diff --git a/cmd/run_with_timeout/run_with_timeout.go b/cmd/run_with_timeout/run_with_timeout.go
index f2caaabd9..deaa842e4 100644
--- a/cmd/run_with_timeout/run_with_timeout.go
+++ b/cmd/run_with_timeout/run_with_timeout.go
@@ -47,7 +47,7 @@ func main() {
 	flag.Parse()
 
 	if flag.NArg() < 1 {
-		fmt.Fprintln(os.Stderr, "command is required")
+		fmt.Fprintf(os.Stderr, "%s: error: command is required\n", os.Args[0])
 		usage()
 	}
 
@@ -55,9 +55,9 @@ func main() {
 		os.Stdin, os.Stdout, os.Stderr)
 	if err != nil {
 		if exitErr, ok := err.(*exec.ExitError); ok {
-			fmt.Fprintln(os.Stderr, "process exited with error:", exitErr.Error())
+			fmt.Fprintf(os.Stderr, "%s: process exited with error: %s\n", os.Args[0], exitErr.Error())
 		} else {
-			fmt.Fprintln(os.Stderr, "error:", err.Error())
+			fmt.Fprintf(os.Stderr, "%s: error: %s\n", os.Args[0], err.Error())
 		}
 		os.Exit(1)
 	}
@@ -115,6 +115,7 @@ func runWithTimeout(command string, args []string, timeout time.Duration, onTime
 	if timeout > 0 {
 		timeoutCh = time.After(timeout)
 	}
+	startTime := time.Now()
 
 	select {
 	case err := <-waitCh:
@@ -126,10 +127,12 @@ func runWithTimeout(command string, args []string, timeout time.Duration, onTime
 		// Continue below.
 	}
 
+	fmt.Fprintf(concurrentStderr, "%s: process timed out after %s\n", os.Args[0], time.Since(startTime))
 	// Process timed out before exiting.
 	defer cmd.Process.Signal(syscall.SIGKILL)
 
 	if onTimeoutCmdStr != "" {
+		fmt.Fprintf(concurrentStderr, "%s: running on_timeout command `%s`\n", os.Args[0], onTimeoutCmdStr)
 		onTimeoutCmd := exec.Command("sh", "-c", onTimeoutCmdStr)
 		onTimeoutCmd.Stdin, onTimeoutCmd.Stdout, onTimeoutCmd.Stderr = stdin, concurrentStdout, concurrentStderr
 		onTimeoutCmd.Env = append(os.Environ(), fmt.Sprintf("PID=%d", cmd.Process.Pid))
diff --git a/cmd/run_with_timeout/run_with_timeout_test.go b/cmd/run_with_timeout/run_with_timeout_test.go
index aebd33600..ed6ec11e7 100644
--- a/cmd/run_with_timeout/run_with_timeout_test.go
+++ b/cmd/run_with_timeout/run_with_timeout_test.go
@@ -17,6 +17,7 @@ package main
 import (
 	"bytes"
 	"io"
+	"regexp"
 	"testing"
 	"time"
 )
@@ -60,7 +61,8 @@ func Test_runWithTimeout(t *testing.T) {
 				args:    []string{"-c", "sleep 1 && echo foo"},
 				timeout: 1 * time.Millisecond,
 			},
-			wantErr: true,
+			wantStderr: ".*: process timed out after .*\n",
+			wantErr:    true,
 		},
 		{
 			name: "on_timeout command",
@@ -71,6 +73,7 @@ func Test_runWithTimeout(t *testing.T) {
 				onTimeoutCmd: "echo bar",
 			},
 			wantStdout: "bar\n",
+			wantStderr: ".*: process timed out after .*\n.*: running on_timeout command `echo bar`\n",
 			wantErr:    true,
 		},
 	}
@@ -86,7 +89,7 @@ func Test_runWithTimeout(t *testing.T) {
 			if gotStdout := stdout.String(); gotStdout != tt.wantStdout {
 				t.Errorf("runWithTimeout() gotStdout = %v, want %v", gotStdout, tt.wantStdout)
 			}
-			if gotStderr := stderr.String(); gotStderr != tt.wantStderr {
+			if gotStderr := stderr.String(); !regexp.MustCompile(tt.wantStderr).MatchString(gotStderr) {
 				t.Errorf("runWithTimeout() gotStderr = %v, want %v", gotStderr, tt.wantStderr)
 			}
 		})
diff --git a/java/config/config.go b/java/config/config.go
index 273084c85..30c6f91aa 100644
--- a/java/config/config.go
+++ b/java/config/config.go
@@ -69,8 +69,6 @@ func init() {
 	pctx.StaticVariable("JavacHeapSize", "2048M")
 	pctx.StaticVariable("JavacHeapFlags", "-J-Xmx${JavacHeapSize}")
 	pctx.StaticVariable("DexFlags", "-JXX:OnError='cat hs_err_pid%p.log' -JXX:CICompilerCount=6 -JXX:+UseDynamicNumberOfGCThreads")
-	// TODO(b/181095653): remove duplicated flags.
-	pctx.StaticVariable("DexJavaFlags", "-XX:OnError='cat hs_err_pid%p.log' -XX:CICompilerCount=6 -XX:+UseDynamicNumberOfGCThreads -Xmx2G")
 
 	pctx.StaticVariable("CommonJdkFlags", strings.Join([]string{
 		`-Xmaxerrs 9999999`,
diff --git a/java/dex.go b/java/dex.go
index 6bf0143b1..7898e9dff 100644
--- a/java/dex.go
+++ b/java/dex.go
@@ -84,11 +84,6 @@ func (d *dexer) effectiveOptimizeEnabled() bool {
 	return BoolDefault(d.dexProperties.Optimize.Enabled, d.dexProperties.Optimize.EnabledByDefault)
 }
 
-func init() {
-	pctx.HostBinToolVariable("runWithTimeoutCmd", "run_with_timeout")
-	pctx.SourcePathVariable("jstackCmd", "${config.JavaToolchain}/jstack")
-}
-
 var d8, d8RE = pctx.MultiCommandRemoteStaticRules("d8",
 	blueprint.RuleParams{
 		Command: `rm -rf "$outDir" && mkdir -p "$outDir" && ` +
@@ -122,10 +117,7 @@ var r8, r8RE = pctx.MultiCommandRemoteStaticRules("r8",
 		Command: `rm -rf "$outDir" && mkdir -p "$outDir" && ` +
 			`rm -f "$outDict" && rm -rf "${outUsageDir}" && ` +
 			`mkdir -p $$(dirname ${outUsage}) && ` +
-			// TODO(b/181095653): remove R8 timeout and go back to config.R8Cmd.
-			`${runWithTimeoutCmd} -timeout 30m -on_timeout '${jstackCmd} $$PID' -- ` +
-			`$r8Template${config.JavaCmd} ${config.DexJavaFlags} -cp ${config.R8Jar} ` +
-			`com.android.tools.r8.compatproguard.CompatProguard -injars $in --output $outDir ` +
+			`$r8Template${config.R8Cmd} ${config.DexFlags} -injars $in --output $outDir ` +
 			`--no-data-resources ` +
 			`-printmapping ${outDict} ` +
 			`-printusage ${outUsage} ` +
@@ -136,10 +128,9 @@ var r8, r8RE = pctx.MultiCommandRemoteStaticRules("r8",
 			`$zipTemplate${config.SoongZipCmd} $zipFlags -o $outDir/classes.dex.jar -C $outDir -f "$outDir/classes*.dex" && ` +
 			`${config.MergeZipsCmd} -D -stripFile "**/*.class" $out $outDir/classes.dex.jar $in`,
 		CommandDeps: []string{
-			"${config.R8Jar}",
+			"${config.R8Cmd}",
 			"${config.SoongZipCmd}",
 			"${config.MergeZipsCmd}",
-			"${runWithTimeoutCmd}",
 		},
 	}, map[string]*remoteexec.REParams{
 		"$r8Template": &remoteexec.REParams{