diff --git a/src/runtime/src/rtio_clocking.rs b/src/runtime/src/rtio_clocking.rs
index 20e2c3d..db4c2e3 100644
--- a/src/runtime/src/rtio_clocking.rs
+++ b/src/runtime/src/rtio_clocking.rs
@@ -35,6 +35,7 @@ fn get_rtio_clock_cfg(cfg: &Config) -> RtioClock {
         }
     }
     else {
+        info!("error reading configuration. Using default internal 125MHz clock");
         RtioClock::Int_125
     }
 }
@@ -105,16 +106,22 @@ fn setup_si5324(timer: &mut GlobalTimer, clk: RtioClock) {
             crystal_ref: true
         });
     }
+    let si5324_ref_input = si5324::Input::Ckin2;
     si5324::setup(unsafe { (&mut i2c::I2C_BUS).as_mut().unwrap() },
-        &si5324_settings.unwrap(), si5324::Input::Ckin2, timer).expect("cannot initialize Si5324");
+        &si5324_settings.unwrap(), si5324_ref_input, timer).expect("cannot initialize Si5324");
 }
 
 pub fn init(timer: &mut GlobalTimer, cfg: &Config) {
 
     let clk = get_rtio_clock_cfg(cfg);
     #[cfg(has_si5324)]
-    setup_si5324(timer, clk);
-
+    {
+        let si5324_ext_input = si5324::Input::Ckin2;
+        match clk {
+            RtioClock::Ext0_Bypass => si5324::bypass(si5324_ext_input).expect("cannot bypass Si5324"),
+            _ => setup_si5324(timer, clk),
+        }
+    }
     #[cfg(has_drtio)]
     init_drtio(timer);