20543: Recommend users install Python packages in a virtualenv

[arvados.git] / lib / crunchrun / crunchrun.go

diff --git a/lib/crunchrun/crunchrun.go b/lib/crunchrun/crunchrun.go
index 3f254496ba488bb3aea553b65d50937e59652096..8e7d3b0d6e9057b21b6ed66959d193889072f2b5 100644 (file)
--- a/lib/crunchrun/crunchrun.go
+++ b/lib/crunchrun/crunchrun.go
@@ -638,7 +638,7 @@ func (runner *ContainerRunner) SetupMounts() (map[string]bindmount, error) {
                        if err != nil {
                                return nil, fmt.Errorf("creating temp dir: %v", err)
                        }
-                       err = gitMount(mnt).extractTree(runner.ContainerArvClient, tmpdir, token)
+                       err = gitMount(mnt).extractTree(runner.containerClient, tmpdir, token)
                        if err != nil {
                                return nil, err
                        }
@@ -1124,6 +1124,7 @@ func (runner *ContainerRunner) WaitFinish() error {
        }
        runner.CrunchLog.Printf("Container exited with status code %d%s", exitcode, extra)
        err = runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
+               "select":    []string{"uuid"},
                "container": arvadosclient.Dict{"exit_code": exitcode},
        }, nil)
        if err != nil {
@@ -1200,7 +1201,10 @@ func (runner *ContainerRunner) updateLogs() {
                }
 
                err = runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
-                       "container": arvadosclient.Dict{"log": saved.PortableDataHash},
+                       "select": []string{"uuid"},
+                       "container": arvadosclient.Dict{
+                               "log": saved.PortableDataHash,
+                       },
                }, nil)
                if err != nil {
                        runner.CrunchLog.Printf("error updating container log to %s: %s", saved.PortableDataHash, err)
@@ -1316,6 +1320,7 @@ func (runner *ContainerRunner) checkSpotInterruptionNotices() {
 
 func (runner *ContainerRunner) updateRuntimeStatus(status arvadosclient.Dict) {
        err := runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
+               "select": []string{"uuid"},
                "container": arvadosclient.Dict{
                        "runtime_status": status,
                },
@@ -1332,7 +1337,9 @@ func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) er
                // 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)
+                       arvadosclient.Dict{
+                               "select": []string{"output"},
+                       }, &runner.Container)
                if err != nil {
                        return err
                }
@@ -1345,7 +1352,6 @@ func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) er
 
        txt, err := (&copier{
                client:        runner.containerClient,
-               arvClient:     runner.ContainerArvClient,
                keepClient:    runner.ContainerKeepClient,
                hostOutputDir: runner.HostOutputDir,
                ctrOutputDir:  runner.Container.OutputPath,
@@ -1371,6 +1377,7 @@ func (runner *ContainerRunner) CaptureOutput(bindmounts map[string]bindmount) er
        var resp arvados.Collection
        err = runner.ContainerArvClient.Create("collections", arvadosclient.Dict{
                "ensure_unique_name": true,
+               "select":             []string{"portable_data_hash"},
                "collection": arvadosclient.Dict{
                        "is_trashed":    true,
                        "name":          "output for " + runner.Container.UUID,
@@ -1497,6 +1504,8 @@ func (runner *ContainerRunner) CommitLogs() error {
        return nil
 }
 
+// Create/update the log collection. Return value has UUID and
+// PortableDataHash fields populated, but others may be blank.
 func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.Collection, err error) {
        runner.logMtx.Lock()
        defer runner.logMtx.Unlock()
@@ -1521,11 +1530,20 @@ func (runner *ContainerRunner) saveLogCollection(final bool) (response arvados.C
        if final {
                updates["is_trashed"] = true
        } else {
-               exp := time.Now().Add(crunchLogUpdatePeriod * 24)
+               // We set trash_at so this collection gets
+               // automatically cleaned up eventually.  It used to be
+               // 12 hours but we had a situation where the API
+               // server was down over a weekend but the containers
+               // kept running such that the log collection got
+               // trashed, so now we make it 2 weeks.  refs #20378
+               exp := time.Now().Add(time.Duration(24*14) * time.Hour)
                updates["trash_at"] = exp
                updates["delete_at"] = exp
        }
-       reqBody := arvadosclient.Dict{"collection": updates}
+       reqBody := arvadosclient.Dict{
+               "select":     []string{"uuid", "portable_data_hash"},
+               "collection": updates,
+       }
        var err2 error
        if runner.logUUID == "" {
                reqBody["ensure_unique_name"] = true
@@ -1560,7 +1578,10 @@ func (runner *ContainerRunner) UpdateContainerRunning(logId string) error {
        return runner.DispatcherArvClient.Update(
                "containers",
                runner.Container.UUID,
-               arvadosclient.Dict{"container": updates},
+               arvadosclient.Dict{
+                       "select":    []string{"uuid"},
+                       "container": updates,
+               },
                nil,
        )
 }
@@ -1598,7 +1619,10 @@ func (runner *ContainerRunner) UpdateContainerFinal() error {
                update["output"] = *runner.OutputPDH
        }
        update["cost"] = runner.calculateCost(time.Now())
-       return runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{"container": update}, nil)
+       return runner.DispatcherArvClient.Update("containers", runner.Container.UUID, arvadosclient.Dict{
+               "select":    []string{"uuid"},
+               "container": update,
+       }, nil)
 }
 
 // IsCancelled returns the value of Cancelled, with goroutine safety.
@@ -1989,7 +2013,9 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
                log.Printf("%s: %v", containerUUID, err)
                return 1
        }
-       api.Retries = 8
+       // arvadosclient now interprets Retries=10 to mean
+       // Timeout=10m, retrying with exponential backoff + jitter.
+       api.Retries = 10
 
        kc, err := keepclient.MakeKeepClient(api)
        if err != nil {
@@ -2077,6 +2103,7 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
                        ContainerUUID: containerUUID,
                        Target:        cr.executor,
                        Log:           cr.CrunchLog,
+                       LogCollection: cr.LogCollection,
                }
                if gwListen == "" {
                        // Direct connection won't work, so we use the
@@ -2087,7 +2114,10 @@ func (command) RunCommand(prog string, args []string, stdin io.Reader, stdout, s
                        cr.gateway.UpdateTunnelURL = func(url string) {
                                cr.gateway.Address = "tunnel " + url
                                cr.DispatcherArvClient.Update("containers", containerUUID,
-                                       arvadosclient.Dict{"container": arvadosclient.Dict{"gateway_address": cr.gateway.Address}}, nil)
+                                       arvadosclient.Dict{
+                                               "select":    []string{"uuid"},
+                                               "container": arvadosclient.Dict{"gateway_address": cr.gateway.Address},
+                                       }, nil)
                        }
                }
                err = cr.gateway.Start()
@@ -2165,7 +2195,9 @@ func hpcConfData(uuid string, configFile string, stderr io.Writer) ConfigData {
                fmt.Fprintf(stderr, "error setting up arvadosclient: %s\n", err)
                return conf
        }
-       arv.Retries = 8
+       // arvadosclient now interprets Retries=10 to mean
+       // Timeout=10m, retrying with exponential backoff + jitter.
+       arv.Retries = 10
        var ctr arvados.Container
        err = arv.Call("GET", "containers", uuid, "", arvadosclient.Dict{"select": []string{"runtime_constraints"}}, &ctr)
        if err != nil {
@@ -2454,6 +2486,7 @@ func (runner *ContainerRunner) handleSIGUSR2(sigchan chan os.Signal) {
        for range sigchan {
                runner.loadPrices()
                update := arvadosclient.Dict{
+                       "select": []string{"uuid"},
                        "container": arvadosclient.Dict{
                                "cost": runner.calculateCost(time.Now()),
                        },