diff --git a/internal/modifier/cdi.go b/internal/modifier/cdi.go
index c7cd8c945..abdd88424 100644
--- a/internal/modifier/cdi.go
+++ b/internal/modifier/cdi.go
@@ -166,38 +166,24 @@ func filterAutomaticDevices(devices []string) []string {
 func newAutomaticCDISpecModifier(logger logger.Interface, cfg *config.Config, devices []string) (oci.SpecModifier, error) {
 	logger.Debugf("Generating in-memory CDI specs for devices %v", devices)
 
-	perModeIdentifiers := make(map[string][]string)
-	perModeDeviceClass := map[string]string{"auto": automaticDeviceClass}
-	uniqueModes := []string{"auto"}
-	seen := make(map[string]bool)
-	for _, device := range devices {
-		mode, id := getModeIdentifier(device)
-		logger.Debugf("Mapped %v to %v: %v", device, mode, id)
-		if !seen[mode] {
-			uniqueModes = append(uniqueModes, mode)
-			seen[mode] = true
-		}
-		if id != "" {
-			perModeIdentifiers[mode] = append(perModeIdentifiers[mode], id)
-		}
-	}
+	cdiModeIdentifiers := cdiModeIdentfiersFromDevices(devices...)
 
-	logger.Debugf("Per-mode identifiers: %v", perModeIdentifiers)
+	logger.Debugf("Per-mode identifiers: %v", cdiModeIdentifiers)
 	var modifiers oci.SpecModifiers
-	for _, mode := range uniqueModes {
+	for _, mode := range cdiModeIdentifiers.modes {
 		cdilib, err := nvcdi.New(
 			nvcdi.WithLogger(logger),
 			nvcdi.WithNVIDIACDIHookPath(cfg.NVIDIACTKConfig.Path),
 			nvcdi.WithDriverRoot(cfg.NVIDIAContainerCLIConfig.Root),
 			nvcdi.WithVendor(automaticDeviceVendor),
-			nvcdi.WithClass(perModeDeviceClass[mode]),
+			nvcdi.WithClass(cdiModeIdentifiers.deviceClassByMode[mode]),
 			nvcdi.WithMode(mode),
 		)
 		if err != nil {
 			return nil, fmt.Errorf("failed to construct CDI library for mode %q: %w", mode, err)
 		}
 
-		spec, err := cdilib.GetSpec(perModeIdentifiers[mode]...)
+		spec, err := cdilib.GetSpec(cdiModeIdentifiers.idsByMode[mode]...)
 		if err != nil {
 			return nil, fmt.Errorf("failed to generate CDI spec for mode %q: %w", mode, err)
 		}
@@ -216,6 +202,35 @@ func newAutomaticCDISpecModifier(logger logger.Interface, cfg *config.Config, de
 	return modifiers, nil
 }
 
+type cdiModeIdentifiers struct {
+	modes             []string
+	idsByMode         map[string][]string
+	deviceClassByMode map[string]string
+}
+
+func cdiModeIdentfiersFromDevices(devices ...string) *cdiModeIdentifiers {
+	perModeIdentifiers := make(map[string][]string)
+	perModeDeviceClass := map[string]string{"auto": automaticDeviceClass}
+	var uniqueModes []string
+	seen := make(map[string]bool)
+	for _, device := range devices {
+		mode, id := getModeIdentifier(device)
+		if !seen[mode] {
+			uniqueModes = append(uniqueModes, mode)
+			seen[mode] = true
+		}
+		if id != "" {
+			perModeIdentifiers[mode] = append(perModeIdentifiers[mode], id)
+		}
+	}
+
+	return &cdiModeIdentifiers{
+		modes:             uniqueModes,
+		idsByMode:         perModeIdentifiers,
+		deviceClassByMode: perModeDeviceClass,
+	}
+}
+
 func getModeIdentifier(device string) (string, string) {
 	if !strings.HasPrefix(device, "mode=") {
 		return "auto", strings.TrimPrefix(device, automaticDevicePrefix)
diff --git a/internal/modifier/cdi_test.go b/internal/modifier/cdi_test.go
index 0163e4ce0..65d2ca37e 100644
--- a/internal/modifier/cdi_test.go
+++ b/internal/modifier/cdi_test.go
@@ -170,3 +170,86 @@ func TestDeviceRequests(t *testing.T) {
 		})
 	}
 }
+
+func Test_cdiModeIdentfiersFromDevices(t *testing.T) {
+	testCases := []struct {
+		description string
+		devices     []string
+		expected    *cdiModeIdentifiers
+	}{
+		{
+			description: "empty device list",
+			devices:     []string{},
+			expected: &cdiModeIdentifiers{
+				modes:             nil,
+				idsByMode:         map[string][]string{},
+				deviceClassByMode: map[string]string{"auto": "gpu"},
+			},
+		},
+		{
+			description: "single automatic device",
+			devices:     []string{"0"},
+			expected: &cdiModeIdentifiers{
+				modes:             []string{"auto"},
+				idsByMode:         map[string][]string{"auto": {"0"}},
+				deviceClassByMode: map[string]string{"auto": "gpu"},
+			},
+		},
+		{
+			description: "multiple automatic devices",
+			devices:     []string{"0", "1"},
+			expected: &cdiModeIdentifiers{
+				modes:             []string{"auto"},
+				idsByMode:         map[string][]string{"auto": {"0", "1"}},
+				deviceClassByMode: map[string]string{"auto": "gpu"},
+			},
+		},
+		{
+			description: "device with explicit mode",
+			devices:     []string{"mode=gds,id=foo"},
+			expected: &cdiModeIdentifiers{
+				modes:             []string{"gds"},
+				idsByMode:         map[string][]string{"gds": {"foo"}},
+				deviceClassByMode: map[string]string{"auto": "gpu"},
+			},
+		},
+		{
+			description: "mixed auto and explicit",
+			devices:     []string{"0", "mode=gds,id=foo", "mode=gdrcopy,id=bar"},
+			expected: &cdiModeIdentifiers{
+				modes: []string{"auto", "gds", "gdrcopy"},
+				idsByMode: map[string][]string{
+					"auto":    {"0"},
+					"gds":     {"foo"},
+					"gdrcopy": {"bar"},
+				},
+				deviceClassByMode: map[string]string{"auto": "gpu"},
+			},
+		},
+		{
+			description: "device with only mode, no id",
+			devices:     []string{"mode=nvswitch"},
+			expected: &cdiModeIdentifiers{
+				modes:             []string{"nvswitch"},
+				idsByMode:         map[string][]string{},
+				deviceClassByMode: map[string]string{"auto": "gpu"},
+			},
+		},
+		{
+			description: "duplicate modes",
+			devices:     []string{"mode=gds,id=x", "mode=gds,id=y", "mode=gds"},
+			expected: &cdiModeIdentifiers{
+				modes:             []string{"gds"},
+				idsByMode:         map[string][]string{"gds": {"x", "y"}},
+				deviceClassByMode: map[string]string{"auto": "gpu"},
+			},
+		},
+	}
+
+	for _, tc := range testCases {
+		t.Run(tc.description, func(t *testing.T) {
+			result := cdiModeIdentfiersFromDevices(tc.devices...)
+			require.EqualValues(t, tc.expected, result)
+		})
+	}
+}
diff --git a/tests/e2e/nvidia-container-toolkit_test.go b/tests/e2e/nvidia-container-toolkit_test.go
index b2487c436..80ff3663c 100644
--- a/tests/e2e/nvidia-container-toolkit_test.go
+++ b/tests/e2e/nvidia-container-toolkit_test.go
@@ -198,6 +198,16 @@ var _ = Describe("docker", Ordered, ContinueOnFailure, func() {
 			Expect(err).ToNot(HaveOccurred())
 			Expect(ldconfigOut).To(ContainSubstring("/usr/local/cuda-12.9/compat/"))
 		})
+
+		It("should create a single ld.so.conf.d config file", func(ctx context.Context) {
+			lsout, _, err := runner.Run("docker run --rm -i -e NVIDIA_DISABLE_REQUIRE=true --runtime=nvidia -e NVIDIA_VISIBLE_DEVICES=runtime.nvidia.com/gpu=all nvcr.io/nvidia/cuda:12.9.0-base-ubi8 bash -c \"ls -l /etc/ld.so.conf.d/00-compat-*.conf\"")
+			Expect(err).ToNot(HaveOccurred())
+			Expect(lsout).To(WithTransform(
+				func(s string) []string {
+					return strings.Split(strings.TrimSpace(s), "\n")
+				}, HaveLen(1),
+			))
+		})
 	})
 
 	When("Disabling device node creation", Ordered, func() {
diff --git a/third_party/libnvidia-container b/third_party/libnvidia-container
index 0964f8171..889a3bb54 160000
--- a/third_party/libnvidia-container
+++ b/third_party/libnvidia-container
@@ -1 +1 @@
-Subproject commit 0964f81717e96ac903e39700908677dcdf72ed5f
+Subproject commit 889a3bb5408c195ed7897ba2cb8341c7d249672f