.Attempts,
Similar: j.Similar,
StdErr: stderr,
StdOut: stdout,
Env: env,
}
if !j.StartTime.IsZero() {
i := j.StartTime.Unix()
js.Started = &i
}
if !j.EndTime.IsZero() {
i := j.EndTime.Unix()
js.Ended = &i
}
return js, nil
}
// JobEssence struct describes the essential aspects of a Job that make it
// unique, used to describe a Job when eg. you want to search for one.
type JobEssence struct {
// JobKey can be set by itself if you already know the "key" of the desired
// job; you can get these keys when you use GetByRepGroup() or
// GetIncomplete() with a limit. When this is set, other properties are
// ignored.
JobKey string
// Cmd always forms an essential part of a Job.
Cmd string
// Cwd should only be set if the Job was created with CwdMatters = true.
Cwd string
// Mounts should only be set if the Job was created with Mounts
MountConfigs MountConfigs
}
// Key returns the same value that key() on the matching Job would give you.
func (j *JobEssence) Key() string {
if j.JobKey != "" {
return j.JobKey
}