// Copyright (C) The Arvados Authors. All rights reserved.
//
// SPDX-License-Identifier: AGPL-3.0
package crunchrun
import (
"bytes"
"context"
"encoding/json"
"errors"
"flag"
"fmt"
"io"
"io/ioutil"
"log"
"net"
"net/http"
"os"
"os/exec"
"os/signal"
"os/user"
"path"
"path/filepath"
"regexp"
"runtime"
"runtime/pprof"
"sort"
"strings"
"sync"
"syscall"
"time"
"git.arvados.org/arvados.git/lib/cmd"
"git.arvados.org/arvados.git/lib/config"
"git.arvados.org/arvados.git/lib/crunchstat"
"git.arvados.org/arvados.git/sdk/go/arvados"
"git.arvados.org/arvados.git/sdk/go/arvadosclient"
"git.arvados.org/arvados.git/sdk/go/ctxlog"
"git.arvados.org/arvados.git/sdk/go/keepclient"
"git.arvados.org/arvados.git/sdk/go/manifest"
"golang.org/x/sys/unix"
)
type command struct{}
var Command = command{}
// ConfigData contains environment variables and (when needed) cluster
// configuration, passed from dispatchcloud to crunch-run on stdin.
type ConfigData struct {
Env map[string]string
KeepBuffers int
Cluster *arvados.Cluster
}
// IArvadosClient is the minimal Arvados API methods used by crunch-run.
type IArvadosClient interface {
Create(resourceType string, parameters arvadosclient.Dict, output interface{}) error
Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error
Call(method, resourceType, uuid, action string, parameters arvadosclient.Dict, output interface{}) error
CallRaw(method string, resourceType string, uuid string, action string, parameters arvadosclient.Dict) (reader io.ReadCloser, err error)
Discovery(key string) (interface{}, error)
}
// ErrCancelled is the error returned when the container is cancelled.
var ErrCancelled = errors.New("Cancelled")
// IKeepClient is the minimal Keep API methods used by crunch-run.
type IKeepClient interface {
BlockWrite(context.Context, arvados.BlockWriteOptions) (arvados.BlockWriteResponse, error)
ReadAt(locator string, p []byte, off int) (int, error)
ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error)
LocalLocator(locator string) (string, error)
ClearBlockCache()
SetStorageClasses(sc []string)
}
// NewLogWriter is a factory function to create a new log writer.
type NewLogWriter func(name string) (io.WriteCloser, error)
type RunArvMount func(cmdline []string, tok string) (*exec.Cmd, error)
type MkTempDir func(string, string) (string, error)
type PsProcess interface {
CmdlineSlice() ([]string, error)
}
// ContainerRunner is the main stateful struct used for a single execution of a
// container.
type ContainerRunner struct {
executor containerExecutor
executorStdin io.Closer
executorStdout io.Closer
executorStderr io.Closer
// Dispatcher client is initialized with the Dispatcher token.
// This is a privileged token used to manage container status
// and logs.
//
// We have both dispatcherClient and DispatcherArvClient
// because there are two different incompatible Arvados Go
// SDKs and we have to use both (hopefully this gets fixed in
// #14467)
dispatcherClient *arvados.Client
DispatcherArvClient IArvadosClient
DispatcherKeepClient IKeepClient
// Container client is initialized with the Container token
// This token controls the permissions of the container, and
// must be used for operations such as reading collections.
//
// Same comment as above applies to
// containerClient/ContainerArvClient.
containerClient *arvados.Client
ContainerArvClient IArvadosClient
ContainerKeepClient IKeepClient
Container arvados.Container
token string
ExitCode *int
NewLogWriter NewLogWriter
CrunchLog *ThrottledLogger
logUUID string
logMtx sync.Mutex
LogCollection arvados.CollectionFileSystem
LogsPDH *string
RunArvMount RunArvMount
MkTempDir MkTempDir
ArvMount *exec.Cmd
ArvMountPoint string
HostOutputDir string
Volumes map[string]struct{}
OutputPDH *string
SigChan chan os.Signal
ArvMountExit chan error
SecretMounts map[string]arvados.Mount
MkArvClient func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error)
finalState string
parentTemp string
keepstoreLogger io.WriteCloser
keepstoreLogbuf *bufThenWrite
statLogger io.WriteCloser
statReporter *crunchstat.Reporter
hoststatLogger io.WriteCloser
hoststatReporter *crunchstat.Reporter
statInterval time.Duration
cgroupRoot string
// What we expect the container's cgroup parent to be.
expectCgroupParent string
// What we tell docker to use as the container's cgroup
// parent. Note: Ideally we would use the same field for both
// expectCgroupParent and setCgroupParent, and just make it
// default to "docker". However, when using docker < 1.10 with
// systemd, specifying a non-empty cgroup parent (even the
// default value "docker") hits a docker bug
// (https://github.com/docker/docker/issues/17126). Using two
// separate fields makes it possible to use the "expect cgroup
// parent to be X" feature even on sites where the "specify
// cgroup parent" feature breaks.
setCgroupParent string
cStateLock sync.Mutex
cCancelled bool // StopContainer() invoked
enableMemoryLimit bool
enableNetwork string // one of "default" or "always"
networkMode string // "none", "host", or "" -- passed through to executor
brokenNodeHook string // script to run if node appears to be broken
arvMountLog *ThrottledLogger
containerWatchdogInterval time.Duration
gateway Gateway
}
// setupSignals sets up signal handling to gracefully terminate the
// underlying container and update state when receiving a TERM, INT or
// QUIT signal.
func (runner *ContainerRunner) setupSignals() {
runner.SigChan = make(chan os.Signal, 1)
signal.Notify(runner.SigChan, syscall.SIGTERM)
signal.Notify(runner.SigChan, syscall.SIGINT)
signal.Notify(runner.SigChan, syscall.SIGQUIT)
go func(sig chan os.Signal) {
for s := range sig {
runner.stop(s)
}
}(runner.SigChan)
}
// stop the underlying container.
func (runner *ContainerRunner) stop(sig os.Signal) {
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
if sig != nil {
runner.CrunchLog.Printf("caught signal: %v", sig)
}
runner.cCancelled = true
runner.CrunchLog.Printf("stopping container")
err := runner.executor.Stop()
if err != nil {
runner.CrunchLog.Printf("error stopping container: %s", err)
}
}
var errorBlacklist = []string{
"(?ms).*[Cc]annot connect to the Docker daemon.*",
"(?ms).*oci runtime error.*starting container process.*container init.*mounting.*to rootfs.*no such file or directory.*",
"(?ms).*grpc: the connection is unavailable.*",
}
func (runner *ContainerRunner) runBrokenNodeHook() {
if runner.brokenNodeHook == "" {
path := filepath.Join(lockdir, brokenfile)
runner.CrunchLog.Printf("Writing %s to mark node as broken", path)
f, err := os.OpenFile(path, os.O_CREATE|os.O_RDWR, 0700)
if err != nil {
runner.CrunchLog.Printf("Error writing %s: %s", path, err)
return
}
f.Close()
} else {
runner.CrunchLog.Printf("Running broken node hook %q", runner.brokenNodeHook)
// run killme script
c := exec.Command(runner.brokenNodeHook)
c.Stdout = runner.CrunchLog
c.Stderr = runner.CrunchLog
err := c.Run()
if err != nil {
runner.CrunchLog.Printf("Error running broken node hook: %v", err)
}
}
}
func (runner *ContainerRunner) checkBrokenNode(goterr error) bool {
for _, d := range errorBlacklist {
if m, e := regexp.MatchString(d, goterr.Error()); m && e == nil {
runner.CrunchLog.Printf("Error suggests node is unable to run containers: %v", goterr)
runner.runBrokenNodeHook()
return true
}
}
return false
}
// LoadImage determines the docker image id from the container record and
// checks if it is available in the local Docker image store. If not, it loads
// the image from Keep.
func (runner *ContainerRunner) LoadImage() (string, error) {
runner.CrunchLog.Printf("Fetching Docker image from collection '%s'", runner.Container.ContainerImage)
d, err := os.Open(runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage)
if err != nil {
return "", err
}
defer d.Close()
allfiles, err := d.Readdirnames(-1)
if err != nil {
return "", err
}
var tarfiles []string
for _, fnm := range allfiles {
if strings.HasSuffix(fnm, ".tar") {
tarfiles = append(tarfiles, fnm)
}
}
if len(tarfiles) == 0 {
return "", fmt.Errorf("image collection does not include a .tar image file")
}
if len(tarfiles) > 1 {
return "", fmt.Errorf("cannot choose from multiple tar files in image collection: %v", tarfiles)
}
imageID := tarfiles[0][:len(tarfiles[0])-4]
imageTarballPath := runner.ArvMountPoint + "/by_id/" + runner.Container.ContainerImage + "/" + imageID + ".tar"
runner.CrunchLog.Printf("Using Docker image id %q", imageID)
runner.CrunchLog.Print("Loading Docker image from keep")
err = runner.executor.LoadImage(imageID, imageTarballPath, runner.Container, runner.ArvMountPoint,
runner.containerClient)
if err != nil {
return "", err
}
return imageID, nil
}
func (runner *ContainerRunner) ArvMountCmd(cmdline []string, token string) (c *exec.Cmd, err error) {
c = exec.Command(cmdline[0], cmdline[1:]...)
// Copy our environment, but override ARVADOS_API_TOKEN with
// the container auth token.
c.Env = nil
for _, s := range os.Environ() {
if !strings.HasPrefix(s, "ARVADOS_API_TOKEN=") {
c.Env = append(c.Env, s)
}
}
c.Env = append(c.Env, "ARVADOS_API_TOKEN="+token)
w, err := runner.NewLogWriter("arv-mount")
if err != nil {
return nil, err
}
runner.arvMountLog = NewThrottledLogger(w)
scanner := logScanner{
Patterns: []string{
"Keep write error",
"Block not found error",
"Unhandled exception during FUSE operation",
},
ReportFunc: runner.reportArvMountWarning,
}
c.Stdout = runner.arvMountLog
c.Stderr = io.MultiWriter(runner.arvMountLog, os.Stderr, &scanner)
runner.CrunchLog.Printf("Running %v", c.Args)
err = c.Start()
if err != nil {
return nil, err
}
statReadme := make(chan bool)
runner.ArvMountExit = make(chan error)
keepStatting := true
go func() {
for keepStatting {
time.Sleep(100 * time.Millisecond)
_, err = os.Stat(fmt.Sprintf("%s/by_id/README", runner.ArvMountPoint))
if err == nil {
keepStatting = false
statReadme <- true
}
}
close(statReadme)
}()
go func() {
mnterr := c.Wait()
if mnterr != nil {
runner.CrunchLog.Printf("Arv-mount exit error: %v", mnterr)
}
runner.ArvMountExit <- mnterr
close(runner.ArvMountExit)
}()
select {
case <-statReadme:
break
case err := <-runner.ArvMountExit:
runner.ArvMount = nil
keepStatting = false
return nil, err
}
return c, nil
}
func (runner *ContainerRunner) SetupArvMountPoint(prefix string) (err error) {
if runner.ArvMountPoint == "" {
runner.ArvMountPoint, err = runner.MkTempDir(runner.parentTemp, prefix)
}
return
}
func copyfile(src string, dst string) (err error) {
srcfile, err := os.Open(src)
if err != nil {
return
}
os.MkdirAll(path.Dir(dst), 0777)
dstfile, err := os.Create(dst)
if err != nil {
return
}
_, err = io.Copy(dstfile, srcfile)
if err != nil {
return
}
err = srcfile.Close()
err2 := dstfile.Close()
if err != nil {
return
}
if err2 != nil {
return err2
}
return nil
}
func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) {
bindmounts := map[string]bindmount{}
err := runner.SetupArvMountPoint("keep")
if err != nil {
return nil, fmt.Errorf("While creating keep mount temp dir: %v", err)
}
token, err := runner.ContainerToken()
if err != nil {
return nil, fmt.Errorf("could not get container token: %s", err)
}
runner.CrunchLog.Printf("container token %q", token)
pdhOnly := true
tmpcount := 0
arvMountCmd := []string{
"arv-mount",
"--foreground",
"--read-write",
"--storage-classes", strings.Join(runner.Container.OutputStorageClasses, ","),
fmt.Sprintf("--crunchstat-interval=%v", runner.statInterval.Seconds())}
if _, isdocker := runner.executor.(*dockerExecutor); isdocker {
arvMountCmd = append(arvMountCmd, "--allow-other")
}
if runner.Container.RuntimeConstraints.KeepCacheRAM > 0 {
arvMountCmd = append(arvMountCmd, "--file-cache", fmt.Sprintf("%d", runner.Container.RuntimeConstraints.KeepCacheRAM))
}
collectionPaths := []string{}
needCertMount := true
type copyFile struct {
src string
bind string
}
var copyFiles []copyFile
var binds []string
for bind := range runner.Container.Mounts {
binds = append(binds, bind)
}
for bind := range runner.SecretMounts {
if _, ok := runner.Container.Mounts[bind]; ok {
return nil, fmt.Errorf("secret mount %q conflicts with regular mount", bind)
}
if runner.SecretMounts[bind].Kind != "json" &&
runner.SecretMounts[bind].Kind != "text" {
return nil, fmt.Errorf("secret mount %q type is %q but only 'json' and 'text' are permitted",
bind, runner.SecretMounts[bind].Kind)
}
binds = append(binds, bind)
}
sort.Strings(binds)
for _, bind := range binds {
mnt, notSecret := runner.Container.Mounts[bind]
if !notSecret {
mnt = runner.SecretMounts[bind]
}
if bind == "stdout" || bind == "stderr" {
// Is it a "file" mount kind?
if mnt.Kind != "file" {
return nil, fmt.Errorf("unsupported mount kind '%s' for %s: only 'file' is supported", mnt.Kind, bind)
}
// Does path start with OutputPath?
prefix := runner.Container.OutputPath
if !strings.HasSuffix(prefix, "/") {
prefix += "/"
}
if !strings.HasPrefix(mnt.Path, prefix) {
return nil, fmt.Errorf("%s path does not start with OutputPath: %s, %s", strings.Title(bind), mnt.Path, prefix)
}
}
if bind == "stdin" {
// Is it a "collection" mount kind?
if mnt.Kind != "collection" && mnt.Kind != "json" {
return nil, fmt.Errorf("unsupported mount kind '%s' for stdin: only 'collection' and 'json' are supported", mnt.Kind)
}
}
if bind == "/etc/arvados/ca-certificates.crt" {
needCertMount = false
}
if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && bind != runner.Container.OutputPath+"/" {
if mnt.Kind != "collection" && mnt.Kind != "text" && mnt.Kind != "json" {
return nil, fmt.Errorf("only mount points of kind 'collection', 'text' or 'json' are supported underneath the output_path for %q, was %q", bind, mnt.Kind)
}
}
switch {
case mnt.Kind == "collection" && bind != "stdin":
var src string
if mnt.UUID != "" && mnt.PortableDataHash != "" {
return nil, fmt.Errorf("cannot specify both 'uuid' and 'portable_data_hash' for a collection mount")
}
if mnt.UUID != "" {
if mnt.Writable {
return nil, fmt.Errorf("writing to existing collections currently not permitted")
}
pdhOnly = false
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.UUID)
} else if mnt.PortableDataHash != "" {
if mnt.Writable && !strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
return nil, fmt.Errorf("can never write to a collection specified by portable data hash")
}
idx := strings.Index(mnt.PortableDataHash, "/")
if idx > 0 {
mnt.Path = path.Clean(mnt.PortableDataHash[idx:])
mnt.PortableDataHash = mnt.PortableDataHash[0:idx]
runner.Container.Mounts[bind] = mnt
}
src = fmt.Sprintf("%s/by_id/%s", runner.ArvMountPoint, mnt.PortableDataHash)
if mnt.Path != "" && mnt.Path != "." {
if strings.HasPrefix(mnt.Path, "./") {
mnt.Path = mnt.Path[2:]
} else if strings.HasPrefix(mnt.Path, "/") {
mnt.Path = mnt.Path[1:]
}
src += "/" + mnt.Path
}
} else {
src = fmt.Sprintf("%s/tmp%d", runner.ArvMountPoint, tmpcount)
arvMountCmd = append(arvMountCmd, "--mount-tmp", fmt.Sprintf("tmp%d", tmpcount))
tmpcount++
}
if mnt.Writable {
if bind == runner.Container.OutputPath {
runner.HostOutputDir = src
bindmounts[bind] = bindmount{HostPath: src}
} else if strings.HasPrefix(bind, runner.Container.OutputPath+"/") {
copyFiles = append(copyFiles, copyFile{src, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
} else {
bindmounts[bind] = bindmount{HostPath: src}
}
} else {
bindmounts[bind] = bindmount{HostPath: src, ReadOnly: true}
}
collectionPaths = append(collectionPaths, src)
case mnt.Kind == "tmp":
var tmpdir string
tmpdir, err = runner.MkTempDir(runner.parentTemp, "tmp")
if err != nil {
return nil, fmt.Errorf("while creating mount temp dir: %v", err)
}
st, staterr := os.Stat(tmpdir)
if staterr != nil {
return nil, fmt.Errorf("while Stat on temp dir: %v", staterr)
}
err = os.Chmod(tmpdir, st.Mode()|os.ModeSetgid|0777)
if staterr != nil {
return nil, fmt.Errorf("while Chmod temp dir: %v", err)
}
bindmounts[bind] = bindmount{HostPath: tmpdir}
if bind == runner.Container.OutputPath {
runner.HostOutputDir = tmpdir
}
case mnt.Kind == "json" || mnt.Kind == "text":
var filedata []byte
if mnt.Kind == "json" {
filedata, err = json.Marshal(mnt.Content)
if err != nil {
return nil, fmt.Errorf("encoding json data: %v", err)
}
} else {
text, ok := mnt.Content.(string)
if !ok {
return nil, fmt.Errorf("content for mount %q must be a string", bind)
}
filedata = []byte(text)
}
tmpdir, err := runner.MkTempDir(runner.parentTemp, mnt.Kind)
if err != nil {
return nil, fmt.Errorf("creating temp dir: %v", err)
}
tmpfn := filepath.Join(tmpdir, "mountdata."+mnt.Kind)
err = ioutil.WriteFile(tmpfn, filedata, 0444)
if err != nil {
return nil, fmt.Errorf("writing temp file: %v", err)
}
if strings.HasPrefix(bind, runner.Container.OutputPath+"/") && (notSecret || runner.Container.Mounts[runner.Container.OutputPath].Kind != "collection") {
// In most cases, if the container
// specifies a literal file inside the
// output path, we copy it into the
// output directory (either a mounted
// collection or a staging area on the
// host fs). If it's a secret, it will
// be skipped when copying output from
// staging to Keep later.
copyFiles = append(copyFiles, copyFile{tmpfn, runner.HostOutputDir + bind[len(runner.Container.OutputPath):]})
} else {
// If a secret is outside OutputPath,
// we bind mount the secret file
// directly just like other mounts. We
// also use this strategy when a
// secret is inside OutputPath but
// OutputPath is a live collection, to
// avoid writing the secret to
// Keep. Attempting to remove a
// bind-mounted secret file from
// inside the container will return a
// "Device or resource busy" error
// that might not be handled well by
// the container, which is why we
// don't use this strategy when
// OutputPath is a staging directory.
bindmounts[bind] = bindmount{HostPath: tmpfn, ReadOnly: true}
}
case mnt.Kind == "git_tree":
tmpdir, err := runner.MkTempDir(runner.parentTemp, "git_tree")
if err != nil {
return nil, fmt.Errorf("creating temp dir: %v", err)
}
err = gitMount(mnt).extractTree(runner.ContainerArvClient, tmpdir, token)
if err != nil {
return nil, err
}
bindmounts[bind] = bindmount{HostPath: tmpdir, ReadOnly: true}
}
}
if runner.HostOutputDir == "" {
return nil, fmt.Errorf("output path does not correspond to a writable mount point")
}
if needCertMount && runner.Container.RuntimeConstraints.API {
for _, certfile := range arvadosclient.CertFiles {
_, err := os.Stat(certfile)
if err == nil {
bindmounts["/etc/arvados/ca-certificates.crt"] = bindmount{HostPath: certfile, ReadOnly: true}
break
}
}
}
if pdhOnly {
// If we are only mounting collections by pdh, make
// sure we don't subscribe to websocket events to
// avoid putting undesired load on the API server
arvMountCmd = append(arvMountCmd, "--mount-by-pdh", "by_id", "--disable-event-listening")
} else {
arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_id")
}
// the by_uuid mount point is used by singularity when writing
// out docker images converted to SIF
arvMountCmd = append(arvMountCmd, "--mount-by-id", "by_uuid")
arvMountCmd = append(arvMountCmd, runner.ArvMountPoint)
runner.ArvMount, err = runner.RunArvMount(arvMountCmd, token)
if err != nil {
return nil, fmt.Errorf("while trying to start arv-mount: %v", err)
}
for _, p := range collectionPaths {
_, err = os.Stat(p)
if err != nil {
return nil, fmt.Errorf("while checking that input files exist: %v", err)
}
}
for _, cp := range copyFiles {
st, err := os.Stat(cp.src)
if err != nil {
return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
}
if st.IsDir() {
err = filepath.Walk(cp.src, func(walkpath string, walkinfo os.FileInfo, walkerr error) error {
if walkerr != nil {
return walkerr
}
target := path.Join(cp.bind, walkpath[len(cp.src):])
if walkinfo.Mode().IsRegular() {
copyerr := copyfile(walkpath, target)
if copyerr != nil {
return copyerr
}
return os.Chmod(target, walkinfo.Mode()|0777)
} else if walkinfo.Mode().IsDir() {
mkerr := os.MkdirAll(target, 0777)
if mkerr != nil {
return mkerr
}
return os.Chmod(target, walkinfo.Mode()|os.ModeSetgid|0777)
} else {
return fmt.Errorf("source %q is not a regular file or directory", cp.src)
}
})
} else if st.Mode().IsRegular() {
err = copyfile(cp.src, cp.bind)
if err == nil {
err = os.Chmod(cp.bind, st.Mode()|0777)
}
}
if err != nil {
return nil, fmt.Errorf("while staging writable file from %q to %q: %v", cp.src, cp.bind, err)
}
}
return bindmounts, nil
}
func (runner *ContainerRunner) stopHoststat() error {
if runner.hoststatReporter == nil {
return nil
}
runner.hoststatReporter.Stop()
err := runner.hoststatLogger.Close()
if err != nil {
return fmt.Errorf("error closing hoststat logs: %v", err)
}
return nil
}
func (runner *ContainerRunner) startHoststat() error {
w, err := runner.NewLogWriter("hoststat")
if err != nil {
return err
}
runner.hoststatLogger = NewThrottledLogger(w)
runner.hoststatReporter = &crunchstat.Reporter{
Logger: log.New(runner.hoststatLogger, "", 0),
CgroupRoot: runner.cgroupRoot,
PollPeriod: runner.statInterval,
}
runner.hoststatReporter.Start()
return nil
}
func (runner *ContainerRunner) startCrunchstat() error {
w, err := runner.NewLogWriter("crunchstat")
if err != nil {
return err
}
runner.statLogger = NewThrottledLogger(w)
runner.statReporter = &crunchstat.Reporter{
CID: runner.executor.CgroupID(),
Logger: log.New(runner.statLogger, "", 0),
CgroupParent: runner.expectCgroupParent,
CgroupRoot: runner.cgroupRoot,
PollPeriod: runner.statInterval,
TempDir: runner.parentTemp,
}
runner.statReporter.Start()
return nil
}
type infoCommand struct {
label string
cmd []string
}
// LogHostInfo logs info about the current host, for debugging and
// accounting purposes. Although it's logged as "node-info", this is
// about the environment where crunch-run is actually running, which
// might differ from what's described in the node record (see
// LogNodeRecord).
func (runner *ContainerRunner) LogHostInfo() (err error) {
w, err := runner.NewLogWriter("node-info")
if err != nil {
return
}
commands := []infoCommand{
{
label: "Host Information",
cmd: []string{"uname", "-a"},
},
{
label: "CPU Information",
cmd: []string{"cat", "/proc/cpuinfo"},
},
{
label: "Memory Information",
cmd: []string{"cat", "/proc/meminfo"},
},
{
label: "Disk Space",
cmd: []string{"df", "-m", "/", os.TempDir()},
},
{
label: "Disk INodes",
cmd: []string{"df", "-i", "/", os.TempDir()},
},
}
// Run commands with informational output to be logged.
for _, command := range commands {
fmt.Fprintln(w, command.label)
cmd := exec.Command(command.cmd[0], command.cmd[1:]...)
cmd.Stdout = w
cmd.Stderr = w
if err := cmd.Run(); err != nil {
err = fmt.Errorf("While running command %q: %v", command.cmd, err)
fmt.Fprintln(w, err)
return err
}
fmt.Fprintln(w, "")
}
err = w.Close()
if err != nil {
return fmt.Errorf("While closing node-info logs: %v", err)
}
return nil
}
// LogContainerRecord gets and saves the raw JSON container record from the API server
func (runner *ContainerRunner) LogContainerRecord() error {
logged, err := runner.logAPIResponse("container", "containers", map[string]interface{}{"filters": [][]string{{"uuid", "=", runner.Container.UUID}}}, nil)
if !logged && err == nil {
err = fmt.Errorf("error: no container record found for %s", runner.Container.UUID)
}
return err
}
// LogNodeRecord logs the current host's InstanceType config entry (or
// the arvados#node record, if running via crunch-dispatch-slurm).
func (runner *ContainerRunner) LogNodeRecord() error {
if it := os.Getenv("InstanceType"); it != "" {
// Dispatched via arvados-dispatch-cloud. Save
// InstanceType config fragment received from
// dispatcher on stdin.
w, err := runner.LogCollection.OpenFile("node.json", os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return err
}
defer w.Close()
_, err = io.WriteString(w, it)
if err != nil {
return err
}
return w.Close()
}
// Dispatched via crunch-dispatch-slurm. Look up
// apiserver's node record corresponding to
// $SLURMD_NODENAME.
hostname := os.Getenv("SLURMD_NODENAME")
if hostname == "" {
hostname, _ = os.Hostname()
}
_, err := runner.logAPIResponse("node", "nodes", map[string]interface{}{"filters": [][]string{{"hostname", "=", hostname}}}, func(resp interface{}) {
// The "info" field has admin-only info when
// obtained with a privileged token, and
// should not be logged.
node, ok := resp.(map[string]interface{})
if ok {
delete(node, "info")
}
})
return err
}
func (runner *ContainerRunner) logAPIResponse(label, path string, params map[string]interface{}, munge func(interface{})) (logged bool, err error) {
writer, err := runner.LogCollection.OpenFile(label+".json", os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return false, err
}
w := &ArvLogWriter{
ArvClient: runner.DispatcherArvClient,
UUID: runner.Container.UUID,
loggingStream: label,
writeCloser: writer,
}
reader, err := runner.DispatcherArvClient.CallRaw("GET", path, "", "", arvadosclient.Dict(params))
if err != nil {
return false, fmt.Errorf("error getting %s record: %v", label, err)
}
defer reader.Close()
dec := json.NewDecoder(reader)
dec.UseNumber()
var resp map[string]interface{}
if err = dec.Decode(&resp); err != nil {
return false, fmt.Errorf("error decoding %s list response: %v", label, err)
}
items, ok := resp["items"].([]interface{})
if !ok {
return false, fmt.Errorf("error decoding %s list response: no \"items\" key in API list response", label)
} else if len(items) < 1 {
return false, nil
}
if munge != nil {
munge(items[0])
}
// Re-encode it using indentation to improve readability
enc := json.NewEncoder(w)
enc.SetIndent("", " ")
if err = enc.Encode(items[0]); err != nil {
return false, fmt.Errorf("error logging %s record: %v", label, err)
}
err = w.Close()
if err != nil {
return false, fmt.Errorf("error closing %s.json in log collection: %v", label, err)
}
return true, nil
}
func (runner *ContainerRunner) getStdoutFile(mntPath string) (*os.File, error) {
stdoutPath := mntPath[len(runner.Container.OutputPath):]
index := strings.LastIndex(stdoutPath, "/")
if index > 0 {
subdirs := stdoutPath[:index]
if subdirs != "" {
st, err := os.Stat(runner.HostOutputDir)
if err != nil {
return nil, fmt.Errorf("While Stat on temp dir: %v", err)
}
stdoutPath := filepath.Join(runner.HostOutputDir, subdirs)
err = os.MkdirAll(stdoutPath, st.Mode()|os.ModeSetgid|0777)
if err != nil {
return nil, fmt.Errorf("While MkdirAll %q: %v", stdoutPath, err)
}
}
}
stdoutFile, err := os.Create(filepath.Join(runner.HostOutputDir, stdoutPath))
if err != nil {
return nil, fmt.Errorf("While creating file %q: %v", stdoutPath, err)
}
return stdoutFile, nil
}
// CreateContainer creates the docker container.
func (runner *ContainerRunner) CreateContainer(imageID string, bindmounts map[string]bindmount) error {
var stdin io.ReadCloser = ioutil.NopCloser(bytes.NewReader(nil))
if mnt, ok := runner.Container.Mounts["stdin"]; ok {
switch mnt.Kind {
case "collection":
var collID string
if mnt.UUID != "" {
collID = mnt.UUID
} else {
collID = mnt.PortableDataHash
}
path := runner.ArvMountPoint + "/by_id/" + collID + "/" + mnt.Path
f, err := os.Open(path)
if err != nil {
return err
}
stdin = f
case "json":
j, err := json.Marshal(mnt.Content)
if err != nil {
return fmt.Errorf("error encoding stdin json data: %v", err)
}
stdin = ioutil.NopCloser(bytes.NewReader(j))
default:
return fmt.Errorf("stdin mount has unsupported kind %q", mnt.Kind)
}
}
var stdout, stderr io.WriteCloser
if mnt, ok := runner.Container.Mounts["stdout"]; ok {
f, err := runner.getStdoutFile(mnt.Path)
if err != nil {
return err
}
stdout = f
} else if w, err := runner.NewLogWriter("stdout"); err != nil {
return err
} else {
stdout = NewThrottledLogger(w)
}
if mnt, ok := runner.Container.Mounts["stderr"]; ok {
f, err := runner.getStdoutFile(mnt.Path)
if err != nil {
return err
}
stderr = f
} else if w, err := runner.NewLogWriter("stderr"); err != nil {
return err
} else {
stderr = NewThrottledLogger(w)
}
env := runner.Container.Environment
enableNetwork := runner.enableNetwork == "always"
if runner.Container.RuntimeConstraints.API {
enableNetwork = true
tok, err := runner.ContainerToken()
if err != nil {
return err
}
env = map[string]string{}
for k, v := range runner.Container.Environment {
env[k] = v
}
env["ARVADOS_API_TOKEN"] = tok
env["ARVADOS_API_HOST"] = os.Getenv("ARVADOS_API_HOST")
env["ARVADOS_API_HOST_INSECURE"] = os.Getenv("ARVADOS_API_HOST_INSECURE")
}
workdir := runner.Container.Cwd
if workdir == "." {
// both "" and "." mean default
workdir = ""
}
ram := runner.Container.RuntimeConstraints.RAM
if !runner.enableMemoryLimit {
ram = 0
}
runner.executorStdin = stdin
runner.executorStdout = stdout
runner.executorStderr = stderr
if runner.Container.RuntimeConstraints.CUDA.DeviceCount > 0 {
nvidiaModprobe(runner.CrunchLog)
}
return runner.executor.Create(containerSpec{
Image: imageID,
VCPUs: runner.Container.RuntimeConstraints.VCPUs,
RAM: ram,
WorkingDir: workdir,
Env: env,
BindMounts: bindmounts,
Command: runner.Container.Command,
EnableNetwork: enableNetwork,
CUDADeviceCount: runner.Container.RuntimeConstraints.CUDA.DeviceCount,
NetworkMode: runner.networkMode,
CgroupParent: runner.setCgroupParent,
Stdin: stdin,
Stdout: stdout,
Stderr: stderr,
})
}
// StartContainer starts the docker container created by CreateContainer.
func (runner *ContainerRunner) StartContainer() error {
runner.CrunchLog.Printf("Starting container")
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
if runner.cCancelled {
return ErrCancelled
}
err := runner.executor.Start()
if err != nil {
var advice string
if m, e := regexp.MatchString("(?ms).*(exec|System error).*(no such file or directory|file not found).*", err.Error()); m && e == nil {
advice = fmt.Sprintf("\nPossible causes: command %q is missing, the interpreter given in #! is missing, or script has Windows line endings.", runner.Container.Command[0])
}
return fmt.Errorf("could not start container: %v%s", err, advice)
}
return nil
}
// WaitFinish waits for the container to terminate, capture the exit code, and
// close the stdout/stderr logging.
func (runner *ContainerRunner) WaitFinish() error {
runner.CrunchLog.Print("Waiting for container to finish")
var timeout <-chan time.Time
if s := runner.Container.SchedulingParameters.MaxRunTime; s > 0 {
timeout = time.After(time.Duration(s) * time.Second)
}
ctx, cancel := context.WithCancel(context.Background())
defer cancel()
go func() {
select {
case <-timeout:
runner.CrunchLog.Printf("maximum run time exceeded. Stopping container.")
runner.stop(nil)
case <-runner.ArvMountExit:
runner.CrunchLog.Printf("arv-mount exited while container is still running. Stopping container.")
runner.stop(nil)
case <-ctx.Done():
}
}()
exitcode, err := runner.executor.Wait(ctx)
if err != nil {
runner.checkBrokenNode(err)
return err
}
runner.ExitCode = &exitcode
extra := ""
if exitcode&0x80 != 0 {
// Convert raw exit status (0x80 + signal number) to a
// string to log after the code, like " (signal 101)"
// or " (signal 9, killed)"
sig := syscall.WaitStatus(exitcode).Signal()
if name := unix.SignalName(sig); name != "" {
extra = fmt.Sprintf(" (signal %d, %s)", sig, name)
} else {
extra = fmt.Sprintf(" (signal %d)", sig)
}
}
runner.CrunchLog.Printf("Container exited with status code %d%s", exitcode, extra)
var returnErr error
if err = runner.executorStdin.Close(); err != nil {
err = fmt.Errorf("error closing container stdin: %s", err)
runner.CrunchLog.Printf("%s", err)
returnErr = err
}
if err = runner.executorStdout.Close(); err != nil {
err = fmt.Errorf("error closing container stdout: %s", err)
runner.CrunchLog.Printf("%s", err)
if returnErr == nil {
returnErr = err
}
}
if err = runner.executorStderr.Close(); err != nil {
err = fmt.Errorf("error closing container stderr: %s", err)
runner.CrunchLog.Printf("%s", err)
if returnErr == nil {
returnErr = err
}
}
if runner.statReporter != nil {
runner.statReporter.Stop()
err = runner.statLogger.Close()
if err != nil {
runner.CrunchLog.Printf("error closing crunchstat logs: %v", err)
}
}
return returnErr
}
func (runner *ContainerRunner) updateLogs() {
ticker := time.NewTicker(crunchLogUpdatePeriod / 360)
defer ticker.Stop()
sigusr1 := make(chan os.Signal, 1)
signal.Notify(sigusr1, syscall.SIGUSR1)
defer signal.Stop(sigusr1)
saveAtTime := time.Now().Add(crunchLogUpdatePeriod)
saveAtSize := crunchLogUpdateSize
var savedSize int64
for {
select {
case <-ticker.C:
case <-sigusr1:
saveAtTime = time.Now()
}
runner.logMtx.Lock()
done := runner.LogsPDH != nil
runner.logMtx.Unlock()
if done {
return
}
size := runner.LogCollection.Size()
if size == savedSize || (time.Now().Before(saveAtTime) && size < saveAtSize) {
continue
}
saveAtTime = time.Now().Add(crunchLogUpdatePeriod)
saveAtSize = runner.LogCollection.Size() + crunchLogUpdateSize
saved, err := runner.saveLogCollection(false)
if err != nil {
runner.CrunchLog.Printf("error updating log collection: %s", err)
continue
}
var updated arvados.Container
err = runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
"container": arvadosclient.Dict{"log": saved.PortableDataHash},
}, &updated)
if err != nil {
runner.CrunchLog.Printf("error updating container log to %s: %s", saved.PortableDataHash, err)
continue
}
savedSize = size
}
}
func (runner *ContainerRunner) reportArvMountWarning(pattern, text string) {
var updated arvados.Container
err := runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
"container": arvadosclient.Dict{
"runtime_status": arvadosclient.Dict{
"warning": "arv-mount: " + pattern,
"warningDetail": text,
},
},
}, &updated)
if err != nil {
runner.CrunchLog.Printf("error updating container runtime_status: %s", err)
}
}
// CaptureOutput saves data from the container's output directory if
// needed, and updates the container output accordingly.
func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) error {
if runner.Container.RuntimeConstraints.API {
// Output may have been set directly by the container, so
// refresh the container record to check.
err := runner.DispatcherArvClient.Get("containers", runner.Container.UUID,
nil, &runner.Container)
if err != nil {
return err
}
if runner.Container.Output != "" {
// Container output is already set.
runner.OutputPDH = &runner.Container.Output
return nil
}
}
txt, err := (&copier{
client: runner.containerClient,
arvClient: runner.ContainerArvClient,
keepClient: runner.ContainerKeepClient,
hostOutputDir: runner.HostOutputDir,
ctrOutputDir: runner.Container.OutputPath,
bindmounts: bindmounts,
mounts: runner.Container.Mounts,
secretMounts: runner.SecretMounts,
logger: runner.CrunchLog,
}).Copy()
if err != nil {
return err
}
if n := len(regexp.MustCompile(` [0-9a-f]+\+\S*\+R`).FindAllStringIndex(txt, -1)); n > 0 {
runner.CrunchLog.Printf("Copying %d data blocks from remote input collections...", n)
fs, err := (&arvados.Collection{ManifestText: txt}).FileSystem(runner.containerClient, runner.ContainerKeepClient)
if err != nil {
return err
}
txt, err = fs.MarshalManifest(".")
if err != nil {
return err
}
}
var resp arvados.Collection
err = runner.ContainerArvClient.Create("collections", arvadosclient.Dict{
"ensure_unique_name": true,
"collection": arvadosclient.Dict{
"is_trashed": true,
"name": "output for " + runner.Container.UUID,
"manifest_text": txt,
},
}, &resp)
if err != nil {
return fmt.Errorf("error creating output collection: %v", err)
}
runner.OutputPDH = &resp.PortableDataHash
return nil
}
func (runner *ContainerRunner) CleanupDirs() {
if runner.ArvMount != nil {
var delay int64 = 8
umount := exec.Command("arv-mount", fmt.Sprintf("--unmount-timeout=%d", delay), "--unmount", runner.ArvMountPoint)
umount.Stdout = runner.CrunchLog
umount.Stderr = runner.CrunchLog
runner.CrunchLog.Printf("Running %v", umount.Args)
umnterr := umount.Start()
if umnterr != nil {
runner.CrunchLog.Printf("Error unmounting: %v", umnterr)
runner.ArvMount.Process.Kill()
} else {
// If arv-mount --unmount gets stuck for any reason, we
// don't want to wait for it forever. Do Wait() in a goroutine
// so it doesn't block crunch-run.
umountExit := make(chan error)
go func() {
mnterr := umount.Wait()
if mnterr != nil {
runner.CrunchLog.Printf("Error unmounting: %v", mnterr)
}
umountExit <- mnterr
}()
for again := true; again; {
again = false
select {
case <-umountExit:
umount = nil
again = true
case <-runner.ArvMountExit:
break
case <-time.After(time.Duration((delay + 1) * int64(time.Second))):
runner.CrunchLog.Printf("Timed out waiting for unmount")
if umount != nil {
umount.Process.Kill()
}
runner.ArvMount.Process.Kill()
}
}
}
runner.ArvMount = nil
}
if runner.ArvMountPoint != "" {
if rmerr := os.Remove(runner.ArvMountPoint); rmerr != nil {
runner.CrunchLog.Printf("While cleaning up arv-mount directory %s: %v", runner.ArvMountPoint, rmerr)
}
runner.ArvMountPoint = ""
}
if rmerr := os.RemoveAll(runner.parentTemp); rmerr != nil {
runner.CrunchLog.Printf("While cleaning up temporary directory %s: %v", runner.parentTemp, rmerr)
}
}
// CommitLogs posts the collection containing the final container logs.
func (runner *ContainerRunner) CommitLogs() error {
func() {
// Hold cStateLock to prevent races on CrunchLog (e.g., stop()).
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
runner.CrunchLog.Print(runner.finalState)
if runner.arvMountLog != nil {
runner.arvMountLog.Close()
}
runner.CrunchLog.Close()
// Closing CrunchLog above allows them to be committed to Keep at this
// point, but re-open crunch log with ArvClient in case there are any
// other further errors (such as failing to write the log to Keep!)
// while shutting down
runner.CrunchLog = NewThrottledLogger(&ArvLogWriter{
ArvClient: runner.DispatcherArvClient,
UUID: runner.Container.UUID,
loggingStream: "crunch-run",
writeCloser: nil,
})
runner.CrunchLog.Immediate = log.New(os.Stderr, runner.Container.UUID+" ", 0)
}()
if runner.keepstoreLogger != nil {
// Flush any buffered logs from our local keepstore
// process. Discard anything logged after this point
// -- it won't end up in the log collection, so
// there's no point writing it to the collectionfs.
runner.keepstoreLogbuf.SetWriter(io.Discard)
runner.keepstoreLogger.Close()
runner.keepstoreLogger = nil
}
if runner.LogsPDH != nil {
// If we have already assigned something to LogsPDH,
// we must be closing the re-opened log, which won't
// end up getting attached to the container record and
// therefore doesn't need to be saved as a collection
// -- it exists only to send logs to other channels.
return nil
}
saved, err := runner.saveLogCollection(true)
if err != nil {
return fmt.Errorf("error saving log collection: %s", err)
}
runner.logMtx.Lock()
defer runner.logMtx.Unlock()
runner.LogsPDH = &saved.PortableDataHash
return nil
}
func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.Collection, err error) {
runner.logMtx.Lock()
defer runner.logMtx.Unlock()
if runner.LogsPDH != nil {
// Already finalized.
return
}
updates := arvadosclient.Dict{
"name": "logs for " + runner.Container.UUID,
}
mt, err1 := runner.LogCollection.MarshalManifest(".")
if err1 == nil {
// Only send updated manifest text if there was no
// error.
updates["manifest_text"] = mt
}
// Even if flushing the manifest had an error, we still want
// to update the log record, if possible, to push the trash_at
// and delete_at times into the future. Details on bug
// #17293.
if final {
updates["is_trashed"] = true
} else {
exp := time.Now().Add(crunchLogUpdatePeriod * 24)
updates["trash_at"] = exp
updates["delete_at"] = exp
}
reqBody := arvadosclient.Dict{"collection": updates}
var err2 error
if runner.logUUID == "" {
reqBody["ensure_unique_name"] = true
err2 = runner.DispatcherArvClient.Create("collections", reqBody, &response)
} else {
err2 = runner.DispatcherArvClient.Update("collections", runner.logUUID, reqBody, &response)
}
if err2 == nil {
runner.logUUID = response.UUID
}
if err1 != nil || err2 != nil {
err = fmt.Errorf("error recording logs: %q, %q", err1, err2)
}
return
}
// UpdateContainerRunning updates the container state to "Running"
func (runner *ContainerRunner) UpdateContainerRunning() error {
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
if runner.cCancelled {
return ErrCancelled
}
return runner.DispatcherArvClient.Update("containers", runner.Container.UUID,
arvadosclient.Dict{"container": arvadosclient.Dict{"state": "Running", "gateway_address": runner.gateway.Address}}, nil)
}
// ContainerToken returns the api_token the container (and any
// arv-mount processes) are allowed to use.
func (runner *ContainerRunner) ContainerToken() (string, error) {
if runner.token != "" {
return runner.token, nil
}
var auth arvados.APIClientAuthorization
err := runner.DispatcherArvClient.Call("GET", "containers", runner.Container.UUID, "auth", nil, &auth)
if err != nil {
return "", err
}
runner.token = fmt.Sprintf("v2/%s/%s/%s", auth.UUID, auth.APIToken, runner.Container.UUID)
return runner.token, nil
}
// UpdateContainerFinal updates the container record state on API
// server to "Complete" or "Cancelled"
func (runner *ContainerRunner) UpdateContainerFinal() error {
update := arvadosclient.Dict{}
update["state"] = runner.finalState
if runner.LogsPDH != nil {
update["log"] = *runner.LogsPDH
}
if runner.finalState == "Complete" {
if runner.ExitCode != nil {
update["exit_code"] = *runner.ExitCode
}
if runner.OutputPDH != nil {
update["output"] = *runner.OutputPDH
}
}
return runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
}
// IsCancelled returns the value of Cancelled, with goroutine safety.
func (runner *ContainerRunner) IsCancelled() bool {
runner.cStateLock.Lock()
defer runner.cStateLock.Unlock()
return runner.cCancelled
}
// NewArvLogWriter creates an ArvLogWriter
func (runner *ContainerRunner) NewArvLogWriter(name string) (io.WriteCloser, error) {
writer, err := runner.LogCollection.OpenFile(name+".txt", os.O_CREATE|os.O_WRONLY, 0666)
if err != nil {
return nil, err
}
return &ArvLogWriter{
ArvClient: runner.DispatcherArvClient,
UUID: runner.Container.UUID,
loggingStream: name,
writeCloser: writer,
}, nil
}
// Run the full container lifecycle.
func (runner *ContainerRunner) Run() (err error) {
runner.CrunchLog.Printf("crunch-run %s started", cmd.Version.String())
runner.CrunchLog.Printf("%s", currentUserAndGroups())
v, _ := exec.Command("arv-mount", "--version").CombinedOutput()
runner.CrunchLog.Printf("Using FUSE mount: %s", v)
runner.CrunchLog.Printf("Using container runtime: %s", runner.executor.Runtime())
runner.CrunchLog.Printf("Executing container: %s", runner.Container.UUID)
hostname, hosterr := os.Hostname()
if hosterr != nil {
runner.CrunchLog.Printf("Error getting hostname '%v'", hosterr)
} else {
runner.CrunchLog.Printf("Executing on host '%s'", hostname)
}
runner.finalState = "Queued"
defer func() {
runner.CleanupDirs()
runner.CrunchLog.Printf("crunch-run finished")
runner.CrunchLog.Close()
}()
err = runner.fetchContainerRecord()
if err != nil {
return
}
if runner.Container.State != "Locked" {
return fmt.Errorf("dispatch error detected: container %q has state %q", runner.Container.UUID, runner.Container.State)
}
var bindmounts map[string]bindmount
defer func() {
// checkErr prints e (unless it's nil) and sets err to
// e (unless err is already non-nil). Thus, if err
// hasn't already been assigned when Run() returns,
// this cleanup func will cause Run() to return the
// first non-nil error that is passed to checkErr().
checkErr := func(errorIn string, e error) {
if e == nil {
return
}
runner.CrunchLog.Printf("error in %s: %v", errorIn, e)
if err == nil {
err = e
}
if runner.finalState == "Complete" {
// There was an error in the finalization.
runner.finalState = "Cancelled"
}
}
// Log the error encountered in Run(), if any
checkErr("Run", err)
if runner.finalState == "Queued" {
runner.UpdateContainerFinal()
return
}
if runner.IsCancelled() {
runner.finalState = "Cancelled"
// but don't return yet -- we still want to
// capture partial output and write logs
}
if bindmounts != nil {
checkErr("CaptureOutput", runner.CaptureOutput(bindmounts))
}
checkErr("stopHoststat", runner.stopHoststat())
checkErr("CommitLogs", runner.CommitLogs())
runner.CleanupDirs()
checkErr("UpdateContainerFinal", runner.UpdateContainerFinal())
}()
runner.setupSignals()
err = runner.startHoststat()
if err != nil {
return
}
// set up FUSE mount and binds
bindmounts, err = runner.SetupMounts()
if err != nil {
runner.finalState = "Cancelled"
err = fmt.Errorf("While setting up mounts: %v", err)
return
}
// check for and/or load image
imageID, err := runner.LoadImage()
if err != nil {
if !runner.checkBrokenNode(err) {
// Failed to load image but not due to a "broken node"
// condition, probably user error.
runner.finalState = "Cancelled"
}
err = fmt.Errorf("While loading container image: %v", err)
return
}
err = runner.CreateContainer(imageID, bindmounts)
if err != nil {
return
}
err = runner.LogHostInfo()
if err != nil {
return
}
err = runner.LogNodeRecord()
if err != nil {
return
}
err = runner.LogContainerRecord()
if err != nil {
return
}
if runner.IsCancelled() {
return
}
err = runner.UpdateContainerRunning()
if err != nil {
return
}
runner.finalState = "Cancelled"
err = runner.startCrunchstat()
if err != nil {
return
}
err = runner.StartContainer()
if err != nil {
runner.checkBrokenNode(err)
return
}
err = runner.WaitFinish()
if err == nil && !runner.IsCancelled() {
runner.finalState = "Complete"
}
return
}
// Fetch the current container record (uuid = runner.Container.UUID)
// into runner.Container.
func (runner *ContainerRunner) fetchContainerRecord() error {
reader, err := runner.DispatcherArvClient.CallRaw("GET", "containers", runner.Container.UUID, "", nil)
if err != nil {
return fmt.Errorf("error fetching container record: %v", err)
}
defer reader.Close()
dec := json.NewDecoder(reader)
dec.UseNumber()
err = dec.Decode(&runner.Container)
if err != nil {
return fmt.Errorf("error decoding container record: %v", err)
}
var sm struct {
SecretMounts map[string]arvados.Mount `json:"secret_mounts"`
}
containerToken, err := runner.ContainerToken()
if err != nil {
return fmt.Errorf("error getting container token: %v", err)
}
runner.ContainerArvClient, runner.ContainerKeepClient,
runner.containerClient, err = runner.MkArvClient(containerToken)
if err != nil {
return fmt.Errorf("error creating container API client: %v", err)
}
runner.ContainerKeepClient.SetStorageClasses(runner.Container.OutputStorageClasses)
runner.DispatcherKeepClient.SetStorageClasses(runner.Container.OutputStorageClasses)
err = runner.ContainerArvClient.Call("GET", "containers", runner.Container.UUID, "secret_mounts", nil, &sm)
if err != nil {
if apierr, ok := err.(arvadosclient.APIServerError); !ok || apierr.HttpStatusCode != 404 {
return fmt.Errorf("error fetching secret_mounts: %v", err)
}
// ok && apierr.HttpStatusCode == 404, which means
// secret_mounts isn't supported by this API server.
}
runner.SecretMounts = sm.SecretMounts
return nil
}
// NewContainerRunner creates a new container runner.
func NewContainerRunner(dispatcherClient *arvados.Client,
dispatcherArvClient IArvadosClient,
dispatcherKeepClient IKeepClient,
containerUUID string) (*ContainerRunner, error) {
cr := &ContainerRunner{
dispatcherClient: dispatcherClient,
DispatcherArvClient: dispatcherArvClient,
DispatcherKeepClient: dispatcherKeepClient,
}
cr.NewLogWriter = cr.NewArvLogWriter
cr.RunArvMount = cr.ArvMountCmd
cr.MkTempDir = ioutil.TempDir
cr.MkArvClient = func(token string) (IArvadosClient, IKeepClient, *arvados.Client, error) {
cl, err := arvadosclient.MakeArvadosClient()
if err != nil {
return nil, nil, nil, err
}
cl.ApiToken = token
kc, err := keepclient.MakeKeepClient(cl)
if err != nil {
return nil, nil, nil, err
}
c2 := arvados.NewClientFromEnv()
c2.AuthToken = token
return cl, kc, c2, nil
}
var err error
cr.LogCollection, err = (&arvados.Collection{}).FileSystem(cr.dispatcherClient, cr.DispatcherKeepClient)
if err != nil {
return nil, err
}
cr.Container.UUID = containerUUID
w, err := cr.NewLogWriter("crunch-run")
if err != nil {
return nil, err
}
cr.CrunchLog = NewThrottledLogger(w)
cr.CrunchLog.Immediate = log.New(os.Stderr, containerUUID+" ", 0)
loadLogThrottleParams(dispatcherArvClient)
go cr.updateLogs()
return cr, nil
}
func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
log := log.New(stderr, "", 0)
flags := flag.NewFlagSet(prog, flag.ContinueOnError)
statInterval := flags.Duration("crunchstat-interval", 10*time.Second, "sampling period for periodic resource usage reporting")
cgroupRoot := flags.String("cgroup-root", "/sys/fs/cgroup", "path to sysfs cgroup tree")
cgroupParent := flags.String("cgroup-parent", "docker", "name of container's parent cgroup (ignored if -cgroup-parent-subsystem is used)")
cgroupParentSubsystem := flags.String("cgroup-parent-subsystem", "", "use current cgroup for given subsystem as parent cgroup for container")
caCertsPath := flags.String("ca-certs", "", "Path to TLS root certificates")
detach := flags.Bool("detach", false, "Detach from parent process and run in the background")
stdinConfig := flags.Bool("stdin-config", false, "Load config and environment variables from JSON message on stdin")
configFile := flags.String("config", arvados.DefaultConfigFile, "filename of cluster config file to try loading if -stdin-config=false (default is $ARVADOS_CONFIG)")
sleep := flags.Duration("sleep", 0, "Delay before starting (testing use only)")
kill := flags.Int("kill", -1, "Send signal to an existing crunch-run process for given UUID")
list := flags.Bool("list", false, "List UUIDs of existing crunch-run processes")
enableMemoryLimit := flags.Bool("enable-memory-limit", true, "tell container runtime to limit container's memory usage")
enableNetwork := flags.String("container-enable-networking", "default", "enable networking \"always\" (for all containers) or \"default\" (for containers that request it)")
networkMode := flags.String("container-network-mode", "default", `Docker network mode for container (use any argument valid for docker --net)`)
memprofile := flags.String("memprofile", "", "write memory profile to `file` after running container")
runtimeEngine := flags.String("runtime-engine", "docker", "container runtime: docker or singularity")
brokenNodeHook := flags.String("broken-node-hook", "", "script to run if node is detected to be broken (for example, Docker daemon is not running)")
flags.Duration("check-containerd", 0, "Ignored. Exists for compatibility with older versions.")
ignoreDetachFlag := false
if len(args) > 0 && args[0] == "-no-detach" {
// This process was invoked by a parent process, which
// has passed along its own arguments, including
// -detach, after the leading -no-detach flag. Strip
// the leading -no-detach flag (it's not recognized by
// flags.Parse()) and ignore the -detach flag that
// comes later.
args = args[1:]
ignoreDetachFlag = true
}
if ok, code := cmd.ParseFlags(flags, prog, args, "container-uuid", stderr); !ok {
return code
} else if !*list && flags.NArg() != 1 {
fmt.Fprintf(stderr, "missing required argument: container-uuid (try -help)\n")
return 2
}
containerUUID := flags.Arg(0)
switch {
case *detach && !ignoreDetachFlag:
return Detach(containerUUID, prog, args, os.Stdin, os.Stdout, os.Stderr)
case *kill >= 0:
return KillProcess(containerUUID, syscall.Signal(*kill), os.Stdout, os.Stderr)
case *list:
return ListProcesses(os.Stdout, os.Stderr)
}
if len(containerUUID) != 27 {
log.Printf("usage: %s [options] UUID", prog)
return 1
}
var keepstoreLogbuf bufThenWrite
var conf ConfigData
if *stdinConfig {
err := json.NewDecoder(stdin).Decode(&conf)
if err != nil {
log.Printf("decode stdin: %s", err)
return 1
}
for k, v := range conf.Env {
err = os.Setenv(k, v)
if err != nil {
log.Printf("setenv(%q): %s", k, err)
return 1
}
}
if conf.Cluster != nil {
// ClusterID is missing from the JSON
// representation, but we need it to generate
// a valid config file for keepstore, so we
// fill it using the container UUID prefix.
conf.Cluster.ClusterID = containerUUID[:5]
}
} else {
conf = hpcConfData(containerUUID, *configFile, io.MultiWriter(&keepstoreLogbuf, stderr))
}
log.Printf("crunch-run %s started", cmd.Version.String())
time.Sleep(*sleep)
if *caCertsPath != "" {
arvadosclient.CertFiles = []string{*caCertsPath}
}
keepstore, err := startLocalKeepstore(conf, io.MultiWriter(&keepstoreLogbuf, stderr))
if err != nil {
log.Print(err)
return 1
}
if keepstore != nil {
defer keepstore.Process.Kill()
}
api, err := arvadosclient.MakeArvadosClient()
if err != nil {
log.Printf("%s: %v", containerUUID, err)
return 1
}
api.Retries = 8
kc, err := keepclient.MakeKeepClient(api)
if err != nil {
log.Printf("%s: %v", containerUUID, err)
return 1
}
kc.BlockCache = &keepclient.BlockCache{MaxBlocks: 2}
kc.Retries = 4
cr, err := NewContainerRunner(arvados.NewClientFromEnv(), api, kc, containerUUID)
if err != nil {
log.Print(err)
return 1
}
if keepstore == nil {
// Log explanation (if any) for why we're not running
// a local keepstore.
var buf bytes.Buffer
keepstoreLogbuf.SetWriter(&buf)
if buf.Len() > 0 {
cr.CrunchLog.Printf("%s", strings.TrimSpace(buf.String()))
}
} else if logWhat := conf.Cluster.Containers.LocalKeepLogsToContainerLog; logWhat == "none" {
cr.CrunchLog.Printf("using local keepstore process (pid %d) at %s", keepstore.Process.Pid, os.Getenv("ARVADOS_KEEP_SERVICES"))
keepstoreLogbuf.SetWriter(io.Discard)
} else {
cr.CrunchLog.Printf("using local keepstore process (pid %d) at %s, writing logs to keepstore.txt in log collection", keepstore.Process.Pid, os.Getenv("ARVADOS_KEEP_SERVICES"))
logwriter, err := cr.NewLogWriter("keepstore")
if err != nil {
log.Print(err)
return 1
}
cr.keepstoreLogger = NewThrottledLogger(logwriter)
var writer io.WriteCloser = cr.keepstoreLogger
if logWhat == "errors" {
writer = &filterKeepstoreErrorsOnly{WriteCloser: writer}
} else if logWhat != "all" {
// should have been caught earlier by
// dispatcher's config loader
log.Printf("invalid value for Containers.LocalKeepLogsToContainerLog: %q", logWhat)
return 1
}
err = keepstoreLogbuf.SetWriter(writer)
if err != nil {
log.Print(err)
return 1
}
cr.keepstoreLogbuf = &keepstoreLogbuf
}
switch *runtimeEngine {
case "docker":
cr.executor, err = newDockerExecutor(containerUUID, cr.CrunchLog.Printf, cr.containerWatchdogInterval)
case "singularity":
cr.executor, err = newSingularityExecutor(cr.CrunchLog.Printf)
default:
cr.CrunchLog.Printf("%s: unsupported RuntimeEngine %q", containerUUID, *runtimeEngine)
cr.CrunchLog.Close()
return 1
}
if err != nil {
cr.CrunchLog.Printf("%s: %v", containerUUID, err)
cr.checkBrokenNode(err)
cr.CrunchLog.Close()
return 1
}
defer cr.executor.Close()
cr.brokenNodeHook = *brokenNodeHook
gwAuthSecret := os.Getenv("GatewayAuthSecret")
os.Unsetenv("GatewayAuthSecret")
if gwAuthSecret == "" {
// not safe to run a gateway service without an auth
// secret
cr.CrunchLog.Printf("Not starting a gateway server (GatewayAuthSecret was not provided by dispatcher)")
} else if gwListen := os.Getenv("GatewayAddress"); gwListen == "" {
// dispatcher did not tell us which external IP
// address to advertise --> no gateway service
cr.CrunchLog.Printf("Not starting a gateway server (GatewayAddress was not provided by dispatcher)")
} else {
cr.gateway = Gateway{
Address: gwListen,
AuthSecret: gwAuthSecret,
ContainerUUID: containerUUID,
Target: cr.executor,
Log: cr.CrunchLog,
}
err = cr.gateway.Start()
if err != nil {
log.Printf("error starting gateway server: %s", err)
return 1
}
}
parentTemp, tmperr := cr.MkTempDir("", "crunch-run."+containerUUID+".")
if tmperr != nil {
log.Printf("%s: %v", containerUUID, tmperr)
return 1
}
cr.parentTemp = parentTemp
cr.statInterval = *statInterval
cr.cgroupRoot = *cgroupRoot
cr.expectCgroupParent = *cgroupParent
cr.enableMemoryLimit = *enableMemoryLimit
cr.enableNetwork = *enableNetwork
cr.networkMode = *networkMode
if *cgroupParentSubsystem != "" {
p, err := findCgroup(*cgroupParentSubsystem)
if err != nil {
log.Printf("fatal: cgroup parent subsystem: %s", err)
return 1
}
cr.setCgroupParent = p
cr.expectCgroupParent = p
}
runerr := cr.Run()
if *memprofile != "" {
f, err := os.Create(*memprofile)
if err != nil {
log.Printf("could not create memory profile: %s", err)
}
runtime.GC() // get up-to-date statistics
if err := pprof.WriteHeapProfile(f); err != nil {
log.Printf("could not write memory profile: %s", err)
}
closeerr := f.Close()
if closeerr != nil {
log.Printf("closing memprofile file: %s", err)
}
}
if runerr != nil {
log.Printf("%s: %v", containerUUID, runerr)
return 1
}
return 0
}
// Try to load ConfigData in hpc (slurm/lsf) environment. This means
// loading the cluster config from the specified file and (if that
// works) getting the runtime_constraints container field from
// controller to determine # VCPUs so we can calculate KeepBuffers.
func hpcConfData(uuid string, configFile string, stderr io.Writer) ConfigData {
var conf ConfigData
conf.Cluster = loadClusterConfigFile(configFile, stderr)
if conf.Cluster == nil {
// skip loading the container record -- we won't be
// able to start local keepstore anyway.
return conf
}
arv, err := arvadosclient.MakeArvadosClient()
if err != nil {
fmt.Fprintf(stderr, "error setting up arvadosclient: %s\n", err)
return conf
}
arv.Retries = 8
var ctr arvados.Container
err = arv.Call("GET", "containers", uuid, "", arvadosclient.Dict{"select": []string{"runtime_constraints"}}, &ctr)
if err != nil {
fmt.Fprintf(stderr, "error getting container record: %s\n", err)
return conf
}
if ctr.RuntimeConstraints.VCPUs > 0 {
conf.KeepBuffers = ctr.RuntimeConstraints.VCPUs * conf.Cluster.Containers.LocalKeepBlobBuffersPerVCPU
}
return conf
}
// Load cluster config file from given path. If an error occurs, log
// the error to stderr and return nil.
func loadClusterConfigFile(path string, stderr io.Writer) *arvados.Cluster {
ldr := config.NewLoader(&bytes.Buffer{}, ctxlog.New(stderr, "plain", "info"))
ldr.Path = path
cfg, err := ldr.Load()
if err != nil {
fmt.Fprintf(stderr, "could not load config file %s: %s\n", path, err)
return nil
}
cluster, err := cfg.GetCluster("")
if err != nil {
fmt.Fprintf(stderr, "could not use config file %s: %s\n", path, err)
return nil
}
fmt.Fprintf(stderr, "loaded config file %s\n", path)
return cluster
}
func startLocalKeepstore(configData ConfigData, logbuf io.Writer) (*exec.Cmd, error) {
if configData.KeepBuffers < 1 {
fmt.Fprintf(logbuf, "not starting a local keepstore process because KeepBuffers=%v in config\n", configData.KeepBuffers)
return nil, nil
}
if configData.Cluster == nil {
fmt.Fprint(logbuf, "not starting a local keepstore process because cluster config file was not loaded\n")
return nil, nil
}
for uuid, vol := range configData.Cluster.Volumes {
if len(vol.AccessViaHosts) > 0 {
fmt.Fprintf(logbuf, "not starting a local keepstore process because a volume (%s) uses AccessViaHosts\n", uuid)
return nil, nil
}
if !vol.ReadOnly && vol.Replication < configData.Cluster.Collections.DefaultReplication {
fmt.Fprintf(logbuf, "not starting a local keepstore process because a writable volume (%s) has replication less than Collections.DefaultReplication (%d < %d)\n", uuid, vol.Replication, configData.Cluster.Collections.DefaultReplication)
return nil, nil
}
}
// Rather than have an alternate way to tell keepstore how
// many buffers to use when starting it this way, we just
// modify the cluster configuration that we feed it on stdin.
configData.Cluster.API.MaxKeepBlobBuffers = configData.KeepBuffers
ln, err := net.Listen("tcp", "localhost:0")
if err != nil {
return nil, err
}
_, port, err := net.SplitHostPort(ln.Addr().String())
if err != nil {
ln.Close()
return nil, err
}
ln.Close()
url := "http://localhost:" + port
fmt.Fprintf(logbuf, "starting keepstore on %s\n", url)
var confJSON bytes.Buffer
err = json.NewEncoder(&confJSON).Encode(arvados.Config{
Clusters: map[string]arvados.Cluster{
configData.Cluster.ClusterID: *configData.Cluster,
},
})
if err != nil {
return nil, err
}
cmd := exec.Command("/proc/self/exe", "keepstore", "-config=-")
if target, err := os.Readlink(cmd.Path); err == nil && strings.HasSuffix(target, ".test") {
// If we're a 'go test' process, running
// /proc/self/exe would start the test suite in a
// child process, which is not what we want.
cmd.Path, _ = exec.LookPath("go")
cmd.Args = append([]string{"go", "run", "../../cmd/arvados-server"}, cmd.Args[1:]...)
cmd.Env = os.Environ()
}
cmd.Stdin = &confJSON
cmd.Stdout = logbuf
cmd.Stderr = logbuf
cmd.Env = append(cmd.Env,
"GOGC=10",
"ARVADOS_SERVICE_INTERNAL_URL="+url)
err = cmd.Start()
if err != nil {
return nil, fmt.Errorf("error starting keepstore process: %w", err)
}
cmdExited := false
go func() {
cmd.Wait()
cmdExited = true
}()
ctx, cancel := context.WithDeadline(context.Background(), time.Now().Add(time.Second*10))
defer cancel()
poll := time.NewTicker(time.Second / 10)
defer poll.Stop()
client := http.Client{}
for range poll.C {
testReq, err := http.NewRequestWithContext(ctx, "GET", url+"/_health/ping", nil)
testReq.Header.Set("Authorization", "Bearer "+configData.Cluster.ManagementToken)
if err != nil {
return nil, err
}
resp, err := client.Do(testReq)
if err == nil {
resp.Body.Close()
if resp.StatusCode == http.StatusOK {
break
}
}
if cmdExited {
return nil, fmt.Errorf("keepstore child process exited")
}
if ctx.Err() != nil {
return nil, fmt.Errorf("timed out waiting for new keepstore process to report healthy")
}
}
os.Setenv("ARVADOS_KEEP_SERVICES", url)
return cmd, nil
}
// return current uid, gid, groups in a format suitable for logging:
// "crunch-run process has uid=1234(arvados) gid=1234(arvados)
// groups=1234(arvados),114(fuse)"
func currentUserAndGroups() string {
u, err := user.Current()
if err != nil {
return fmt.Sprintf("error getting current user ID: %s", err)
}
s := fmt.Sprintf("crunch-run process has uid=%s(%s) gid=%s", u.Uid, u.Username, u.Gid)
if g, err := user.LookupGroupId(u.Gid); err == nil {
s += fmt.Sprintf("(%s)", g.Name)
}
s += " groups="
if gids, err := u.GroupIds(); err == nil {
for i, gid := range gids {
if i > 0 {
s += ","
}
s += gid
if g, err := user.LookupGroupId(gid); err == nil {
s += fmt.Sprintf("(%s)", g.Name)
}
}
}
return s
}