import (
"bufio"
"bytes"
- "context"
"crypto/md5"
"encoding/json"
"errors"
"net"
"os"
"os/exec"
- "path/filepath"
"runtime/pprof"
"sort"
"strings"
"git.curoverse.com/arvados.git/sdk/go/arvados"
"git.curoverse.com/arvados.git/sdk/go/arvadosclient"
+ "git.curoverse.com/arvados.git/sdk/go/arvadostest"
"git.curoverse.com/arvados.git/sdk/go/manifest"
+ "golang.org/x/net/context"
dockertypes "github.com/docker/docker/api/types"
dockercontainer "github.com/docker/docker/api/types/container"
TestingT(t)
}
-type TestSuite struct{}
-
// Gocheck boilerplate
var _ = Suite(&TestSuite{})
+type TestSuite struct {
+ docker *TestDockerClient
+}
+
+func (s *TestSuite) SetUpTest(c *C) {
+ s.docker = NewTestDockerClient()
+}
+
type ArvTestClient struct {
Total int64
Calls int
logReader io.ReadCloser
logWriter io.WriteCloser
fn func(t *TestDockerClient)
- finish int
+ exitCode int
stop chan bool
cwd string
env []string
api *ArvTestClient
realTemp string
+ calledWait bool
}
-func NewTestDockerClient(exitCode int) *TestDockerClient {
+func NewTestDockerClient() *TestDockerClient {
t := &TestDockerClient{}
t.logReader, t.logWriter = io.Pipe()
- t.finish = exitCode
t.stop = make(chan bool, 1)
t.cwd = "/"
return t
}
func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error {
+ if t.exitCode == 3 {
+ return errors.New(`Error response from daemon: oci runtime error: container_linux.go:247: starting container process caused "process_linux.go:359: container init caused \"rootfs_linux.go:54: mounting \\\"/tmp/keep453790790/by_id/99999999999999999999999999999999+99999/myGenome\\\" to rootfs \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged\\\" at \\\"/tmp/docker/overlay2/9999999999999999999999999999999999999999999999999999999999999999/merged/keep/99999999999999999999999999999999+99999/myGenome\\\" caused \\\"no such file or directory\\\"\""`)
+ }
+ if t.exitCode == 4 {
+ return errors.New(`panic: standard_init_linux.go:175: exec user process caused "no such file or directory"`)
+ }
+ if t.exitCode == 5 {
+ return errors.New(`Error response from daemon: Cannot start container 41f26cbc43bcc1280f4323efb1830a394ba8660c9d1c2b564ba42bf7f7694845: [8] System error: no such file or directory`)
+ }
+ if t.exitCode == 6 {
+ return errors.New(`Error response from daemon: Cannot start container 58099cd76c834f3dc2a4fb76c8028f049ae6d4fdf0ec373e1f2cfea030670c2d: [8] System error: exec: "foobar": executable file not found in $PATH`)
+ }
+
if container == "abcde" {
- go t.fn(t)
+ // t.fn gets executed in ContainerWait
return nil
} else {
return errors.New("Invalid container id")
}
}
-func (t *TestDockerClient) ContainerStop(ctx context.Context, container string, timeout *time.Duration) error {
+func (t *TestDockerClient) ContainerRemove(ctx context.Context, container string, options dockertypes.ContainerRemoveOptions) error {
t.stop <- true
return nil
}
func (t *TestDockerClient) ContainerWait(ctx context.Context, container string, condition dockercontainer.WaitCondition) (<-chan dockercontainer.ContainerWaitOKBody, <-chan error) {
- body := make(chan dockercontainer.ContainerWaitOKBody)
+ t.calledWait = true
+ body := make(chan dockercontainer.ContainerWaitOKBody, 1)
err := make(chan error)
go func() {
- body <- dockercontainer.ContainerWaitOKBody{StatusCode: int64(t.finish)}
- close(body)
- close(err)
+ t.fn(t)
+ body <- dockercontainer.ContainerWaitOKBody{StatusCode: int64(t.exitCode)}
}()
return body, err
}
func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) {
+ if t.exitCode == 2 {
+ return dockertypes.ImageInspect{}, nil, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
+ }
+
if t.imageLoaded == image {
return dockertypes.ImageInspect{}, nil, nil
} else {
}
func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) {
+ if t.exitCode == 2 {
+ return dockertypes.ImageLoadResponse{}, fmt.Errorf("Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running?")
+ }
_, err := io.Copy(ioutil.Discard, input)
if err != nil {
return dockertypes.ImageLoadResponse{}, err
func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string,
parameters arvadosclient.Dict) (reader io.ReadCloser, err error) {
var j []byte
- if method == "GET" && resourceType == "containers" && action == "" && !client.callraw {
- j, err = json.Marshal(client.Container)
+ if method == "GET" && resourceType == "nodes" && uuid == "" && action == "" {
+ j = []byte(`{
+ "kind": "arvados#nodeList",
+ "items": [{
+ "uuid": "zzzzz-7ekkf-2z3mc76g2q73aio",
+ "hostname": "compute2",
+ "properties": {"total_cpu_cores": 16}
+ }]}`)
+ } else if method == "GET" && resourceType == "containers" && action == "" && !client.callraw {
+ if uuid == "" {
+ j, err = json.Marshal(map[string]interface{}{
+ "items": []interface{}{client.Container},
+ "kind": "arvados#nodeList",
+ })
+ } else {
+ j, err = json.Marshal(client.Container)
+ }
} else {
j = []byte(`{
"command": ["sleep", "1"],
len int64
}
+func (fw FileWrapper) Readdir(n int) ([]os.FileInfo, error) {
+ return nil, errors.New("not implemented")
+}
+
+func (fw FileWrapper) Seek(int64, int) (int64, error) {
+ return 0, errors.New("not implemented")
+}
+
func (fw FileWrapper) Size() int64 {
return fw.len
}
-func (fw FileWrapper) Seek(int64, int) (int64, error) {
+func (fw FileWrapper) Stat() (os.FileInfo, error) {
+ return nil, errors.New("not implemented")
+}
+
+func (fw FileWrapper) Truncate(int64) error {
+ return errors.New("not implemented")
+}
+
+func (fw FileWrapper) Write([]byte) (int, error) {
return 0, errors.New("not implemented")
}
func (s *TestSuite) TestLoadImage(c *C) {
kc := &KeepTestClient{}
- docker := NewTestDockerClient(0)
- cr := NewContainerRunner(&ArvTestClient{}, kc, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr := NewContainerRunner(&ArvTestClient{}, kc, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
_, err := cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
func (KeepReadErrorTestClient) ClearBlockCache() {
}
-type ErrorReader struct{}
+type ErrorReader struct {
+ FileWrapper
+}
func (ErrorReader) Read(p []byte) (n int, err error) {
return 0, errors.New("ErrorReader")
}
-func (ErrorReader) Close() error {
- return nil
-}
-
-func (ErrorReader) Size() int64 {
- return 0
-}
-
func (ErrorReader) Seek(int64, int) (int64, error) {
return 0, errors.New("ErrorReader")
}
func (s *TestSuite) TestLoadImageKeepError(c *C) {
// (2) Keep error
- docker := NewTestDockerClient(0)
- cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
cr.Container.ContainerImage = hwPDH
err := cr.LoadImage()
func (s *TestSuite) TestLoadImageKeepReadError(c *C) {
// (4) Collection doesn't contain image
- docker := NewTestDockerClient(0)
- cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
cr.Container.ContainerImage = hwPDH
err := cr.LoadImage()
}
func (s *TestSuite) TestRunContainer(c *C) {
- docker := NewTestDockerClient(0)
- docker.fn = func(t *TestDockerClient) {
+ s.docker.fn = func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, "Hello world\n"))
t.logWriter.Close()
}
- cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
var logs TestLogs
cr.NewLogWriter = logs.NewTestLoggingWriter
// Used by the TestFullRun*() test below to DRY up boilerplate setup to do full
// dress rehearsal of the Run() function, starting from a JSON container record.
-func FullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
+func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, exitCode int, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, realTemp string) {
rec := arvados.Container{}
err := json.Unmarshal([]byte(record), &rec)
c.Check(err, IsNil)
- docker := NewTestDockerClient(exitCode)
- docker.fn = fn
- docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
+ s.docker.exitCode = exitCode
+ s.docker.fn = fn
+ s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
api = &ArvTestClient{Container: rec}
- docker.api = api
- cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ s.docker.api = api
+ cr = NewContainerRunner(api, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
cr.statInterval = 100 * time.Millisecond
am := &ArvMountCmdLine{}
cr.RunArvMount = am.ArvMountTest
c.Assert(err, IsNil)
defer os.RemoveAll(realTemp)
- docker.realTemp = realTemp
+ s.docker.realTemp = realTemp
tempcount := 0
cr.MkTempDir = func(_ string, prefix string) (string, error) {
if api.CalledWith("container.state", "Complete") != nil {
c.Check(err, IsNil)
}
- c.Check(api.WasSetRunning, Equals, true)
-
- c.Check(api.Content[api.Calls-1]["container"].(arvadosclient.Dict)["log"], NotNil)
+ if exitCode != 2 {
+ c.Check(api.WasSetRunning, Equals, true)
+ c.Check(api.Content[api.Calls-2]["container"].(arvadosclient.Dict)["log"], NotNil)
+ }
if err != nil {
for k, v := range api.Logs {
}
func (s *TestSuite) TestFullRunHello(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["echo", "hello world"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestCrunchstat(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["sleep", "1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestNodeInfoLog(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ os.Setenv("SLURMD_NODENAME", "compute2")
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["sleep", "1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
c.Check(api.CalledWith("container.exit_code", 0), NotNil)
c.Check(api.CalledWith("container.state", "Complete"), NotNil)
+ c.Assert(api.Logs["node"], NotNil)
+ json := api.Logs["node"].String()
+ c.Check(json, Matches, `(?ms).*"uuid": *"zzzzz-7ekkf-2z3mc76g2q73aio".*`)
+ c.Check(json, Matches, `(?ms).*"total_cpu_cores": *16.*`)
+ c.Check(json, Not(Matches), `(?ms).*"info":.*`)
+
c.Assert(api.Logs["node-info"], NotNil)
- c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Host Information.*`)
- c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*CPU Information.*`)
- c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Memory Information.*`)
- c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk Space.*`)
- c.Check(api.Logs["node-info"].String(), Matches, `(?ms).*Disk INodes.*`)
+ json = api.Logs["node-info"].String()
+ c.Check(json, Matches, `(?ms).*Host Information.*`)
+ c.Check(json, Matches, `(?ms).*CPU Information.*`)
+ c.Check(json, Matches, `(?ms).*Memory Information.*`)
+ c.Check(json, Matches, `(?ms).*Disk Space.*`)
+ c.Check(json, Matches, `(?ms).*Disk INodes.*`)
}
func (s *TestSuite) TestContainerRecordLog(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["sleep", "1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestFullRunStderr(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["pwd"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
}
func (s *TestSuite) TestFullRunSetCwd(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["pwd"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
func (s *TestSuite) TestStopOnSignal(c *C) {
s.testStopContainer(c, func(cr *ContainerRunner) {
go func() {
- for !cr.cStarted {
+ for !s.docker.calledWait {
time.Sleep(time.Millisecond)
}
cr.SigChan <- syscall.SIGINT
err := json.Unmarshal([]byte(record), &rec)
c.Check(err, IsNil)
- docker := NewTestDockerClient(0)
- docker.fn = func(t *TestDockerClient) {
+ s.docker.fn = func(t *TestDockerClient) {
<-t.stop
t.logWriter.Write(dockerLog(1, "foo\n"))
t.logWriter.Close()
}
- docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
+ s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
api := &ArvTestClient{Container: rec}
- cr := NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr := NewContainerRunner(api, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil }
setup(cr)
c.Check(api.CalledWith("container.log", nil), NotNil)
c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
- c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "foo\n"), Equals, true)
+ c.Check(api.Logs["stdout"].String(), Matches, "(?ms).*foo\n$")
}
func (s *TestSuite) TestFullRunSetEnv(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $FROBIZ"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
c.Assert(err, IsNil)
stubCertPath := stubCert(certTemp)
+ cr.parentTemp = realTemp
+
defer os.RemoveAll(realTemp)
defer os.RemoveAll(certTemp)
}
checkEmpty := func() {
- filepath.Walk(realTemp, func(path string, _ os.FileInfo, err error) error {
- c.Check(path, Equals, realTemp)
- c.Check(err, IsNil)
- return nil
- })
+ // Should be deleted.
+ _, err := os.Stat(realTemp)
+ c.Assert(os.IsNotExist(err), Equals, true)
+
+ // Now recreate it for the next test.
+ c.Assert(os.Mkdir(realTemp, 0777), IsNil)
}
{
cr.Container.Mounts = make(map[string]arvados.Mount)
cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"}
cr.OutputPath = "/tmp"
-
+ cr.statInterval = 5 * time.Second
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
+ "--read-write", "--crunchstat-interval=5",
+ "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp"})
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/out", realTemp + "/3:/tmp"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
+ "--read-write", "--crunchstat-interval=5",
+ "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/out", realTemp + "/tmp3:/tmp"})
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
+ "--read-write", "--crunchstat-interval=5",
+ "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", stubCertPath + ":/etc/arvados/ca-certificates.crt:ro"})
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
+ "--read-write", "--crunchstat-interval=5",
+ "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/tmp0:/keeptmp"})
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
+ "--read-write", "--crunchstat-interval=5",
+ "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
sort.StringSlice(cr.Binds).Sort()
c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
realTemp + "/keep1/tmp0:/keepout"})
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
+ "--read-write", "--crunchstat-interval=5",
+ "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
sort.StringSlice(cr.Binds).Sort()
c.Check(cr.Binds, DeepEquals, []string{realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53:/keepinp:ro",
realTemp + "/keep1/tmp0:/keepout"})
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, IsNil)
sort.StringSlice(cr.Binds).Sort()
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2/mountdata.json:/mnt/test.json:ro"})
- content, err := ioutil.ReadFile(realTemp + "/2/mountdata.json")
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/json2/mountdata.json:/mnt/test.json:ro"})
+ content, err := ioutil.ReadFile(realTemp + "/json2/mountdata.json")
c.Check(err, IsNil)
c.Check(content, DeepEquals, []byte(test.out))
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, IsNil)
- c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other", "--read-write", "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
- c.Check(cr.Binds, DeepEquals, []string{realTemp + "/2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
+ c.Check(am.Cmd, DeepEquals, []string{"--foreground", "--allow-other",
+ "--read-write", "--crunchstat-interval=5",
+ "--file-cache", "512", "--mount-tmp", "tmp0", "--mount-by-pdh", "by_id", realTemp + "/keep1"})
+ c.Check(cr.Binds, DeepEquals, []string{realTemp + "/tmp2:/tmp", realTemp + "/keep1/tmp0:/tmp/foo:ro"})
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
- // Writable mount points are not allowed underneath output_dir mount point
+ // Writable mount points copied to output_dir mount point
{
i = 0
cr.ArvMountPoint = ""
cr.Container.Mounts = make(map[string]arvados.Mount)
cr.Container.Mounts = map[string]arvados.Mount{
- "/tmp": {Kind: "tmp"},
- "/tmp/foo": {Kind: "collection", Writable: true},
+ "/tmp": {Kind: "tmp"},
+ "/tmp/foo": {Kind: "collection",
+ PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53",
+ Writable: true},
+ "/tmp/bar": {Kind: "collection",
+ PortableDataHash: "59389a8f9ee9d399be35462a0f92541d+53",
+ Path: "baz",
+ Writable: true},
}
cr.OutputPath = "/tmp"
+ os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541c+53", os.ModePerm)
+ os.MkdirAll(realTemp+"/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz", os.ModePerm)
+
+ rf, _ := os.Create(realTemp + "/keep1/by_id/59389a8f9ee9d399be35462a0f92541d+53/baz/quux")
+ rf.Write([]byte("bar"))
+ rf.Close()
+
err := cr.SetupMounts()
- c.Check(err, NotNil)
- c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`)
+ c.Check(err, IsNil)
+ _, err = os.Stat(cr.HostOutputDir + "/foo")
+ c.Check(err, IsNil)
+ _, err = os.Stat(cr.HostOutputDir + "/bar/quux")
+ c.Check(err, IsNil)
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, NotNil)
c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`)
+ os.RemoveAll(cr.ArvMountPoint)
cr.CleanupDirs()
checkEmpty()
}
err := cr.SetupMounts()
c.Check(err, NotNil)
c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`)
+ os.RemoveAll(cr.ArvMountPoint)
+ cr.CleanupDirs()
+ checkEmpty()
+ }
+
+ // git_tree mounts
+ {
+ i = 0
+ cr.ArvMountPoint = ""
+ (*GitMountSuite)(nil).useTestGitServer(c)
+ cr.token = arvadostest.ActiveToken
+ cr.Container.Mounts = make(map[string]arvados.Mount)
+ cr.Container.Mounts = map[string]arvados.Mount{
+ "/tip": {
+ Kind: "git_tree",
+ UUID: arvadostest.Repository2UUID,
+ Commit: "fd3531f42995344f36c30b79f55f27b502f3d344",
+ Path: "/",
+ },
+ "/non-tip": {
+ Kind: "git_tree",
+ UUID: arvadostest.Repository2UUID,
+ Commit: "5ebfab0522851df01fec11ec55a6d0f4877b542e",
+ Path: "/",
+ },
+ }
+ cr.OutputPath = "/tmp"
+
+ err := cr.SetupMounts()
+ c.Check(err, IsNil)
+
+ // dirMap[mountpoint] == tmpdir
+ dirMap := make(map[string]string)
+ for _, bind := range cr.Binds {
+ tokens := strings.Split(bind, ":")
+ dirMap[tokens[1]] = tokens[0]
+
+ if cr.Container.Mounts[tokens[1]].Writable {
+ c.Check(len(tokens), Equals, 2)
+ } else {
+ c.Check(len(tokens), Equals, 3)
+ c.Check(tokens[2], Equals, "ro")
+ }
+ }
+
+ data, err := ioutil.ReadFile(dirMap["/tip"] + "/dir1/dir2/file with mode 0644")
+ c.Check(err, IsNil)
+ c.Check(string(data), Equals, "\000\001\002\003")
+ _, err = ioutil.ReadFile(dirMap["/tip"] + "/file only on testbranch")
+ c.Check(err, FitsTypeOf, &os.PathError{})
+ c.Check(os.IsNotExist(err), Equals, true)
+
+ data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/dir1/dir2/file with mode 0644")
+ c.Check(err, IsNil)
+ c.Check(string(data), Equals, "\000\001\002\003")
+ data, err = ioutil.ReadFile(dirMap["/non-tip"] + "/file only on testbranch")
+ c.Check(err, IsNil)
+ c.Check(string(data), Equals, "testfile\n")
+
cr.CleanupDirs()
checkEmpty()
}
"runtime_constraints": {}
}`
- api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
+ api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
})
}
// Used by the TestStdoutWithWrongPath*()
-func StdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
+func (s *TestSuite) stdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner, err error) {
rec := arvados.Container{}
err = json.Unmarshal([]byte(record), &rec)
c.Check(err, IsNil)
- docker := NewTestDockerClient(0)
- docker.fn = fn
- docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
+ s.docker.fn = fn
+ s.docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{})
api = &ArvTestClient{Container: rec}
- cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+ cr = NewContainerRunner(api, &KeepTestClient{}, s.docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
am := &ArvMountCmdLine{}
cr.RunArvMount = am.ArvMountTest
}
func (s *TestSuite) TestStdoutWithWrongPath(c *C) {
- _, _, err := StdoutErrorRunHelper(c, `{
+ _, _, err := s.stdoutErrorRunHelper(c, `{
"mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "file", "path":"/tmpa.out"} },
"output_path": "/tmp"
}`, func(t *TestDockerClient) {})
}
func (s *TestSuite) TestStdoutWithWrongKindTmp(c *C) {
- _, _, err := StdoutErrorRunHelper(c, `{
+ _, _, err := s.stdoutErrorRunHelper(c, `{
"mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "tmp", "path":"/tmp/a.out"} },
"output_path": "/tmp"
}`, func(t *TestDockerClient) {})
}
func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) {
- _, _, err := StdoutErrorRunHelper(c, `{
+ _, _, err := s.stdoutErrorRunHelper(c, `{
"mounts": {"/tmp": {"kind": "tmp"}, "stdout": {"kind": "collection", "path":"/tmp/a.out"} },
"output_path": "/tmp"
}`, func(t *TestDockerClient) {})
func (s *TestSuite) TestFullRunWithAPI(c *C) {
os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
defer os.Unsetenv("ARVADOS_API_HOST")
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
func (s *TestSuite) TestFullRunSetOutput(c *C) {
os.Setenv("ARVADOS_API_HOST", "test.arvados.org")
defer os.Unsetenv("ARVADOS_API_HOST")
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": "/bin",
extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"}
- api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
})
"a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt",
}
- api, runner, realtemp := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ api, runner, realtemp := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
})
- c.Check(runner.Binds, DeepEquals, []string{realtemp + "/2:/tmp",
+ c.Check(runner.Binds, DeepEquals, []string{realtemp + "/tmp2:/tmp",
realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt:/tmp/foo/bar:ro",
realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt:/tmp/foo/baz/sub2file2:ro",
realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1:/tmp/foo/sub1:ro",
"b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
}
- api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
})
"a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt",
}
- api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- os.Symlink("/keep/foo/sub1file2", t.realTemp+"/2/baz")
- os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz2")
- os.Symlink("/keep/foo2/subdir1", t.realTemp+"/2/baz3")
- os.Mkdir(t.realTemp+"/2/baz4", 0700)
- os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/2/baz4/baz5")
+ api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ os.Symlink("/keep/foo/sub1file2", t.realTemp+"/tmp2/baz")
+ os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/tmp2/baz2")
+ os.Symlink("/keep/foo2/subdir1", t.realTemp+"/tmp2/baz3")
+ os.Mkdir(t.realTemp+"/tmp2/baz4", 0700)
+ os.Symlink("/keep/foo2/subdir1/file2_in_subdir1.txt", t.realTemp+"/tmp2/baz4/baz5")
t.logWriter.Close()
})
extraMounts := []string{}
- api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- os.Symlink("/etc/hosts", t.realTemp+"/2/baz")
+ api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ os.Symlink("/etc/hosts", t.realTemp+"/tmp2/baz")
t.logWriter.Close()
})
extraMounts := []string{}
- api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
- rf, _ := os.Create(t.realTemp + "/2/realfile")
+ api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ rf, _ := os.Create(t.realTemp + "/tmp2/realfile")
rf.Write([]byte("foo"))
rf.Close()
- os.Mkdir(t.realTemp+"/2/realdir", 0700)
- rf, _ = os.Create(t.realTemp + "/2/realdir/subfile")
+ os.Mkdir(t.realTemp+"/tmp2/realdir", 0700)
+ rf, _ = os.Create(t.realTemp + "/tmp2/realdir/subfile")
rf.Write([]byte("bar"))
rf.Close()
- os.Symlink("/tmp/realfile", t.realTemp+"/2/file1")
- os.Symlink("realfile", t.realTemp+"/2/file2")
- os.Symlink("/tmp/file1", t.realTemp+"/2/file3")
- os.Symlink("file2", t.realTemp+"/2/file4")
- os.Symlink("realdir", t.realTemp+"/2/dir1")
- os.Symlink("/tmp/realdir", t.realTemp+"/2/dir2")
+ os.Symlink("/tmp/realfile", t.realTemp+"/tmp2/file1")
+ os.Symlink("realfile", t.realTemp+"/tmp2/file2")
+ os.Symlink("/tmp/file1", t.realTemp+"/tmp2/file3")
+ os.Symlink("file2", t.realTemp+"/tmp2/file4")
+ os.Symlink("realdir", t.realTemp+"/tmp2/dir1")
+ os.Symlink("/tmp/realdir", t.realTemp+"/tmp2/dir2")
t.logWriter.Close()
})
"b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt",
}
- api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
+ api, _, _ := s.fullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
})
"runtime_constraints": {}
}`
- api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
+ api, _, _ := s.fullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) {
t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n"))
t.logWriter.Close()
})
}
func (s *TestSuite) TestStderrMount(c *C) {
- api, _, _ := FullRunHelper(c, `{
+ api, _, _ := s.fullRunHelper(c, `{
"command": ["/bin/sh", "-c", "echo hello;exit 1"],
"container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
"cwd": ".",
_, err = cr.UploadOutputFile(realTemp+"/"+v, info, err, []string{}, nil, "", "", 0)
c.Assert(err, NotNil)
}
+
+func (s *TestSuite) TestFullBrokenDocker1(c *C) {
+ tf, err := ioutil.TempFile("", "brokenNodeHook-")
+ c.Assert(err, IsNil)
+ defer os.Remove(tf.Name())
+
+ tf.Write([]byte(`#!/bin/sh
+exec echo killme
+`))
+ tf.Close()
+ os.Chmod(tf.Name(), 0700)
+
+ ech := tf.Name()
+ brokenNodeHook = &ech
+
+ api, _, _ := s.fullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 2, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Queued"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
+
+}
+
+func (s *TestSuite) TestFullBrokenDocker2(c *C) {
+ ech := ""
+ brokenNodeHook = &ech
+
+ api, _, _ := s.fullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 2, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Queued"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*No broken node hook.*")
+}
+
+func (s *TestSuite) TestFullBrokenDocker3(c *C) {
+ ech := ""
+ brokenNodeHook = &ech
+
+ api, _, _ := s.fullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 3, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
+}
+
+func (s *TestSuite) TestBadCommand1(c *C) {
+ ech := ""
+ brokenNodeHook = &ech
+
+ api, _, _ := s.fullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 4, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
+}
+
+func (s *TestSuite) TestBadCommand2(c *C) {
+ ech := ""
+ brokenNodeHook = &ech
+
+ api, _, _ := s.fullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 5, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
+}
+
+func (s *TestSuite) TestBadCommand3(c *C) {
+ ech := ""
+ brokenNodeHook = &ech
+
+ api, _, _ := s.fullRunHelper(c, `{
+ "command": ["echo", "hello world"],
+ "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122",
+ "cwd": ".",
+ "environment": {},
+ "mounts": {"/tmp": {"kind": "tmp"} },
+ "output_path": "/tmp",
+ "priority": 1,
+ "runtime_constraints": {}
+}`, nil, 6, func(t *TestDockerClient) {
+ t.logWriter.Write(dockerLog(1, "hello world\n"))
+ t.logWriter.Close()
+ })
+
+ c.Check(api.CalledWith("container.state", "Cancelled"), NotNil)
+ c.Check(api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
+}