X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/ebb2559b3a09636ff687316bbe512e0e8a86b168..e4f03346d4498a77d252d2ffb08d1e0246785b5e:/services/crunch-run/crunchrun_test.go diff --git a/services/crunch-run/crunchrun_test.go b/services/crunch-run/crunchrun_test.go index b9856aca29..5bfbf796f0 100644 --- a/services/crunch-run/crunchrun_test.go +++ b/services/crunch-run/crunchrun_test.go @@ -1,28 +1,36 @@ package main import ( + "bufio" "bytes" + "context" "crypto/md5" "encoding/json" "errors" "fmt" - "git.curoverse.com/arvados.git/sdk/go/arvados" - "git.curoverse.com/arvados.git/sdk/go/arvadosclient" - "git.curoverse.com/arvados.git/sdk/go/keepclient" - "git.curoverse.com/arvados.git/sdk/go/manifest" - "github.com/curoverse/dockerclient" - . "gopkg.in/check.v1" "io" "io/ioutil" + "net" "os" "os/exec" "path/filepath" + "runtime/pprof" "sort" "strings" "sync" "syscall" "testing" "time" + + "git.curoverse.com/arvados.git/sdk/go/arvados" + "git.curoverse.com/arvados.git/sdk/go/arvadosclient" + "git.curoverse.com/arvados.git/sdk/go/keepclient" + "git.curoverse.com/arvados.git/sdk/go/manifest" + + dockertypes "github.com/docker/docker/api/types" + dockercontainer "github.com/docker/docker/api/types/container" + dockernetwork "github.com/docker/docker/api/types/network" + . "gopkg.in/check.v1" ) // Gocheck boilerplate @@ -40,9 +48,9 @@ type ArvTestClient struct { Calls int Content []arvadosclient.Dict arvados.Container - Logs map[string]*bytes.Buffer - WasSetRunning bool + Logs map[string]*bytes.Buffer sync.Mutex + WasSetRunning bool } type KeepTestClient struct { @@ -57,6 +65,12 @@ var hwImageId = "9c31ee32b3d15268a0754e8edc74d4f815ee014b693bc5109058e431dd5caea var otherManifest = ". 68a84f561b1d1708c6baff5e019a9ab3+46+Ae5d0af96944a3690becb1decdf60cc1c937f556d@5693216f 0:46:md5sum.txt\n" var otherPDH = "a3e8f74c6f101eae01fa08bfb4e49b3a+54" +var normalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt\n./subdir1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt\n./subdir1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt\n" +var normalizedWithSubdirsPDH = "a0def87f80dd594d4675809e83bd4f15+367" + +var denormalizedManifestWithSubdirs = ". 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 0:9:file1_in_main.txt 9:18:file2_in_main.txt 0:27:zzzzz-8i9sb-bcdefghijkdhvnk.log.txt 0:10:subdir1/file1_in_subdir1.txt 10:17:subdir1/file2_in_subdir1.txt\n" +var denormalizedWithSubdirsPDH = "b0def87f80dd594d4675809e83bd4f15+367" + var fakeAuthUUID = "zzzzz-gj3su-55pqoyepgi2glem" var fakeAuthToken = "a3ltuwzqcu2u4sc0q7yhpc2w7s00fdcqecg5d6e0u3pfohmbjt" @@ -65,55 +79,49 @@ type TestDockerClient struct { logReader io.ReadCloser logWriter io.WriteCloser fn func(t *TestDockerClient) - finish chan dockerclient.WaitResult + finish int stop chan bool cwd string env []string api *ArvTestClient } -func NewTestDockerClient() *TestDockerClient { +func NewTestDockerClient(exitCode int) *TestDockerClient { t := &TestDockerClient{} t.logReader, t.logWriter = io.Pipe() - t.finish = make(chan dockerclient.WaitResult) + t.finish = exitCode t.stop = make(chan bool) t.cwd = "/" return t } -func (t *TestDockerClient) StopContainer(id string, timeout int) error { - t.stop <- true - return nil +type MockConn struct { + net.Conn } -func (t *TestDockerClient) InspectImage(id string) (*dockerclient.ImageInfo, error) { - if t.imageLoaded == id { - return &dockerclient.ImageInfo{}, nil - } else { - return nil, errors.New("") - } +func (m *MockConn) Write(b []byte) (int, error) { + return len(b), nil } -func (t *TestDockerClient) LoadImage(reader io.Reader) error { - _, err := io.Copy(ioutil.Discard, reader) - if err != nil { - return err - } else { - t.imageLoaded = hwImageId - return nil - } +func NewMockConn() *MockConn { + c := &MockConn{} + return c } -func (t *TestDockerClient) CreateContainer(config *dockerclient.ContainerConfig, name string, authConfig *dockerclient.AuthConfig) (string, error) { +func (t *TestDockerClient) ContainerAttach(ctx context.Context, container string, options dockertypes.ContainerAttachOptions) (dockertypes.HijackedResponse, error) { + return dockertypes.HijackedResponse{Conn: NewMockConn(), Reader: bufio.NewReader(t.logReader)}, nil +} + +func (t *TestDockerClient) ContainerCreate(ctx context.Context, config *dockercontainer.Config, hostConfig *dockercontainer.HostConfig, networkingConfig *dockernetwork.NetworkingConfig, containerName string) (dockercontainer.ContainerCreateCreatedBody, error) { if config.WorkingDir != "" { t.cwd = config.WorkingDir } t.env = config.Env - return "abcde", nil + return dockercontainer.ContainerCreateCreatedBody{ID: "abcde"}, nil } -func (t *TestDockerClient) StartContainer(id string, config *dockerclient.HostConfig) error { - if id == "abcde" { +func (t *TestDockerClient) ContainerStart(ctx context.Context, container string, options dockertypes.ContainerStartOptions) error { + if container == "abcde" { go t.fn(t) return nil } else { @@ -121,15 +129,34 @@ func (t *TestDockerClient) StartContainer(id string, config *dockerclient.HostCo } } -func (t *TestDockerClient) AttachContainer(id string, options *dockerclient.AttachOptions) (io.ReadCloser, error) { - return t.logReader, nil +func (t *TestDockerClient) ContainerStop(ctx context.Context, container string, timeout *time.Duration) error { + t.stop <- true + return nil } -func (t *TestDockerClient) Wait(id string) <-chan dockerclient.WaitResult { - return t.finish +func (t *TestDockerClient) ContainerWait(ctx context.Context, container string) (int64, error) { + return int64(t.finish), nil +} + +func (t *TestDockerClient) ImageInspectWithRaw(ctx context.Context, image string) (dockertypes.ImageInspect, []byte, error) { + if t.imageLoaded == image { + return dockertypes.ImageInspect{}, nil, nil + } else { + return dockertypes.ImageInspect{}, nil, errors.New("") + } +} + +func (t *TestDockerClient) ImageLoad(ctx context.Context, input io.Reader, quiet bool) (dockertypes.ImageLoadResponse, error) { + _, err := io.Copy(ioutil.Discard, input) + if err != nil { + return dockertypes.ImageLoadResponse{}, err + } else { + t.imageLoaded = hwImageId + return dockertypes.ImageLoadResponse{Body: ioutil.NopCloser(input)}, nil + } } -func (*TestDockerClient) RemoveImage(name string, force bool) ([]*dockerclient.ImageDelete, error) { +func (*TestDockerClient) ImageRemove(ctx context.Context, image string, options dockertypes.ImageRemoveOptions) ([]dockertypes.ImageDeleteResponseItem, error) { return nil, nil } @@ -176,12 +203,31 @@ func (client *ArvTestClient) Call(method, resourceType, uuid, action string, par } } +func (client *ArvTestClient) CallRaw(method, resourceType, uuid, action string, + parameters arvadosclient.Dict) (reader io.ReadCloser, err error) { + j := []byte(`{ + "command": ["sleep", "1"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": ".", + "environment": {}, + "mounts": {"/tmp": {"kind": "tmp"} }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }`) + return ioutil.NopCloser(bytes.NewReader(j)), nil +} + func (client *ArvTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error { if resourceType == "collections" { if uuid == hwPDH { output.(*arvados.Collection).ManifestText = hwManifest } else if uuid == otherPDH { output.(*arvados.Collection).ManifestText = otherManifest + } else if uuid == normalizedWithSubdirsPDH { + output.(*arvados.Collection).ManifestText = normalizedManifestWithSubdirs + } else if uuid == denormalizedWithSubdirsPDH { + output.(*arvados.Collection).ManifestText = denormalizedManifestWithSubdirs } } if resourceType == "containers" { @@ -203,7 +249,16 @@ func (client *ArvTestClient) Update(resourceType string, uuid string, parameters return nil } -var discoveryMap = map[string]interface{}{"defaultTrashLifetime": float64(1209600)} +var discoveryMap = map[string]interface{}{ + "defaultTrashLifetime": float64(1209600), + "crunchLimitLogBytesPerJob": float64(67108864), + "crunchLogThrottleBytes": float64(65536), + "crunchLogThrottlePeriod": float64(60), + "crunchLogThrottleLines": float64(1024), + "crunchLogPartialLineThrottlePeriod": float64(5), + "crunchLogBytesPerEvent": float64(4096), + "crunchLogSecondsBetweenEvents": float64(1), +} func (client *ArvTestClient) Discovery(key string) (interface{}, error) { return discoveryMap[key], nil @@ -245,23 +300,31 @@ func (fw FileWrapper) Len() uint64 { return fw.len } -func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error) { +func (fw FileWrapper) Seek(int64, int) (int64, error) { + return 0, errors.New("not implemented") +} + +func (client *KeepTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) { if filename == hwImageId+".tar" { rdr := ioutil.NopCloser(&bytes.Buffer{}) client.Called = true return FileWrapper{rdr, 1321984}, nil + } else if filename == "/file1_in_main.txt" { + rdr := ioutil.NopCloser(strings.NewReader("foo")) + client.Called = true + return FileWrapper{rdr, 3}, nil } return nil, nil } func (s *TestSuite) TestLoadImage(c *C) { kc := &KeepTestClient{} - docker := NewTestDockerClient() + docker := NewTestDockerClient(0) cr := NewContainerRunner(&ArvTestClient{}, kc, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz") - _, err := cr.Docker.RemoveImage(hwImageId, true) + _, err := cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{}) - _, err = cr.Docker.InspectImage(hwImageId) + _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId) c.Check(err, NotNil) cr.Container.ContainerImage = hwPDH @@ -274,13 +337,13 @@ func (s *TestSuite) TestLoadImage(c *C) { c.Check(err, IsNil) defer func() { - cr.Docker.RemoveImage(hwImageId, true) + cr.Docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{}) }() c.Check(kc.Called, Equals, true) c.Check(cr.ContainerConfig.Image, Equals, hwImageId) - _, err = cr.Docker.InspectImage(hwImageId) + _, _, err = cr.Docker.ImageInspectWithRaw(nil, hwImageId) c.Check(err, IsNil) // (2) Test using image that's already loaded @@ -306,6 +369,11 @@ func (ArvErrorTestClient) Call(method, resourceType, uuid, action string, parame return errors.New("ArvError") } +func (ArvErrorTestClient) CallRaw(method, resourceType, uuid, action string, + parameters arvadosclient.Dict) (reader io.ReadCloser, err error) { + return nil, errors.New("ArvError") +} + func (ArvErrorTestClient) Get(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) error { return errors.New("ArvError") } @@ -324,7 +392,7 @@ func (KeepErrorTestClient) PutHB(hash string, buf []byte) (string, int, error) { return "", 0, errors.New("KeepError") } -func (KeepErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error) { +func (KeepErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) { return nil, errors.New("KeepError") } @@ -348,7 +416,11 @@ func (ErrorReader) Len() uint64 { return 0 } -func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.ReadCloserWithLen, error) { +func (ErrorReader) Seek(int64, int) (int64, error) { + return 0, errors.New("ErrorReader") +} + +func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (keepclient.Reader, error) { return ErrorReader{}, nil } @@ -363,7 +435,7 @@ func (s *TestSuite) TestLoadImageArvError(c *C) { func (s *TestSuite) TestLoadImageKeepError(c *C) { // (2) Keep error - docker := NewTestDockerClient() + docker := NewTestDockerClient(0) cr := NewContainerRunner(&ArvTestClient{}, KeepErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz") cr.Container.ContainerImage = hwPDH @@ -382,7 +454,7 @@ func (s *TestSuite) TestLoadImageCollectionError(c *C) { func (s *TestSuite) TestLoadImageKeepReadError(c *C) { // (4) Collection doesn't contain image - docker := NewTestDockerClient() + docker := NewTestDockerClient(0) cr := NewContainerRunner(&ArvTestClient{}, KeepReadErrorTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz") cr.Container.ContainerImage = hwPDH @@ -423,11 +495,10 @@ func dockerLog(fd byte, msg string) []byte { } func (s *TestSuite) TestRunContainer(c *C) { - docker := NewTestDockerClient() + docker := NewTestDockerClient(0) docker.fn = func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, "Hello world\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{} } cr := NewContainerRunner(&ArvTestClient{}, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz") @@ -465,6 +536,7 @@ func (s *TestSuite) TestCommitLogs(c *C) { c.Check(err, IsNil) c.Check(api.Calls, Equals, 2) + c.Check(api.Content[1]["ensure_unique_name"], Equals, true) c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz") c.Check(api.Content[1]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n") c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60") @@ -505,7 +577,7 @@ func (s *TestSuite) TestUpdateContainerCancelled(c *C) { api := &ArvTestClient{} kc := &KeepTestClient{} cr := NewContainerRunner(api, kc, nil, "zzzzz-zzzzz-zzzzzzzzzzzzzzz") - cr.Cancelled = true + cr.cCancelled = true cr.finalState = "Cancelled" err := cr.UpdateContainerFinal() @@ -518,14 +590,14 @@ func (s *TestSuite) TestUpdateContainerCancelled(c *C) { // 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, fn func(t *TestDockerClient)) (api *ArvTestClient, cr *ContainerRunner) { +func 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() + docker := NewTestDockerClient(exitCode) docker.fn = fn - docker.RemoveImage(hwImageId, true) + docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{}) api = &ArvTestClient{Container: rec} docker.api = api @@ -534,6 +606,31 @@ func FullRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvT am := &ArvMountCmdLine{} cr.RunArvMount = am.ArvMountTest + realTemp, err = ioutil.TempDir("", "crunchrun_test1-") + c.Assert(err, IsNil) + defer os.RemoveAll(realTemp) + + tempcount := 0 + cr.MkTempDir = func(_ string, prefix string) (string, error) { + tempcount++ + d := fmt.Sprintf("%s/%s%d", realTemp, prefix, tempcount) + err := os.Mkdir(d, os.ModePerm) + if err != nil && strings.Contains(err.Error(), ": file exists") { + // Test case must have pre-populated the tempdir + err = nil + } + return d, err + } + + if extraMounts != nil && len(extraMounts) > 0 { + err := cr.SetupArvMountPoint("keep") + c.Check(err, IsNil) + + for _, m := range extraMounts { + os.MkdirAll(cr.ArvMountPoint+"/by_id/"+m, os.ModePerm) + } + } + err = cr.Run() c.Check(err, IsNil) c.Check(api.WasSetRunning, Equals, true) @@ -551,7 +648,7 @@ func FullRunHelper(c *C, record string, fn func(t *TestDockerClient)) (api *ArvT } func (s *TestSuite) TestFullRunHello(c *C) { - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["echo", "hello world"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": ".", @@ -560,10 +657,9 @@ func (s *TestSuite) TestFullRunHello(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {} -}`, func(t *TestDockerClient) { +}`, nil, 0, func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, "hello world\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) @@ -573,7 +669,7 @@ func (s *TestSuite) TestFullRunHello(c *C) { } func (s *TestSuite) TestCrunchstat(c *C) { - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["sleep", "1"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": ".", @@ -582,10 +678,9 @@ func (s *TestSuite) TestCrunchstat(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {} - }`, func(t *TestDockerClient) { + }`, nil, 0, func(t *TestDockerClient) { time.Sleep(time.Second) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) @@ -605,8 +700,58 @@ func (s *TestSuite) TestCrunchstat(c *C) { c.Check(api.Logs["crunchstat"].String(), Matches, `(?ms).*cgroup stats files never appeared for abcde\n`) } +func (s *TestSuite) TestNodeInfoLog(c *C) { + api, _, _ := FullRunHelper(c, `{ + "command": ["sleep", "1"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": ".", + "environment": {}, + "mounts": {"/tmp": {"kind": "tmp"} }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }`, nil, 0, + func(t *TestDockerClient) { + time.Sleep(time.Second) + t.logWriter.Close() + }) + + c.Check(api.CalledWith("container.exit_code", 0), NotNil) + c.Check(api.CalledWith("container.state", "Complete"), NotNil) + + 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.*`) +} + +func (s *TestSuite) TestContainerRecordLog(c *C) { + api, _, _ := FullRunHelper(c, `{ + "command": ["sleep", "1"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": ".", + "environment": {}, + "mounts": {"/tmp": {"kind": "tmp"} }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }`, nil, 0, + func(t *TestDockerClient) { + time.Sleep(time.Second) + t.logWriter.Close() + }) + + c.Check(api.CalledWith("container.exit_code", 0), NotNil) + c.Check(api.CalledWith("container.state", "Complete"), NotNil) + + c.Assert(api.Logs["container"], NotNil) + c.Check(api.Logs["container"].String(), Matches, `(?ms).*container_image.*`) +} + func (s *TestSuite) TestFullRunStderr(c *C) { - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["/bin/sh", "-c", "echo hello ; echo world 1>&2 ; exit 1"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": ".", @@ -615,11 +760,10 @@ func (s *TestSuite) TestFullRunStderr(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {} -}`, func(t *TestDockerClient) { +}`, nil, 1, func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, "hello\n")) t.logWriter.Write(dockerLog(2, "world\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 1} }) final := api.CalledWith("container.state", "Complete") @@ -632,7 +776,7 @@ func (s *TestSuite) TestFullRunStderr(c *C) { } func (s *TestSuite) TestFullRunDefaultCwd(c *C) { - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["pwd"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": ".", @@ -641,10 +785,9 @@ func (s *TestSuite) TestFullRunDefaultCwd(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {} -}`, func(t *TestDockerClient) { +}`, nil, 0, func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, t.cwd+"\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 0} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) @@ -654,7 +797,7 @@ func (s *TestSuite) TestFullRunDefaultCwd(c *C) { } func (s *TestSuite) TestFullRunSetCwd(c *C) { - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["pwd"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": "/bin", @@ -663,10 +806,9 @@ func (s *TestSuite) TestFullRunSetCwd(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {} -}`, func(t *TestDockerClient) { +}`, nil, 0, func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, t.cwd+"\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 0} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) @@ -674,7 +816,28 @@ func (s *TestSuite) TestFullRunSetCwd(c *C) { c.Check(strings.HasSuffix(api.Logs["stdout"].String(), "/bin\n"), Equals, true) } -func (s *TestSuite) TestCancel(c *C) { +func (s *TestSuite) TestStopOnSignal(c *C) { + s.testStopContainer(c, func(cr *ContainerRunner) { + go func() { + for !cr.cStarted { + time.Sleep(time.Millisecond) + } + cr.SigChan <- syscall.SIGINT + }() + }) +} + +func (s *TestSuite) TestStopOnArvMountDeath(c *C) { + s.testStopContainer(c, func(cr *ContainerRunner) { + cr.ArvMountExit = make(chan error) + go func() { + cr.ArvMountExit <- exec.Command("true").Run() + close(cr.ArvMountExit) + }() + }) +} + +func (s *TestSuite) testStopContainer(c *C, setup func(cr *ContainerRunner)) { record := `{ "command": ["/bin/sh", "-c", "echo foo && sleep 30 && echo bar"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", @@ -690,45 +853,42 @@ func (s *TestSuite) TestCancel(c *C) { err := json.Unmarshal([]byte(record), &rec) c.Check(err, IsNil) - docker := NewTestDockerClient() + docker := NewTestDockerClient(0) docker.fn = func(t *TestDockerClient) { <-t.stop t.logWriter.Write(dockerLog(1, "foo\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 0} } - docker.RemoveImage(hwImageId, true) + docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{}) api := &ArvTestClient{Container: rec} cr := NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz") - am := &ArvMountCmdLine{} - cr.RunArvMount = am.ArvMountTest + cr.RunArvMount = func([]string, string) (*exec.Cmd, error) { return nil, nil } + setup(cr) + done := make(chan error) go func() { - for cr.ContainerID == "" { - time.Sleep(time.Millisecond) - } - cr.SigChan <- syscall.SIGINT + done <- cr.Run() }() - - err = cr.Run() - - c.Check(err, IsNil) - if err != nil { - for k, v := range api.Logs { - c.Log(k) - c.Log(v.String()) - } + select { + case <-time.After(20 * time.Second): + pprof.Lookup("goroutine").WriteTo(os.Stderr, 1) + c.Fatal("timed out") + case err = <-done: + c.Check(err, IsNil) + } + for k, v := range api.Logs { + c.Log(k) + c.Log(v.String()) } 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) - } func (s *TestSuite) TestFullRunSetEnv(c *C) { - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["/bin/sh", "-c", "echo $FROBIZ"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": "/bin", @@ -737,10 +897,9 @@ func (s *TestSuite) TestFullRunSetEnv(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {} -}`, func(t *TestDockerClient) { +}`, nil, 0, func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 0} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) @@ -805,6 +964,7 @@ func (s *TestSuite) TestSetupMounts(c *C) { { i = 0 + cr.ArvMountPoint = "" cr.Container.Mounts = make(map[string]arvados.Mount) cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"} cr.OutputPath = "/tmp" @@ -819,6 +979,7 @@ func (s *TestSuite) TestSetupMounts(c *C) { { i = 0 + cr.ArvMountPoint = "" cr.Container.Mounts = make(map[string]arvados.Mount) cr.Container.Mounts["/tmp"] = arvados.Mount{Kind: "tmp"} cr.OutputPath = "/tmp" @@ -838,6 +999,7 @@ func (s *TestSuite) TestSetupMounts(c *C) { { i = 0 + cr.ArvMountPoint = "" cr.Container.Mounts = map[string]arvados.Mount{ "/keeptmp": {Kind: "collection", Writable: true}, } @@ -855,6 +1017,7 @@ func (s *TestSuite) TestSetupMounts(c *C) { { i = 0 + cr.ArvMountPoint = "" cr.Container.Mounts = map[string]arvados.Mount{ "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"}, "/keepout": {Kind: "collection", Writable: true}, @@ -876,6 +1039,7 @@ func (s *TestSuite) TestSetupMounts(c *C) { { i = 0 + cr.ArvMountPoint = "" cr.Container.RuntimeConstraints.KeepCacheRAM = 512 cr.Container.Mounts = map[string]arvados.Mount{ "/keepinp": {Kind: "collection", PortableDataHash: "59389a8f9ee9d399be35462a0f92541c+53"}, @@ -905,6 +1069,7 @@ func (s *TestSuite) TestSetupMounts(c *C) { {in: map[string]int{"foo": 123}, out: `{"foo":123}`}, } { i = 0 + cr.ArvMountPoint = "" cr.Container.Mounts = map[string]arvados.Mount{ "/mnt/test.json": {Kind: "json", Content: test.in}, } @@ -918,6 +1083,79 @@ func (s *TestSuite) TestSetupMounts(c *C) { cr.CleanupDirs() checkEmpty() } + + // Read-only mount points are allowed underneath 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"}, + } + cr.OutputPath = "/tmp" + + os.MkdirAll(realTemp+"/keep1/tmp0", os.ModePerm) + + 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"}) + cr.CleanupDirs() + checkEmpty() + } + + // Writable mount points are not allowed underneath 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}, + } + cr.OutputPath = "/tmp" + + err := cr.SetupMounts() + c.Check(err, NotNil) + c.Check(err, ErrorMatches, `Writable mount points are not permitted underneath the output_path.*`) + cr.CleanupDirs() + checkEmpty() + } + + // Only mount points of kind 'collection' are allowed underneath 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: "json"}, + } + cr.OutputPath = "/tmp" + + err := cr.SetupMounts() + c.Check(err, NotNil) + c.Check(err, ErrorMatches, `Only mount points of kind 'collection' are supported underneath the output_path.*`) + cr.CleanupDirs() + checkEmpty() + } + + // Only mount point of kind 'collection' is allowed for stdin + { + i = 0 + cr.ArvMountPoint = "" + cr.Container.Mounts = make(map[string]arvados.Mount) + cr.Container.Mounts = map[string]arvados.Mount{ + "stdin": {Kind: "tmp"}, + } + + err := cr.SetupMounts() + c.Check(err, NotNil) + c.Check(err, ErrorMatches, `Unsupported mount kind 'tmp' for stdin.*`) + cr.CleanupDirs() + checkEmpty() + } } func (s *TestSuite) TestStdout(c *C) { @@ -932,10 +1170,9 @@ func (s *TestSuite) TestStdout(c *C) { "runtime_constraints": {} }` - api, _ := FullRunHelper(c, helperRecord, func(t *TestDockerClient) { + api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 0} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) @@ -949,9 +1186,9 @@ func StdoutErrorRunHelper(c *C, record string, fn func(t *TestDockerClient)) (ap err = json.Unmarshal([]byte(record), &rec) c.Check(err, IsNil) - docker := NewTestDockerClient() + docker := NewTestDockerClient(0) docker.fn = fn - docker.RemoveImage(hwImageId, true) + docker.ImageRemove(nil, hwImageId, dockertypes.ImageRemoveOptions{}) api = &ArvTestClient{Container: rec} cr = NewContainerRunner(api, &KeepTestClient{}, docker, "zzzzz-zzzzz-zzzzzzzzzzzzzzz") @@ -995,7 +1232,7 @@ func (s *TestSuite) TestStdoutWithWrongKindCollection(c *C) { func (s *TestSuite) TestFullRunWithAPI(c *C) { os.Setenv("ARVADOS_API_HOST", "test.arvados.org") defer os.Unsetenv("ARVADOS_API_HOST") - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": "/bin", @@ -1004,10 +1241,9 @@ func (s *TestSuite) TestFullRunWithAPI(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {"API": true} -}`, func(t *TestDockerClient) { +}`, nil, 0, func(t *TestDockerClient) { t.logWriter.Write(dockerLog(1, t.env[1][17:]+"\n")) t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 0} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) @@ -1019,7 +1255,7 @@ func (s *TestSuite) TestFullRunWithAPI(c *C) { func (s *TestSuite) TestFullRunSetOutput(c *C) { os.Setenv("ARVADOS_API_HOST", "test.arvados.org") defer os.Unsetenv("ARVADOS_API_HOST") - api, _ := FullRunHelper(c, `{ + api, _, _ := FullRunHelper(c, `{ "command": ["/bin/sh", "-c", "echo $ARVADOS_API_HOST"], "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", "cwd": "/bin", @@ -1028,13 +1264,241 @@ func (s *TestSuite) TestFullRunSetOutput(c *C) { "output_path": "/tmp", "priority": 1, "runtime_constraints": {"API": true} -}`, func(t *TestDockerClient) { +}`, nil, 0, func(t *TestDockerClient) { t.api.Container.Output = "d4ab34d3d4f8a72f5c4973051ae69fab+122" t.logWriter.Close() - t.finish <- dockerclient.WaitResult{ExitCode: 0} }) c.Check(api.CalledWith("container.exit_code", 0), NotNil) c.Check(api.CalledWith("container.state", "Complete"), NotNil) c.Check(api.CalledWith("container.output", "d4ab34d3d4f8a72f5c4973051ae69fab+122"), NotNil) } + +func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) { + helperRecord := `{ + "command": ["/bin/sh", "-c", "echo $FROBIZ"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": "/bin", + "environment": {"FROBIZ": "bilbo"}, + "mounts": { + "/tmp": {"kind": "tmp"}, + "/tmp/foo": {"kind": "collection", + "portable_data_hash": "a3e8f74c6f101eae01fa08bfb4e49b3a+54", + "exclude_from_output": true + }, + "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} + }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }` + + extraMounts := []string{"a3e8f74c6f101eae01fa08bfb4e49b3a+54"} + + api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) { + t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n")) + t.logWriter.Close() + }) + + c.Check(api.CalledWith("container.exit_code", 0), NotNil) + c.Check(api.CalledWith("container.state", "Complete"), NotNil) + c.Check(api.CalledWith("collection.manifest_text", "./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out\n"), NotNil) +} + +func (s *TestSuite) TestStdoutWithMultipleMountPointsUnderOutputDir(c *C) { + helperRecord := `{ + "command": ["/bin/sh", "-c", "echo $FROBIZ"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": "/bin", + "environment": {"FROBIZ": "bilbo"}, + "mounts": { + "/tmp": {"kind": "tmp"}, + "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/file2_in_main.txt"}, + "/tmp/foo/sub1": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1"}, + "/tmp/foo/sub1file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/file2_in_subdir1.txt"}, + "/tmp/foo/baz/sub2file2": {"kind": "collection", "portable_data_hash": "a0def87f80dd594d4675809e83bd4f15+367", "path":"/subdir1/subdir2/file2_in_subdir2.txt"}, + "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} + }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }` + + extraMounts := []string{ + "a0def87f80dd594d4675809e83bd4f15+367/file2_in_main.txt", + "a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt", + "a0def87f80dd594d4675809e83bd4f15+367/subdir1/subdir2/file2_in_subdir2.txt", + } + + api, runner, realtemp := 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", + 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", + realtemp + "/keep1/by_id/a0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt:/tmp/foo/sub1file2:ro", + }) + + c.Check(api.CalledWith("container.exit_code", 0), NotNil) + c.Check(api.CalledWith("container.state", "Complete"), NotNil) + for _, v := range api.Content { + if v["collection"] != nil { + c.Check(v["ensure_unique_name"], Equals, true) + collection := v["collection"].(arvadosclient.Dict) + if strings.Index(collection["name"].(string), "output") == 0 { + manifest := collection["manifest_text"].(string) + + c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out +./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 9:18:bar 9:18:sub1file2 +./foo/baz 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 9:18:sub2file2 +./foo/sub1 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396cabcdefghij6419876543234@569fa8c4 0:9:file1_in_subdir1.txt 9:18:file2_in_subdir1.txt +./foo/sub1/subdir2 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0bcdefghijk544332211@569fa8c5 0:9:file1_in_subdir2.txt 9:18:file2_in_subdir2.txt +`) + } + } + } +} + +func (s *TestSuite) TestStdoutWithMountPointsUnderOutputDirDenormalizedManifest(c *C) { + helperRecord := `{ + "command": ["/bin/sh", "-c", "echo $FROBIZ"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": "/bin", + "environment": {"FROBIZ": "bilbo"}, + "mounts": { + "/tmp": {"kind": "tmp"}, + "/tmp/foo/bar": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt"}, + "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} + }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }` + + extraMounts := []string{ + "b0def87f80dd594d4675809e83bd4f15+367/subdir1/file2_in_subdir1.txt", + } + + api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) { + t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n")) + t.logWriter.Close() + }) + + c.Check(api.CalledWith("container.exit_code", 0), NotNil) + c.Check(api.CalledWith("container.state", "Complete"), NotNil) + for _, v := range api.Content { + if v["collection"] != nil { + collection := v["collection"].(arvadosclient.Dict) + if strings.Index(collection["name"].(string), "output") == 0 { + manifest := collection["manifest_text"].(string) + + c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out +./foo 3e426d509afffb85e06c4c96a7c15e91+27+Aa124ac75e5168396c73c0abcdefgh11234567890@569fa8c3 10:17:bar +`) + } + } + } +} + +func (s *TestSuite) TestStdinCollectionMountPoint(c *C) { + helperRecord := `{ + "command": ["/bin/sh", "-c", "echo $FROBIZ"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": "/bin", + "environment": {"FROBIZ": "bilbo"}, + "mounts": { + "/tmp": {"kind": "tmp"}, + "stdin": {"kind": "collection", "portable_data_hash": "b0def87f80dd594d4675809e83bd4f15+367", "path": "/file1_in_main.txt"}, + "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} + }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }` + + extraMounts := []string{ + "b0def87f80dd594d4675809e83bd4f15+367/file1_in_main.txt", + } + + api, _, _ := FullRunHelper(c, helperRecord, extraMounts, 0, func(t *TestDockerClient) { + t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n")) + t.logWriter.Close() + }) + + c.Check(api.CalledWith("container.exit_code", 0), NotNil) + c.Check(api.CalledWith("container.state", "Complete"), NotNil) + for _, v := range api.Content { + if v["collection"] != nil { + collection := v["collection"].(arvadosclient.Dict) + if strings.Index(collection["name"].(string), "output") == 0 { + manifest := collection["manifest_text"].(string) + c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out +`) + } + } + } +} + +func (s *TestSuite) TestStdinJsonMountPoint(c *C) { + helperRecord := `{ + "command": ["/bin/sh", "-c", "echo $FROBIZ"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": "/bin", + "environment": {"FROBIZ": "bilbo"}, + "mounts": { + "/tmp": {"kind": "tmp"}, + "stdin": {"kind": "json", "content": "foo"}, + "stdout": {"kind": "file", "path": "/tmp/a/b/c.out"} + }, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} + }` + + api, _, _ := FullRunHelper(c, helperRecord, nil, 0, func(t *TestDockerClient) { + t.logWriter.Write(dockerLog(1, t.env[0][7:]+"\n")) + t.logWriter.Close() + }) + + c.Check(api.CalledWith("container.exit_code", 0), NotNil) + c.Check(api.CalledWith("container.state", "Complete"), NotNil) + for _, v := range api.Content { + if v["collection"] != nil { + collection := v["collection"].(arvadosclient.Dict) + if strings.Index(collection["name"].(string), "output") == 0 { + manifest := collection["manifest_text"].(string) + c.Check(manifest, Equals, `./a/b 307372fa8fd5c146b22ae7a45b49bc31+6 0:6:c.out +`) + } + } + } +} + +func (s *TestSuite) TestStderrMount(c *C) { + api, _, _ := FullRunHelper(c, `{ + "command": ["/bin/sh", "-c", "echo hello;exit 1"], + "container_image": "d4ab34d3d4f8a72f5c4973051ae69fab+122", + "cwd": ".", + "environment": {}, + "mounts": {"/tmp": {"kind": "tmp"}, + "stdout": {"kind": "file", "path": "/tmp/a/out.txt"}, + "stderr": {"kind": "file", "path": "/tmp/b/err.txt"}}, + "output_path": "/tmp", + "priority": 1, + "runtime_constraints": {} +}`, nil, 1, func(t *TestDockerClient) { + t.logWriter.Write(dockerLog(1, "hello\n")) + t.logWriter.Write(dockerLog(2, "oops\n")) + t.logWriter.Close() + }) + + final := api.CalledWith("container.state", "Complete") + c.Assert(final, NotNil) + c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1) + c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil) + + c.Check(api.CalledWith("collection.manifest_text", "./a b1946ac92492d2347c6235b4d2611184+6 0:6:out.txt\n./b 38af5c54926b620264ab1501150cf189+5 0:5:err.txt\n"), NotNil) +}