OK, we've been fighting this for a while and we think we narrowed it down to 
being a problem with the E320 (NOTE: we are running the E320 in network mode, 
not embedded)

Some background:
1) external reference input is from an octo clock (so it the 1pps input) on 
many different ports
        a) also tried to use a  Symmetricom box for external reference and had 
the same problems

3) the same code we are testing with works when using an x310 instead of an 
e320, with inputs from the same octoclock

4) the code basically does this:
        a) sets the reference source to external
        b) checks to see if the reference is locked (and it keeps doing this 
until we get a "locked" response, using the uhd commands to do this)

5) for the e320, the locked status never returns (when running the x310 with 
this code, it sometimes responds with unlocked, but after a few checks it comes 
back ok)

6) I tried some of the Ettus (UHD) test code
        a) running the "sync_to_gps" program did work - the reference was able 
to lock to the internal (gps) reference
        b) "test_clock_synch"  returns similiar errors to what we get with our 
program (see below):
Checking USRP devices for lock.
 * 318B08B: false
WARNING: One or more devices not locked.
Querying Clock for time and setting USRP times...
[WARNING] [MPM.PeriphManager] Reference Clock reporting unlocked. MB_CLOCK_CTRL 
reg: 0x00000002
Running 10 comparisons at random intervals.
Comparison #1
 * Clock time: 1563463644
 * 318B08B time: 1563463644
Comparison #2
 * Clock time: 1563463652
 * 318B08B time: 1563463652
Comparison #3
 * Clock time: 1563463657
 * 318B08B time: 1563463657
Comparison #4
 * Clock time: 1563463664
 * 318B08B time: 1563463664
Comparison #5
 * Clock time: 1563463666
 * 318B08B time: 1563463666
Comparison #6
 * Clock time: 1563463671
 * 318B08B time: 1563463671
Comparison #7
 * Clock time: 1563463676
 * 318B08B time: 1563463676
Comparison #8
 * Clock time: 1563463686
 * 318B08B time: 1563463686
Comparison #9
 * Clock time: 1563463689
 * 318B08B time: 1563463689
Comparison #10
 * Clock time: 1563463691
 * 318B08B time: 1563463691

Number of matches: 10/10


7) we ran the same tests at a sister site that has four E320s, and they all 
exhibited the same issues

8)Finally, a uhd_usrp_probe command returns this:

[INFO] [UHD] linux; GNU C++ version 4.8.5 20150623 (Red Hat 4.8.5-36); 
Boost_105300; UHD_3.14.1.0-9-g2aa5289d
[INFO] [MPMD] Initializing 1 device(s) in parallel with args: 
mgmt_addr=192.168.10.3,type=e3xx,product=e320,serial=318B08B,claimed=False,addr=192.168.10.3
[WARNING] [MPM.PeriphManager] Reference Clock reporting unlocked. MB_CLOCK_CTRL 
reg: 0x00000002
... many of these warnings repeating ...
[WARNING] [MPM.PeriphManager] Reference Clock reporting unlocked. MB_CLOCK_CTRL 
reg: 0x00000002
[WARNING] [MPM.RPCServer] A timeout event occured!
[INFO] [0/DmaFIFO_0] Initializing block control (NOC ID: 0xF1F0D00000000000)
[INFO] [0/DmaFIFO_0] BIST passed (Throughput: 1324 MB/s)
[INFO] [0/DmaFIFO_0] BIST passed (Throughput: 1322 MB/s)
[INFO] [0/Radio_0] Initializing block control (NOC ID: 0x12AD100000003320)
[INFO] [0/DDC_0] Initializing block control (NOC ID: 0xDDC0000000000000)
[INFO] [MPM.PeriphManager] init() called with device args 
`product=e320,mgmt_addr=192.168.10.3'.
[INFO] [0/DUC_0] Initializing block control (NOC ID: 0xD0C0000000000002)
[INFO] [0/Radio_0] Performing CODEC loopback test...
[INFO] [0/Radio_0] CODEC loopback test passed
[INFO] [0/Radio_0] Performing CODEC loopback test...
[INFO] [0/Radio_0] CODEC loopback test passed
  _____________________________________________________
 /
|       Device: E300-Series Device
|     _____________________________________________________
|    /
|   |       Mboard: ni-e320-318B08B
|   |   eeprom_version: 2
|   |   mpm_version: 3.14.0.0-g6875d061
|   |   pid: 58144
|   |   product: e320
|   |   rev: 2
|   |   rpc_connection: remote
|   |   serial: 318B08B
|   |   type: e3xx
|   |   MPM Version: 1.2
|   |   FPGA Version: 3.1
|   |   FPGA git hash: e39334f.clean
|   |   RFNoC capable: Yes
|   |
|   |   Time sources:  internal, external, gpsdo
|   |   Clock sources: external, internal, gpsdo
|   |   Sensors: gps_sky, gps_locked, temp_rf_channelA, temp_rf_channelB, 
temp_internal, fan, temp_main_power, ref_locked, gps_gpgga, temp_fpga, gps_tpv, 
gps_time
|   |     _____________________________________________________
|   |    /
|   |   |       RX Dboard: A
|   |   |     _____________________________________________________
|   |   |    /
|   |   |   |       RX Frontend: 0
|   |   |   |   Name: Neon
|   |   |   |   Antennas: RX2, TX/RX
|   |   |   |   Sensors: lo_locked, ad9361_temperature, rssi, lo_lock
|   |   |   |   Freq range: 70.000 to 6000.000 MHz
|   |   |   |   Gain range PGA: 0.0 to 76.0 step 1.0 dB
|   |   |   |   Bandwidth range: 20000000.0 to 40000000.0 step 0.0 Hz
|   |   |   |   Connection Type: IQ
|   |   |   |   Uses LO offset: No
|   |   |     _____________________________________________________
|   |   |    /
|   |   |   |       RX Frontend: 1
|   |   |   |   Name: Neon
|   |   |   |   Antennas: RX2, TX/RX
|   |   |   |   Sensors: lo_locked, ad9361_temperature, rssi, lo_lock
|   |   |   |   Freq range: 70.000 to 6000.000 MHz
|   |   |   |   Gain range PGA: 0.0 to 76.0 step 1.0 dB
|   |   |   |   Bandwidth range: 20000000.0 to 40000000.0 step 0.0 Hz
|   |   |   |   Connection Type: IQ
|   |   |   |   Uses LO offset: No
|   |   |     _____________________________________________________
|   |   |    /
|   |   |   |       RX Codec: A
|   |   |   |   Name: AD9361 Dual ADC
|   |   |   |   Gain Elements: None
|   |     _____________________________________________________
|   |    /
|   |   |       TX Dboard: A
|   |   |     _____________________________________________________
|   |   |    /
|   |   |   |       TX Frontend: 0
|   |   |   |   Name: Neon
|   |   |   |   Antennas: TX/RX
|   |   |   |   Sensors: lo_locked, ad9361_temperature
|   |   |   |   Freq range: 47.000 to 6000.000 MHz
|   |   |   |   Gain range PGA: 0.0 to 89.8 step 0.2 dB
|   |   |   |   Bandwidth range: 20000000.0 to 40000000.0 step 0.0 Hz
|   |   |   |   Connection Type: IQ
|   |   |   |   Uses LO offset: No
|   |   |     _____________________________________________________
|   |   |    /
|   |   |   |       TX Frontend: 1
|   |   |   |   Name: Neon
|   |   |   |   Antennas: TX/RX
|   |   |   |   Sensors: lo_locked, ad9361_temperature
|   |   |   |   Freq range: 47.000 to 6000.000 MHz
|   |   |   |   Gain range PGA: 0.0 to 89.8 step 0.2 dB
|   |   |   |   Bandwidth range: 20000000.0 to 40000000.0 step 0.0 Hz
|   |   |   |   Connection Type: IQ
|   |   |   |   Uses LO offset: No
|   |   |     _____________________________________________________
|   |   |    /
|   |   |   |       TX Codec: A
|   |   |   |   Name: AD9361 Dual DAC
|   |   |   |   Gain Elements: None
|   |     _____________________________________________________
|   |    /
|   |   |       RFNoC blocks on this device:
|   |   |
|   |   |   * DmaFIFO_0
|   |   |   * Radio_0
|   |   |   * DDC_0
|   |   |   * DUC_0


We've spent about 2 weeks on this and tried every combo of things we could 
think of and everything works on our other Ettus devices, but the E320 just 
doesn't seem to play nice at all.  Are there any thoughts on what the issue is 
(my gut is saying a configuration in UHD).
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