Merge branch '21666-provision-test-improvement'
[arvados.git] / lib / crunchrun / crunchrun_test.go
index 30f3ea4bb46ddedf7dbd814ad8b602d40bb95672..e51dfe629bc6b8922b31f6e28b46e00295e0f323 100644 (file)
@@ -12,8 +12,8 @@ import (
        "errors"
        "fmt"
        "io"
+       "io/fs"
        "io/ioutil"
-       "log"
        "math/rand"
        "net/http"
        "net/http/httptest"
@@ -39,8 +39,6 @@ import (
        "git.arvados.org/arvados.git/sdk/go/manifest"
 
        . "gopkg.in/check.v1"
-       git_client "gopkg.in/src-d/go-git.v4/plumbing/transport/client"
-       git_http "gopkg.in/src-d/go-git.v4/plumbing/transport/http"
 )
 
 // Gocheck boilerplate
@@ -113,6 +111,7 @@ func (s *TestSuite) SetUpTest(c *C) {
        err = ioutil.WriteFile(s.keepmount+"/by_id/"+fakeInputCollectionPDH+"/input.json", []byte(`{"input":true}`), 0644)
        c.Assert(err, IsNil)
        s.runner.ArvMountPoint = s.keepmount
+       os.Setenv("InstanceType", `{"ProviderType":"a1.2xlarge","Price":1.2}`)
 }
 
 type ArvTestClient struct {
@@ -121,7 +120,6 @@ type ArvTestClient struct {
        Content []arvadosclient.Dict
        arvados.Container
        secretMounts []byte
-       Logs         map[string]*bytes.Buffer
        sync.Mutex
        WasSetRunning bool
        callraw       bool
@@ -129,8 +127,8 @@ type ArvTestClient struct {
 
 type KeepTestClient struct {
        Called         bool
-       Content        []byte
        StorageClasses []string
+       blocks         sync.Map
 }
 
 type stubExecutor struct {
@@ -207,14 +205,7 @@ func (client *ArvTestClient) Create(resourceType string,
        client.Content = append(client.Content, parameters)
 
        if resourceType == "logs" {
-               et := parameters["log"].(arvadosclient.Dict)["event_type"].(string)
-               if client.Logs == nil {
-                       client.Logs = make(map[string]*bytes.Buffer)
-               }
-               if client.Logs[et] == nil {
-                       client.Logs[et] = &bytes.Buffer{}
-               }
-               client.Logs[et].Write([]byte(parameters["log"].(arvadosclient.Dict)["properties"].(map[string]string)["text"]))
+               panic("logs.create called")
        }
 
        if resourceType == "collections" && output != nil {
@@ -311,20 +302,14 @@ func (client *ArvTestClient) Update(resourceType string, uuid string, parameters
        } else if resourceType == "collections" && output != nil {
                mt := parameters["collection"].(arvadosclient.Dict)["manifest_text"].(string)
                output.(*arvados.Collection).UUID = uuid
-               output.(*arvados.Collection).PortableDataHash = fmt.Sprintf("%x", md5.Sum([]byte(mt)))
+               output.(*arvados.Collection).PortableDataHash = arvados.PortableDataHash(mt)
        }
        return nil
 }
 
 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),
+       "crunchLogUpdateSize":   float64(crunchLogUpdateSize),
+       "crunchLogUpdatePeriod": float64(crunchLogUpdatePeriod.Seconds()),
 }
 
 func (client *ArvTestClient) Discovery(key string) (interface{}, error) {
@@ -358,21 +343,30 @@ func (client *KeepTestClient) LocalLocator(locator string) (string, error) {
 }
 
 func (client *KeepTestClient) BlockWrite(_ context.Context, opts arvados.BlockWriteOptions) (arvados.BlockWriteResponse, error) {
-       client.Content = opts.Data
+       locator := fmt.Sprintf("%x+%d", md5.Sum(opts.Data), len(opts.Data))
+       client.blocks.Store(locator, append([]byte(nil), opts.Data...))
        return arvados.BlockWriteResponse{
-               Locator: fmt.Sprintf("%x+%d", md5.Sum(opts.Data), len(opts.Data)),
+               Locator: locator,
        }, nil
 }
 
-func (client *KeepTestClient) ReadAt(string, []byte, int) (int, error) {
-       return 0, errors.New("not implemented")
-}
-
-func (client *KeepTestClient) ClearBlockCache() {
+func (client *KeepTestClient) ReadAt(locator string, dst []byte, offset int) (int, error) {
+       loaded, ok := client.blocks.Load(locator)
+       if !ok {
+               return 0, os.ErrNotExist
+       }
+       data := loaded.([]byte)
+       if offset >= len(data) {
+               return 0, io.EOF
+       }
+       return copy(dst, data[offset:]), nil
 }
 
 func (client *KeepTestClient) Close() {
-       client.Content = nil
+       client.blocks.Range(func(locator, value interface{}) bool {
+               client.blocks.Delete(locator)
+               return true
+       })
 }
 
 func (client *KeepTestClient) SetStorageClasses(sc []string) {
@@ -594,33 +588,10 @@ func (ErrorReader) Seek(int64, int) (int64, error) {
        return 0, errors.New("ErrorReader")
 }
 
-func (KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
+func (*KeepReadErrorTestClient) ManifestFileReader(m manifest.Manifest, filename string) (arvados.File, error) {
        return ErrorReader{}, nil
 }
 
-type ClosableBuffer struct {
-       bytes.Buffer
-}
-
-func (*ClosableBuffer) Close() error {
-       return nil
-}
-
-type TestLogs struct {
-       Stdout ClosableBuffer
-       Stderr ClosableBuffer
-}
-
-func (tl *TestLogs) NewTestLoggingWriter(logstr string) (io.WriteCloser, error) {
-       if logstr == "stdout" {
-               return &tl.Stdout, nil
-       }
-       if logstr == "stderr" {
-               return &tl.Stderr, nil
-       }
-       return nil, errors.New("???")
-}
-
 func dockerLog(fd byte, msg string) []byte {
        by := []byte(msg)
        header := make([]byte, 8+len(by))
@@ -636,8 +607,6 @@ func (s *TestSuite) TestRunContainer(c *C) {
                return 0
        }
 
-       var logs TestLogs
-       s.runner.NewLogWriter = logs.NewTestLoggingWriter
        s.runner.Container.ContainerImage = arvadostest.DockerImage112PDH
        s.runner.Container.Command = []string{"./hw"}
        s.runner.Container.OutputStorageClasses = []string{"default"}
@@ -654,8 +623,8 @@ func (s *TestSuite) TestRunContainer(c *C) {
        err = s.runner.WaitFinish()
        c.Assert(err, IsNil)
 
-       c.Check(logs.Stdout.String(), Matches, ".*Hello world\n")
-       c.Check(logs.Stderr.String(), Equals, "")
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, `Hello world\n`)
+       c.Check(logFileContent(c, s.runner, "stderr.txt"), Matches, ``)
 }
 
 func (s *TestSuite) TestCommitLogs(c *C) {
@@ -664,7 +633,9 @@ func (s *TestSuite) TestCommitLogs(c *C) {
        defer kc.Close()
        cr, err := NewContainerRunner(s.client, api, kc, "zzzzz-zzzzz-zzzzzzzzzzzzzzz")
        c.Assert(err, IsNil)
-       cr.CrunchLog.Timestamper = (&TestTimestamper{}).Timestamp
+       f, err := cr.openLogFile("crunch-run")
+       c.Assert(err, IsNil)
+       cr.CrunchLog = newLogWriter(newTestTimestamper(f))
 
        cr.CrunchLog.Print("Hello world!")
        cr.CrunchLog.Print("Goodbye")
@@ -673,10 +644,10 @@ func (s *TestSuite) TestCommitLogs(c *C) {
        err = cr.CommitLogs()
        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(api.Calls, Equals, 1)
+       c.Check(api.Content[0]["ensure_unique_name"], Equals, true)
+       c.Check(api.Content[0]["collection"].(arvadosclient.Dict)["name"], Equals, "logs for zzzzz-zzzzz-zzzzzzzzzzzzzzz")
+       c.Check(api.Content[0]["collection"].(arvadosclient.Dict)["manifest_text"], Equals, ". 744b2e4553123b02fa7b452ec5c18993+123 0:123:crunch-run.txt\n")
        c.Check(*cr.LogsPDH, Equals, "63da7bdacf08c40f604daad80c261e9a+60")
 }
 
@@ -797,10 +768,7 @@ func (s *TestSuite) fullRunHelper(c *C, record string, extraMounts []string, fn
        }
 
        if err != nil {
-               for k, v := range s.api.Logs {
-                       c.Log(k)
-                       c.Log(v.String())
-               }
+               dumpAllLogFiles(c, s.runner)
        }
 
        return s.api, s.runner, realTemp
@@ -835,7 +803,7 @@ func (s *TestSuite) TestFullRunHello(c *C) {
 
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
-       c.Check(s.api.Logs["stdout"].String(), Matches, ".*hello world\n")
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, "hello world\n")
        c.Check(s.testDispatcherKeepClient.StorageClasses, DeepEquals, []string{"default"})
        c.Check(s.testContainerKeepClient.StorageClasses, DeepEquals, []string{"default"})
 }
@@ -908,6 +876,48 @@ func (s *TestSuite) testSpotInterruptionNotice(c *C, failureRate float64) {
        spotInterruptionCheckInterval = time.Second / 8
        ec2MetadataBaseURL = stub.URL
 
+       checkedLogs := false
+       checkLogs := func() {
+               checkedLogs = true
+               c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*Checking for spot interruptions every 125ms using instance metadata at http://.*`)
+               c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*Error checking spot interruptions: 503 Service Unavailable.*`)
+               if failureRate == 1 {
+                       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*Giving up on checking spot interruptions after too many consecutive failures.*`)
+                       return
+               }
+               text := `Cloud provider scheduled instance stop at ` + stoptime.Load().(time.Time).Format(time.RFC3339)
+               c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*`+text+`.*`)
+               c.Check(s.api.CalledWith("container.runtime_status.warning", "preemption notice"), NotNil)
+               c.Check(s.api.CalledWith("container.runtime_status.warningDetail", text), NotNil)
+               c.Check(s.api.CalledWith("container.runtime_status.preemptionNotice", text), NotNil)
+
+               // Check that the log collection was saved, and the
+               // container record updated with the new PDH,
+               // immediately after the preemption notice was
+               // received -- i.e., while the container is still
+               // running.
+               lastpdh := ""
+               saved := make(map[string]string) // pdh => manifest_text
+               for _, call := range s.api.Content {
+                       if ctr, ok := call["container"].(arvadosclient.Dict); ok {
+                               if pdh, ok := ctr["log"].(string); ok {
+                                       lastpdh = pdh
+                               }
+                       }
+                       if coll, ok := call["collection"].(arvadosclient.Dict); ok {
+                               mt, _ := coll["manifest_text"].(string)
+                               if strings.Contains(mt, ":crunch-run.txt") {
+                                       saved[arvados.PortableDataHash(mt)] = mt
+                               }
+                       }
+               }
+               logfs, err := (&arvados.Collection{ManifestText: saved[lastpdh]}).FileSystem(s.runner.dispatcherClient, s.runner.DispatcherKeepClient)
+               c.Assert(err, IsNil)
+               log, err := fs.ReadFile(arvados.FS(logfs), "crunch-run.txt")
+               c.Check(err, IsNil)
+               c.Check(string(log), Matches, `(?ms).*\Q`+text+`\E.*`)
+       }
+
        go s.runner.checkSpotInterruptionNotices()
        s.fullRunHelper(c, `{
     "command": ["sleep", "3"],
@@ -924,19 +934,10 @@ func (s *TestSuite) testSpotInterruptionNotice(c *C, failureRate float64) {
                stoptime.Store(time.Now().Add(time.Minute).UTC())
                token = "different-fake-ec2-metadata-token"
                time.Sleep(time.Second)
+               checkLogs()
                return 0
        })
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Checking for spot interruptions every 125ms using instance metadata at http://.*`)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Error checking spot interruptions: 503 Service Unavailable.*`)
-       if failureRate == 1 {
-               c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Giving up on checking spot interruptions after too many consecutive failures.*`)
-       } else {
-               text := `Cloud provider scheduled instance stop at ` + stoptime.Load().(time.Time).Format(time.RFC3339)
-               c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*`+text+`.*`)
-               c.Check(s.api.CalledWith("container.runtime_status.warning", "preemption notice"), NotNil)
-               c.Check(s.api.CalledWith("container.runtime_status.warningDetail", text), NotNil)
-               c.Check(s.api.CalledWith("container.runtime_status.preemptionNotice", text), NotNil)
-       }
+       c.Check(checkedLogs, Equals, true)
 }
 
 func (s *TestSuite) TestRunTimeExceeded(c *C) {
@@ -957,7 +958,7 @@ func (s *TestSuite) TestRunTimeExceeded(c *C) {
        })
 
        c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*maximum run time exceeded.*")
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, "(?ms).*maximum run time exceeded.*")
 }
 
 func (s *TestSuite) TestContainerWaitFails(c *C) {
@@ -975,7 +976,7 @@ func (s *TestSuite) TestContainerWaitFails(c *C) {
        })
 
        c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Container is not running.*")
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, "(?ms).*Container is not running.*")
 }
 
 func (s *TestSuite) TestCrunchstat(c *C) {
@@ -998,17 +999,15 @@ func (s *TestSuite) TestCrunchstat(c *C) {
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
 
-       c.Assert(s.api.Logs["crunchstat"], NotNil)
-       c.Check(s.api.Logs["crunchstat"].String(), Matches, `(?ms).*mem \d+ swap \d+ pgmajfault \d+ rss.*`)
+       c.Check(logFileContent(c, s.runner, "crunchstat.txt"), Matches, `(?ms).*mem \d+ swap \d+ pgmajfault \d+ rss.*`)
 
        // Check that we called (*crunchstat.Reporter)Stop().
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Maximum crunch-run memory rss usage was \d+ bytes\n.*`)
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*Maximum crunch-run memory rss usage was \d+ bytes\n.*`)
 }
 
 func (s *TestSuite) TestNodeInfoLog(c *C) {
-       os.Setenv("SLURMD_NODENAME", "compute2")
        s.fullRunHelper(c, `{
-               "command": ["sleep", "1"],
+               "command": ["true"],
                "container_image": "`+arvadostest.DockerImage112PDH+`",
                "cwd": ".",
                "environment": {},
@@ -1018,26 +1017,22 @@ func (s *TestSuite) TestNodeInfoLog(c *C) {
                "runtime_constraints": {},
                "state": "Locked"
        }`, nil, func() int {
-               time.Sleep(time.Second)
                return 0
        })
 
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
 
-       c.Assert(s.api.Logs["node"], NotNil)
-       json := s.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":.*`)
+       json := logFileContent(c, s.runner, "node.json")
+       c.Check(json, Matches, `(?ms).*"ProviderType": *"a1\.2xlarge".*`)
+       c.Check(json, Matches, `(?ms).*"Price": *1\.2.*`)
 
-       c.Assert(s.api.Logs["node-info"], NotNil)
-       json = s.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.*`)
+       nodeinfo := logFileContent(c, s.runner, "node-info.txt")
+       c.Check(nodeinfo, Matches, `(?ms).*Host Information.*`)
+       c.Check(nodeinfo, Matches, `(?ms).*CPU Information.*`)
+       c.Check(nodeinfo, Matches, `(?ms).*Memory Information.*`)
+       c.Check(nodeinfo, Matches, `(?ms).*Disk Space.*`)
+       c.Check(nodeinfo, Matches, `(?ms).*Disk INodes.*`)
 }
 
 func (s *TestSuite) TestLogVersionAndRuntime(c *C) {
@@ -1055,11 +1050,10 @@ func (s *TestSuite) TestLogVersionAndRuntime(c *C) {
                return 0
        })
 
-       c.Assert(s.api.Logs["crunch-run"], NotNil)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*crunch-run \S+ \(go\S+\) start.*`)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*crunch-run process has uid=\d+\(.+\) gid=\d+\(.+\) groups=\d+\(.+\)(,\d+\(.+\))*\n.*`)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Executing container: zzzzz-zzzzz-zzzzzzzzzzzzzzz.*`)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Using container runtime: stub.*`)
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*crunch-run \S+ \(go\S+\) start.*`)
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*crunch-run process has uid=\d+\(.+\) gid=\d+\(.+\) groups=\d+\(.+\)(,\d+\(.+\))*\n.*`)
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*Executing container: zzzzz-zzzzz-zzzzzzzzzzzzzzz.*`)
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*Using container runtime: stub.*`)
 }
 
 func (s *TestSuite) testLogRSSThresholds(c *C, ram int64, expected []int, notExpected int) {
@@ -1075,8 +1069,9 @@ func (s *TestSuite) testLogRSSThresholds(c *C, ram int64, expected []int, notExp
                "runtime_constraints": {"ram": `+fmt.Sprintf("%d", ram)+`},
                "state": "Locked"
        }`, nil, func() int { return 0 })
-       c.Logf("=== crunchstat logs\n%s\n", s.api.Logs["crunchstat"].String())
-       logs := s.api.Logs["crunch-run"].String()
+       logs := logFileContent(c, s.runner, "crunch-run.txt")
+       c.Log("=== crunchstat logs")
+       c.Log(logs)
        pattern := logLineStart + `Container using over %d%% of memory \(rss %d/%d bytes\)`
        var threshold int
        for _, threshold = range expected {
@@ -1114,7 +1109,7 @@ func (s *TestSuite) TestLogMaximaAfterRun(c *C) {
         "runtime_constraints": {"ram": `+fmt.Sprintf("%d", s.debian12MemoryCurrent*10)+`},
         "state": "Locked"
     }`, nil, func() int { return 0 })
-       logs := s.api.Logs["crunch-run"].String()
+       logs := logFileContent(c, s.runner, "crunch-run.txt")
        for _, expected := range []string{
                `Maximum disk usage was \d+%, \d+/\d+ bytes`,
                fmt.Sprintf(`Maximum container memory swap usage was %d bytes`, s.debian12SwapCurrent),
@@ -1182,8 +1177,7 @@ func (s *TestSuite) TestContainerRecordLog(c *C) {
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
 
-       c.Assert(s.api.Logs["container"], NotNil)
-       c.Check(s.api.Logs["container"].String(), Matches, `(?ms).*container_image.*`)
+       c.Check(logFileContent(c, s.runner, "container.json"), Matches, `(?ms).*container_image.*`)
 }
 
 func (s *TestSuite) TestFullRunStderr(c *C) {
@@ -1208,8 +1202,8 @@ func (s *TestSuite) TestFullRunStderr(c *C) {
        c.Check(final["container"].(arvadosclient.Dict)["exit_code"], Equals, 1)
        c.Check(final["container"].(arvadosclient.Dict)["log"], NotNil)
 
-       c.Check(s.api.Logs["stdout"].String(), Matches, ".*hello\n")
-       c.Check(s.api.Logs["stderr"].String(), Matches, ".*world\n")
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, ".*hello\n")
+       c.Check(logFileContent(c, s.runner, "stderr.txt"), Matches, ".*world\n")
 }
 
 func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
@@ -1230,8 +1224,7 @@ func (s *TestSuite) TestFullRunDefaultCwd(c *C) {
 
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
-       c.Log(s.api.Logs["stdout"])
-       c.Check(s.api.Logs["stdout"].String(), Matches, `.*workdir=""\n`)
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, `.*workdir=""`)
 }
 
 func (s *TestSuite) TestFullRunSetCwd(c *C) {
@@ -1252,7 +1245,7 @@ func (s *TestSuite) TestFullRunSetCwd(c *C) {
 
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
-       c.Check(s.api.Logs["stdout"].String(), Matches, ".*/bin\n")
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, ".*/bin\n")
 }
 
 func (s *TestSuite) TestFullRunSetOutputStorageClasses(c *C) {
@@ -1274,7 +1267,7 @@ func (s *TestSuite) TestFullRunSetOutputStorageClasses(c *C) {
 
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
-       c.Check(s.api.Logs["stdout"].String(), Matches, ".*/bin\n")
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, ".*/bin\n")
        c.Check(s.testDispatcherKeepClient.StorageClasses, DeepEquals, []string{"foo", "bar"})
        c.Check(s.testContainerKeepClient.StorageClasses, DeepEquals, []string{"foo", "bar"})
 }
@@ -1371,14 +1364,11 @@ func (s *TestSuite) testStopContainer(c *C) {
        case err = <-done:
                c.Check(err, IsNil)
        }
-       for k, v := range s.api.Logs {
-               c.Log(k)
-               c.Log(v.String(), "\n")
-       }
+       dumpAllLogFiles(c, s.runner)
 
        c.Check(s.api.CalledWith("container.log", nil), NotNil)
        c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
-       c.Check(s.api.Logs["stdout"].String(), Matches, "(?ms).*foo\n$")
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, "(?ms).*foo\n$")
 }
 
 func (s *TestSuite) TestFullRunSetEnv(c *C) {
@@ -1399,7 +1389,7 @@ func (s *TestSuite) TestFullRunSetEnv(c *C) {
 
        c.Check(s.api.CalledWith("container.exit_code", 0), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
-       c.Check(s.api.Logs["stdout"].String(), Matches, `.*map\[FROBIZ:bilbo\]\n`)
+       c.Check(logFileContent(c, s.runner, "stdout.txt"), Matches, `.*map\[FROBIZ:bilbo\]`)
 }
 
 type ArvMountCmdLine struct {
@@ -1413,11 +1403,11 @@ func (am *ArvMountCmdLine) ArvMountTest(c []string, token string) (*exec.Cmd, er
        return nil, nil
 }
 
-func stubCert(temp string) string {
+func stubCert(c *C, temp string) string {
        path := temp + "/ca-certificates.crt"
-       crt, _ := os.Create(path)
-       crt.Close()
-       arvadosclient.CertFiles = []string{path}
+       err := os.WriteFile(path, []byte{}, 0666)
+       c.Assert(err, IsNil)
+       os.Setenv("SSL_CERT_FILE", path)
        return path
 }
 
@@ -1432,7 +1422,7 @@ func (s *TestSuite) TestSetupMounts(c *C) {
 
        realTemp := c.MkDir()
        certTemp := c.MkDir()
-       stubCertPath := stubCert(certTemp)
+       stubCertPath := stubCert(c, certTemp)
        cr.parentTemp = realTemp
 
        i := 0
@@ -1743,54 +1733,6 @@ func (s *TestSuite) TestSetupMounts(c *C) {
                cr.CleanupDirs()
                checkEmpty()
        }
-
-       // git_tree mounts
-       {
-               i = 0
-               cr.ArvMountPoint = ""
-               git_client.InstallProtocol("https", git_http.NewClient(arvados.InsecureHTTPClient))
-               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.Container.OutputPath = "/tmp"
-
-               bindmounts, err := cr.SetupMounts()
-               c.Check(err, IsNil)
-
-               for path, mount := range bindmounts {
-                       c.Check(mount.ReadOnly, Equals, !cr.Container.Mounts[path].Writable, Commentf("%s %#v", path, mount))
-               }
-
-               data, err := ioutil.ReadFile(bindmounts["/tip"].HostPath + "/dir1/dir2/file with mode 0644")
-               c.Check(err, IsNil)
-               c.Check(string(data), Equals, "\000\001\002\003")
-               _, err = ioutil.ReadFile(bindmounts["/tip"].HostPath + "/file only on testbranch")
-               c.Check(err, FitsTypeOf, &os.PathError{})
-               c.Check(os.IsNotExist(err), Equals, true)
-
-               data, err = ioutil.ReadFile(bindmounts["/non-tip"].HostPath + "/dir1/dir2/file with mode 0644")
-               c.Check(err, IsNil)
-               c.Check(string(data), Equals, "\000\001\002\003")
-               data, err = ioutil.ReadFile(bindmounts["/non-tip"].HostPath + "/file only on testbranch")
-               c.Check(err, IsNil)
-               c.Check(string(data), Equals, "testfile\n")
-
-               cr.CleanupDirs()
-               checkEmpty()
-       }
 }
 
 func (s *TestSuite) TestStdout(c *C) {
@@ -1872,7 +1814,7 @@ func (s *TestSuite) TestFullRunWithAPI(c *C) {
        })
        c.Check(s.api.CalledWith("container.exit_code", 3), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*status code 3\n.*`)
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*status code 3\n.*`)
 }
 
 func (s *TestSuite) TestFullRunSetOutput(c *C) {
@@ -1927,7 +1869,7 @@ func (s *TestSuite) TestArvMountRuntimeStatusWarning(c *C) {
        c.Check(s.api.CalledWith("container.runtime_status.warning", "arv-mount: Keep write error"), NotNil)
        c.Check(s.api.CalledWith("container.runtime_status.warningDetail", "Test: Keep write error: I am a teapot"), NotNil)
        c.Check(s.api.CalledWith("container.state", "Complete"), NotNil)
-       c.Check(s.api.Logs["crunch-run"].String(), Matches, `(?ms).*Container exited with status code 137 \(signal 9, SIGKILL\).*`)
+       c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, `(?ms).*Container exited with status code 137 \(signal 9, SIGKILL\).*`)
 }
 
 func (s *TestSuite) TestStdoutWithExcludeFromOutputMountPointUnderOutputDir(c *C) {
@@ -2237,13 +2179,14 @@ func (s *TestSuite) TestFullBrokenDocker(c *C) {
     "state": "Locked"
 }`, nil, func() int { return 0 })
                c.Check(s.api.CalledWith("container.state", nextState), NotNil)
-               c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*unable to run containers.*")
+               logs := logFileContent(c, s.runner, "crunch-run.txt")
+               c.Check(logs, Matches, "(?ms).*unable to run containers.*")
                if s.runner.brokenNodeHook != "" {
-                       c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Running broken node hook.*")
-                       c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*killme.*")
-                       c.Check(s.api.Logs["crunch-run"].String(), Not(Matches), "(?ms).*Writing /var/lock/crunch-run-broken to mark node as broken.*")
+                       c.Check(logs, Matches, "(?ms).*Running broken node hook.*")
+                       c.Check(logs, Matches, "(?ms).*killme.*")
+                       c.Check(logs, Not(Matches), "(?ms).*Writing /var/lock/crunch-run-broken to mark node as broken.*")
                } else {
-                       c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Writing /var/lock/crunch-run-broken to mark node as broken.*")
+                       c.Check(logs, Matches, "(?ms).*Writing /var/lock/crunch-run-broken to mark node as broken.*")
                }
        }
 }
@@ -2268,7 +2211,7 @@ func (s *TestSuite) TestBadCommand(c *C) {
     "state": "Locked"
 }`, nil, func() int { return 0 })
                c.Check(s.api.CalledWith("container.state", "Cancelled"), NotNil)
-               c.Check(s.api.Logs["crunch-run"].String(), Matches, "(?ms).*Possible causes:.*is missing.*")
+               c.Check(logFileContent(c, s.runner, "crunch-run.txt"), Matches, "(?ms).*Possible causes:.*is missing.*")
        }
 }
 
@@ -2378,7 +2321,7 @@ func (s *TestSuite) TestCalculateCost(c *C) {
        cr := s.runner
        cr.costStartTime = now.Add(-time.Hour)
        var logbuf bytes.Buffer
-       cr.CrunchLog.Immediate = log.New(&logbuf, "", 0)
+       cr.CrunchLog = newLogWriter(&logbuf)
 
        // if there's no InstanceType env var, cost is calculated as 0
        os.Unsetenv("InstanceType")
@@ -2389,7 +2332,6 @@ func (s *TestSuite) TestCalculateCost(c *C) {
        // hasn't found any data), cost is calculated based on
        // InstanceType env var
        os.Setenv("InstanceType", `{"Price":1.2}`)
-       defer os.Unsetenv("InstanceType")
        cost = cr.calculateCost(now)
        c.Check(cost, Equals, 1.2)
 
@@ -2435,7 +2377,6 @@ func (s *TestSuite) TestSIGUSR2CostUpdate(c *C) {
        c.Assert(err, IsNil)
 
        os.Setenv("InstanceType", `{"Price":2.2}`)
-       defer os.Unsetenv("InstanceType")
        defer func(s string) { lockdir = s }(lockdir)
        lockdir = c.MkDir()
 
@@ -2506,3 +2447,20 @@ type FakeProcess struct {
 func (fp FakeProcess) CmdlineSlice() ([]string, error) {
        return fp.cmdLine, nil
 }
+
+func logFileContent(c *C, cr *ContainerRunner, fnm string) string {
+       buf, err := fs.ReadFile(arvados.FS(cr.LogCollection), fnm)
+       c.Assert(err, IsNil)
+       return string(buf)
+}
+
+func dumpAllLogFiles(c *C, cr *ContainerRunner) {
+       d, err := cr.LogCollection.OpenFile("/", os.O_RDONLY, 0)
+       c.Assert(err, IsNil)
+       fis, err := d.Readdir(-1)
+       c.Assert(err, IsNil)
+       for _, fi := range fis {
+               c.Logf("=== %s", fi.Name())
+               c.Log(logFileContent(c, cr, fi.Name()))
+       }
+}