X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0662b235357dd40b5d27efd06b60044ddcec06f6..dece16822124a86dd2f57b7d3b25ca1aa7d75600:/sdk/go/crunchrunner/crunchrunner.go diff --git a/sdk/go/crunchrunner/crunchrunner.go b/sdk/go/crunchrunner/crunchrunner.go index 8e24e18fda..ca16fc6561 100644 --- a/sdk/go/crunchrunner/crunchrunner.go +++ b/sdk/go/crunchrunner/crunchrunner.go @@ -1,15 +1,24 @@ +// Copyright (C) The Arvados Authors. All rights reserved. +// +// SPDX-License-Identifier: Apache-2.0 + package main import ( + "encoding/json" "fmt" - "git.curoverse.com/arvados.git/sdk/go/arvadosclient" - "git.curoverse.com/arvados.git/sdk/go/keepclient" + "io" + "io/ioutil" "log" "os" "os/exec" "os/signal" "strings" "syscall" + + "git.curoverse.com/arvados.git/sdk/go/arvados" + "git.curoverse.com/arvados.git/sdk/go/arvadosclient" + "git.curoverse.com/arvados.git/sdk/go/keepclient" ) type TaskDef struct { @@ -17,10 +26,12 @@ type TaskDef struct { Env map[string]string `json:"task.env"` Stdin string `json:"task.stdin"` Stdout string `json:"task.stdout"` + Stderr string `json:"task.stderr"` Vwd map[string]string `json:"task.vwd"` SuccessCodes []int `json:"task.successCodes"` PermanentFailCodes []int `json:"task.permanentFailCodes"` TemporaryFailCodes []int `json:"task.temporaryFailCodes"` + KeepTmpOutput bool `json:"task.keepTmpOutput"` } type Tasks struct { @@ -28,17 +39,17 @@ type Tasks struct { } type Job struct { - Script_parameters Tasks `json:"script_parameters"` + ScriptParameters Tasks `json:"script_parameters"` } type Task struct { - Job_uuid string `json:"job_uuid"` - Created_by_job_task_uuid string `json:"created_by_job_task_uuid"` - Parameters TaskDef `json:"parameters"` - Sequence int `json:"sequence"` - Output string `json:"output"` - Success bool `json:"success"` - Progress float32 `json:"sequence"` + JobUUID string `json:"job_uuid"` + CreatedByJobTaskUUID string `json:"created_by_job_task_uuid"` + Parameters TaskDef `json:"parameters"` + Sequence int `json:"sequence"` + Output string `json:"output"` + Success bool `json:"success"` + Progress float32 `json:"sequence"` } type IArvadosClient interface { @@ -46,17 +57,21 @@ type IArvadosClient interface { Update(resourceType string, uuid string, parameters arvadosclient.Dict, output interface{}) (err error) } -func setupDirectories(crunchtmpdir, taskUuid string) (tmpdir, outdir string, err error) { +func setupDirectories(crunchtmpdir, taskUUID string, keepTmp bool) (tmpdir, outdir string, err error) { tmpdir = crunchtmpdir + "/tmpdir" err = os.Mkdir(tmpdir, 0700) if err != nil { return "", "", err } - outdir = crunchtmpdir + "/outdir" - err = os.Mkdir(outdir, 0700) - if err != nil { - return "", "", err + if keepTmp { + outdir = os.Getenv("TASK_KEEPMOUNT_TMP") + } else { + outdir = crunchtmpdir + "/outdir" + err = os.Mkdir(outdir, 0700) + if err != nil { + return "", "", err + } } return tmpdir, outdir, nil @@ -77,15 +92,39 @@ func checkOutputFilename(outdir, fn string) error { return nil } -func setupCommand(cmd *exec.Cmd, taskp TaskDef, outdir string, replacements map[string]string) (stdin, stdout string, err error) { +func copyFile(dst, src string) error { + in, err := os.Open(src) + if err != nil { + return err + } + defer in.Close() + + out, err := os.Create(dst) + if err != nil { + return err + } + defer out.Close() + + _, err = io.Copy(out, in) + return err +} + +func setupCommand(cmd *exec.Cmd, taskp TaskDef, outdir string, replacements map[string]string) (stdin, stdout, stderr string, err error) { if taskp.Vwd != nil { for k, v := range taskp.Vwd { v = substitute(v, replacements) err = checkOutputFilename(outdir, k) if err != nil { - return "", "", err + return "", "", "", err + } + if taskp.KeepTmpOutput { + err = copyFile(v, outdir+"/"+k) + } else { + err = os.Symlink(v, outdir+"/"+k) + } + if err != nil { + return "", "", "", err } - os.Symlink(v, outdir+"/"+k) } } @@ -94,25 +133,40 @@ func setupCommand(cmd *exec.Cmd, taskp TaskDef, outdir string, replacements map[ stdin = substitute(taskp.Stdin, replacements) cmd.Stdin, err = os.Open(stdin) if err != nil { - return "", "", err + return "", "", "", err } } if taskp.Stdout != "" { err = checkOutputFilename(outdir, taskp.Stdout) if err != nil { - return "", "", err + return "", "", "", err } // Set up stdout redirection stdout = outdir + "/" + taskp.Stdout cmd.Stdout, err = os.Create(stdout) if err != nil { - return "", "", err + return "", "", "", err } } else { cmd.Stdout = os.Stdout } + if taskp.Stderr != "" { + err = checkOutputFilename(outdir, taskp.Stderr) + if err != nil { + return "", "", "", err + } + // Set up stderr redirection + stderr = outdir + "/" + taskp.Stderr + cmd.Stderr, err = os.Create(stderr) + if err != nil { + return "", "", "", err + } + } else { + cmd.Stderr = os.Stderr + } + if taskp.Env != nil { // Set up subprocess environment cmd.Env = os.Environ() @@ -121,7 +175,7 @@ func setupCommand(cmd *exec.Cmd, taskp TaskDef, outdir string, replacements map[ cmd.Env = append(cmd.Env, k+"="+v) } } - return stdin, stdout, nil + return stdin, stdout, stderr, nil } // Set up signal handlers. Go sends signal notifications to a "signal @@ -161,9 +215,25 @@ func substitute(inp string, subst map[string]string) string { return inp } +func getKeepTmp(outdir string) (manifest string, err error) { + fn, err := os.Open(outdir + "/" + ".arvados#collection") + if err != nil { + return "", err + } + defer fn.Close() + + buf, err := ioutil.ReadAll(fn) + if err != nil { + return "", err + } + collection := arvados.Collection{} + err = json.Unmarshal(buf, &collection) + return collection.ManifestText, err +} + func runner(api IArvadosClient, kc IKeepClient, - jobUuid, taskUuid, crunchtmpdir, keepmount string, + jobUUID, taskUUID, crunchtmpdir, keepmount string, jobStruct Job, taskStruct Task) error { var err error @@ -172,34 +242,35 @@ func runner(api IArvadosClient, // If this is task 0 and there are multiple tasks, dispatch subtasks // and exit. if taskStruct.Sequence == 0 { - if len(jobStruct.Script_parameters.Tasks) == 1 { - taskp = jobStruct.Script_parameters.Tasks[0] + if len(jobStruct.ScriptParameters.Tasks) == 1 { + taskp = jobStruct.ScriptParameters.Tasks[0] } else { - for _, task := range jobStruct.Script_parameters.Tasks { + for _, task := range jobStruct.ScriptParameters.Tasks { err := api.Create("job_tasks", map[string]interface{}{ - "job_task": Task{Job_uuid: jobUuid, - Created_by_job_task_uuid: taskUuid, - Sequence: 1, - Parameters: task}}, + "job_task": Task{ + JobUUID: jobUUID, + CreatedByJobTaskUUID: taskUUID, + Sequence: 1, + Parameters: task}}, nil) if err != nil { return TempFail{err} } } - err = api.Update("job_tasks", taskUuid, + err = api.Update("job_tasks", taskUUID, map[string]interface{}{ - "job_task": Task{ - Output: "", - Success: true, - Progress: 1.0}}, + "job_task": map[string]interface{}{ + "output": "", + "success": true, + "progress": 1.0}}, nil) return nil } } var tmpdir, outdir string - tmpdir, outdir, err = setupDirectories(crunchtmpdir, taskUuid) + tmpdir, outdir, err = setupDirectories(crunchtmpdir, taskUUID, taskp.KeepTmpOutput) if err != nil { return TempFail{err} } @@ -209,6 +280,10 @@ func runner(api IArvadosClient, "$(task.outdir)": outdir, "$(task.keep)": keepmount} + log.Printf("crunchrunner: $(task.tmpdir)=%v", tmpdir) + log.Printf("crunchrunner: $(task.outdir)=%v", outdir) + log.Printf("crunchrunner: $(task.keep)=%v", keepmount) + // Set up subprocess for k, v := range taskp.Command { taskp.Command[k] = substitute(v, replacements) @@ -218,8 +293,8 @@ func runner(api IArvadosClient, cmd.Dir = outdir - var stdin, stdout string - stdin, stdout, err = setupCommand(cmd, taskp, outdir, replacements) + var stdin, stdout, stderr string + stdin, stdout, stderr, err = setupCommand(cmd, taskp, outdir, replacements) if err != nil { return err } @@ -231,7 +306,10 @@ func runner(api IArvadosClient, if stdout != "" { stdout = " > " + stdout } - log.Printf("Running %v%v%v", cmd.Args, stdin, stdout) + if stderr != "" { + stderr = " 2> " + stderr + } + log.Printf("Running %v%v%v%v", cmd.Args, stdin, stdout, stderr) var caughtSignal os.Signal sigChan := setupSignals(cmd) @@ -287,13 +365,18 @@ func runner(api IArvadosClient, } // Upload output directory - manifest, err := WriteTree(kc, outdir) + var manifest string + if taskp.KeepTmpOutput { + manifest, err = getKeepTmp(outdir) + } else { + manifest, err = WriteTree(kc, outdir) + } if err != nil { return TempFail{err} } // Set status - err = api.Update("job_tasks", taskUuid, + err = api.Update("job_tasks", taskUUID, map[string]interface{}{ "job_task": Task{ Output: manifest, @@ -317,31 +400,31 @@ func main() { log.Fatal(err) } - jobUuid := os.Getenv("JOB_UUID") - taskUuid := os.Getenv("TASK_UUID") + jobUUID := os.Getenv("JOB_UUID") + taskUUID := os.Getenv("TASK_UUID") tmpdir := os.Getenv("TASK_WORK") keepmount := os.Getenv("TASK_KEEPMOUNT") var jobStruct Job var taskStruct Task - err = api.Get("jobs", jobUuid, nil, &jobStruct) + err = api.Get("jobs", jobUUID, nil, &jobStruct) if err != nil { log.Fatal(err) } - err = api.Get("job_tasks", taskUuid, nil, &taskStruct) + err = api.Get("job_tasks", taskUUID, nil, &taskStruct) if err != nil { log.Fatal(err) } var kc IKeepClient - kc, err = keepclient.MakeKeepClient(&api) + kc, err = keepclient.MakeKeepClient(api) if err != nil { log.Fatal(err) } syscall.Umask(0022) - err = runner(api, kc, jobUuid, taskUuid, tmpdir, keepmount, jobStruct, taskStruct) + err = runner(api, kc, jobUUID, taskUUID, tmpdir, keepmount, jobStruct, taskStruct) if err == nil { os.Exit(0)