Problem of PPS+NMEA for the synchronization of Jeston xavier NX

I have a Ublox ZED-F9P and Jetson, I enabled the PPS+NMEA in Jetson and input NMEA and PPS in the Jetson, however, I also used Chrony and GPSD as the deamon to synchronize my system time to PPS.

However, I noticed that the difference between PPS and my system time was jumped like:

Timestamp: 1720271466.0081768, PPS-Clock Difference: 0.006760120391845703

Timestamp: 1720271466.9999745, PPS-Clock Difference: 0.006780862808227539

Timestamp: 1720271468.0073886, PPS-Clock Difference: 0.006812334060668945

Timestamp: 1720271469.0007286, PPS-Clock Difference: 0.006842851638793945

Timestamp: 1720271470.0055888, PPS-Clock Difference: 0.00687408447265625

Timestamp: 1720271471.0012033, PPS-Clock Difference: 0.006923198699951172

Timestamp: 1720271472.9935737, PPS-Clock Difference: 1.0069923400878906

Timestamp: 1720271473.988717, PPS-Clock Difference: 1.0070548057556152

Timestamp: 1720271474.9976366, PPS-Clock Difference: 0.007140159606933594

Timestamp: 1720271476.9939167, PPS-Clock Difference: 1.0071022510528564

Timestamp: 1720271478.0124972, PPS-Clock Difference: 0.007025957107543945

Timestamp: 1720271478.9996452, PPS-Clock Difference: 0.006987571716308594

Timestamp: 1720271480.0062253, PPS-Clock Difference: 0.006937742233276367

Timestamp: 1720271481.0000224, PPS-Clock Difference: 0.0068895816802978516

Timestamp: 1720271482.9898431, PPS-Clock Difference: 1.0068442821502686

Timestamp: 1720271484.9938395, PPS-Clock Difference: 1.0068144798278809

Timestamp: 1720271486.0035696, PPS-Clock Difference: 0.006811618804931641

Timestamp: 1720271487.0000994, PPS-Clock Difference: 0.0068056583404541016

Timestamp: 1720271488.0096858, PPS-Clock Difference: 0.006804704666137695

Timestamp: 1720271489.0003412, PPS-Clock Difference: 0.006803274154663086

Timestamp: 1720271490.0116658, PPS-Clock Difference: 0.0068051815032958984

Timestamp: 1720271491.9939423, PPS-Clock Difference: 1.006800889968872

Timestamp: 1720271493.00087, PPS-Clock Difference: 0.006792783737182617

Timestamp: 1720271494.003225, PPS-Clock Difference: 0.006788492202758789

Timestamp: 1720271495.000403, PPS-Clock Difference: 0.006785392761230469

Timestamp: 1720271496.0079112, PPS-Clock Difference: 0.006781578063964844

Timestamp: 1720271497.000441, PPS-Clock Difference: 0.00677800178527832

Timestamp: 1720271498.0118775, PPS-Clock Difference: 0.006777524948120117

Timestamp: 1720271499.0002327, PPS-Clock Difference: 0.0067827701568603516

Timestamp: 1720271500.9894478, PPS-Clock Difference: 1.0067920684814453

Timestamp: 1720271502.0108378, PPS-Clock Difference: 0.0068264007568359375

Timestamp: 1720271503.0003114, PPS-Clock Difference: 0.006857156753540039

Timestamp: 1720271504.0072558, PPS-Clock Difference: 0.0069065093994140625

Timestamp: 1720271504.9999986, PPS-Clock Difference: 0.0069580078125

Timestamp: 1720271506.0063345, PPS-Clock Difference: 0.007006168365478516

Timestamp: 1720271506.9998312, PPS-Clock Difference: 0.00704503059387207

Timestamp: 1720271508.0159929, PPS-Clock Difference: 0.007086038589477539

Timestamp: 1720271509.9935262, PPS-Clock Difference: 1.0071132183074951

Timestamp: 1720271510.9986787, PPS-Clock Difference: 0.007178306579589844

Timestamp: 1720271512.0048263, PPS-Clock Difference: 0.00717926025390625

Timestamp: 1720271512.9992213, PPS-Clock Difference: 0.007177114486694336

Timestamp: 1720271514.0095427, PPS-Clock Difference: 0.007177829742431641

Timestamp: 1720271514.9997566, PPS-Clock Difference: 0.00717616081237793

Timestamp: 1720271516.0063536, PPS-Clock Difference: 0.007174015045166016

Timestamp: 1720271516.9995775, PPS-Clock Difference: 0.007170915603637695

Timestamp: 1720271518.0069094, PPS-Clock Difference: 0.007170677185058594

Timestamp: 1720271519.001263, PPS-Clock Difference: 0.007177114486694336

Timestamp: 1720271520.015941, PPS-Clock Difference: 0.007191181182861328

Timestamp: 1720271521.0009513, PPS-Clock Difference: 0.007202863693237305

Timestamp: 1720271522.0097504, PPS-Clock Difference: 0.0072174072265625

Timestamp: 1720271523.000543, PPS-Clock Difference: 0.007246494293212891

Timestamp: 1720271524.0086722, PPS-Clock Difference: 0.0072917938232421875 Some times the difference was just: 0.007246494293212891s but sometimes was: 1.0071022510528564s. I will appreciate if you can give me some ideas. Thx

I have something to add here:When I used ppstest command I noticed that I can get all the pps but when I used gpsline I noticed that sometimes I will lose the PPS, like here:

In the ppstest command:

source 0 - assert 1720382519.989777374, sequence: 195899 - clear 0.000000000, sequence: 0

source 0 - assert 1720382520.989773128, sequence: 195900 - clear 0.000000000, sequence: 0

source 0 - assert 1720382521.989769714, sequence: 195901 - clear 0.000000000, sequence: 0

but in the gpsline I just have:

{“class”:“PPS”,“device”:“/dev/pps1”,“real_sec”:1720382519, “real_nsec”:0,“clock_sec”:1720382518,“clock_nsec”:989777145,“precision”:-20}

{“class”:“TPV”,“device”:“/dev/ttyTHS0”,“mode”:2,“time”:“2024-07-07T20:01:59.000Z”,“ept”:0.005,“lat”:51.804730167,“lon”:10.342598667,“track”:0.0000,“speed”:0.001}

{“class”:“PPS”,“device”:“/dev/pps1”,“real_sec”:1720382520, “real_nsec”:0,“clock_sec”:1720382519,“clock_nsec”:989777374,“precision”:-20}

{“class”:“TPV”,“device”:“/dev/ttyTHS0”,“mode”:2,“time”:“2024-07-07T20:02:00.000Z”,“ept”:0.005,“lat”:51.804730167,“lon”:10.342598500,“track”:0.0000,“speed”:0.003}

{“class”:“TPV”,“device”:“/dev/ttyTHS0”,“mode”:2,“time”:“2024-07-07T20:02:01.000Z”,“ept”:0.005,“lat”:51.804730167,“lon”:10.342598667,“track”:0.0000,“speed”:0.002}

{“class”:“PPS”,“device”:“/dev/pps1”,“real_sec”:1720382522, “real_nsec”:0,“clock_sec”:1720382520,“clock_nsec”:989773128,“precision”:-20}

Seems to be I lose the pps in: 1720382521s. Do you think is it the problem of Kernel or? Thanks!

Hi yu.lan,

Are you using the devkit or custom board for Xavier NX?
What’s your Jetpack version in use?

It seems you lost a timestamp here.

Have you confirmed that your Ublox ZED-F9P output the timestamp to Xavier NX through /dev/ttyTHS0 at this moment?
Is there any error showing in dmesg?

Hi, many thanks for your quick reply! I used the devkit for Xavier NX.
The jetpack version is: Jetpack 4.6.2.
Yes, the TX/RX (UART1) was used to connnect Jetson and Ublox ZED-F9P, the port was /dev/ttyTHS0

For the dmesg I got the output:
[324443.777516] pps pps1: PPS event at 1720510269.991666993
[324443.777527] pps pps1: capture assert seq #323649
[324443.777654] pps pps1: PPS_FETCH
[324443.777663] pps pps1: timeout 3.000000000
[324443.777807] pps pps1: PPS_FETCH
[324443.777821] pps pps1: timeout 3.000000000
[324444.728595] pps pps0: PPS event at 1720510270.942784089
[324444.728637] pps pps0: capture assert seq #316839
[324444.777506] pps pps1: PPS event at 1720510270.991699525
[324444.777518] pps pps1: capture assert seq #323650
[324444.777640] pps pps1: PPS_FETCH
[324444.777650] pps pps1: timeout 3.000000000
[324444.777846] pps pps1: PPS_FETCH
[324444.777892] pps pps1: timeout 3.000000000
[324445.752582] pps pps0: PPS event at 1720510271.966802880
[324445.752594] pps pps0: capture assert seq #316840
[324445.777491] pps pps1: PPS event at 1720510271.991714495
[324445.777502] pps pps1: capture assert seq #323651
[324445.777623] pps pps1: PPS_FETCH
[324445.777634] pps pps1: timeout 3.000000000
[324445.777927] pps pps1: PPS_FETCH
[324445.777937] pps pps1: timeout 3.000000000
[324446.776572] pps pps0: PPS event at 1720510272.990812875
[324446.776589] pps pps0: capture assert seq #316841
[324446.777470] pps pps1: PPS event at 1720510272.991721950
[324446.777477] pps pps1: capture assert seq #323652
[324446.777588] pps pps1: PPS_FETCH
[324446.777596] pps pps1: timeout 3.000000000
[324446.777783] pps pps1: PPS_FETCH
[324446.777833] pps pps1: timeout 3.000000000
[324447.777475] pps pps1: PPS event at 1720510273.991732349
[324447.777486] pps pps1: capture assert seq #323653
[324447.777590] pps pps1: PPS_FETCH
[324447.777599] pps pps1: timeout 3.000000000
[324447.777799] pps pps1: PPS_FETCH
[324447.777807] pps pps1: timeout 3.000000000
[324447.800542] pps pps0: PPS event at 1720510274.014799958
[324447.800598] pps pps0: capture assert seq #316842
[324448.777466] pps pps1: PPS event at 1720510274.991741788
[324448.777478] pps pps1: capture assert seq #323654
[324448.777617] pps pps1: PPS_FETCH
[324448.777626] pps pps1: timeout 3.000000000
[324448.777872] pps pps1: PPS_FETCH
[324448.777880] pps pps1: timeout 3.000000000
[324448.824511] pps pps0: PPS event at 1720510275.038793729
[324448.824587] pps pps0: capture assert seq #316843
[324449.777456] pps pps1: PPS event at 1720510275.991753615
[324449.777472] pps pps1: capture assert seq #323655
[324449.777566] pps pps1: PPS_FETCH
[324449.777577] pps pps1: timeout 3.000000000
[324449.778479] pps pps1: PPS_FETCH
[324449.778490] pps pps1: timeout 3.000000000
[324449.848507] pps pps0: PPS event at 1720510276.062796597
[324449.848524] pps pps0: capture assert seq #316844
[324450.777446] pps pps1: PPS event at 1720510276.991753121
[324450.777465] pps pps1: capture assert seq #323656
[324450.777597] pps pps1: PPS_FETCH
[324450.777609] pps pps1: timeout 3.000000000
[324450.779260] pps pps1: PPS_FETCH
[324450.779281] pps pps1: timeout 3.000000000
[324450.872470] pps pps0: PPS event at 1720510277.086783372
[324450.872485] pps pps0: capture assert seq #316845
[324451.560621] pps pps2: PPS_FETCH
[324451.560636] pps pps2: timeout 3.000000000
[324451.777428] pps pps1: PPS event at 1720510277.991753683
[324451.777439] pps pps1: capture assert seq #323657
[324451.777546] pps pps1: PPS_FETCH
[324451.777560] pps pps1: timeout 3.000000000
[324451.777816] pps pps1: PPS_FETCH
[324451.777830] pps pps1: timeout 3.000000000
[324451.896468] pps pps0: PPS event at 1720510278.110794629
[324451.896515] pps pps0: capture assert seq #316846
[324452.777456] pps pps1: PPS event at 1720510278.991793990
[324452.777468] pps pps1: capture assert seq #323658
[324452.777584] pps pps1: PPS_FETCH
[324452.777593] pps pps1: timeout 3.000000000
[324452.777767] pps pps1: PPS_FETCH
[324452.777775] pps pps1: timeout 3.000000000
[324452.920447] pps pps0: PPS event at 1720510279.134782652
[324452.920486] pps pps0: capture assert seq #316847
[324453.777428] pps pps1: PPS event at 1720510279.991797345
[324453.777441] pps pps1: capture assert seq #323659
[324453.777548] pps pps1: PPS_FETCH
[324453.777602] pps pps1: timeout 3.000000000
[324453.778044] pps pps1: PPS_FETCH
[324453.778055] pps pps1: timeout 3.000000000
[324453.944407] pps pps0: PPS event at 1720510280.158791720
[324453.944454] pps pps0: capture assert seq #316848
[324454.616486] pps pps2: PPS_FETCH
[324454.616500] pps pps2: timeout 3.000000000
[324454.777405] pps pps1: PPS event at 1720510280.991845745
[324454.777416] pps pps1: capture assert seq #323660
[324454.777797] pps pps1: PPS_FETCH
[324454.777807] pps pps1: timeout 3.000000000
[324454.777893] pps pps1: PPS_FETCH
[324454.777903] pps pps1: timeout 3.000000000
[324454.968326] pps pps0: PPS event at 1720510281.182783560
[324454.968339] pps pps0: capture assert seq #316849
[324455.777389] pps pps1: PPS event at 1720510281.991893697
[324455.777401] pps pps1: capture assert seq #323661
[324455.777531] pps pps1: PPS_FETCH
[324455.777544] pps pps1: timeout 3.000000000
[324455.778044] pps pps1: PPS_FETCH
[324455.778053] pps pps1: timeout 3.000000000
[324455.992265] pps pps0: PPS event at 1720510282.206787145
[324455.992310] pps pps0: capture assert seq #316850
[324456.777380] pps pps1: PPS event at 1720510282.991952273
[324456.777391] pps pps1: capture assert seq #323662
[324456.777549] pps pps1: PPS_FETCH
[324456.777560] pps pps1: timeout 3.000000000
[324456.777719] pps pps1: PPS_FETCH
[324456.777729] pps pps1: timeout 3.000000000
[324457.016198] pps pps0: PPS event at 1720510283.230787914
[324457.016211] pps pps0: capture assert seq #316851
[324457.688204] pps pps2: PPS_FETCH
[324457.688218] pps pps2: timeout 3.000000000
[324457.777371] pps pps1: PPS event at 1720510283.991995289
[324457.777383] pps pps1: capture assert seq #323663
[324457.777506] pps pps1: PPS_FETCH
[324457.777517] pps pps1: timeout 3.000000000
[324457.777746] pps pps1: PPS_FETCH
[324457.777756] pps pps1: timeout 3.000000000
[324458.040151] pps pps0: PPS event at 1720510284.254786777
[324458.040164] pps pps0: capture assert seq #316852
[324458.777364] pps pps1: PPS event at 1720510284.992028836
[324458.777376] pps pps1: capture assert seq #323664
[324458.777497] pps pps1: PPS_FETCH
[324458.777547] pps pps1: timeout 3.000000000
[324458.777850] pps pps1: PPS_FETCH
[324458.777860] pps pps1: timeout 3.000000000
[324459.064116] pps pps0: PPS event at 1720510285.278790116
[324459.064161] pps pps0: capture assert seq #316853
[324459.777349] pps pps1: PPS event at 1720510285.992048878
[324459.777362] pps pps1: capture assert seq #323665
[324459.777464] pps pps1: PPS_FETCH
[324459.777475] pps pps1: timeout 3.000000000
[324459.777481] pps pps1: PPS_FETCH
[324459.777492] pps pps1: timeout 3.000000000
[324460.088069] pps pps0: PPS event at 1720510286.302784175
[324460.088086] pps pps0: capture assert seq #316854
[324460.760096] pps pps2: PPS_FETCH
[324460.760110] pps pps2: timeout 3.000000000
[324460.777335] pps pps1: PPS event at 1720510286.992075193
[324460.777347] pps pps1: capture assert seq #323666
[324460.777470] pps pps1: PPS_FETCH
[324460.777481] pps pps1: timeout 3.000000000
[324460.777723] pps pps1: PPS_FETCH
[324460.777732] pps pps1: timeout 3.000000000
[324461.112041] pps pps0: PPS event at 1720510287.326795610
[324461.112055] pps pps0: capture assert seq #316855
[324461.777328] pps pps1: PPS event at 1720510287.992099913
[324461.777341] pps pps1: capture assert seq #323667
[324461.777467] pps pps1: PPS_FETCH
[324461.777477] pps pps1: timeout 3.000000000
[324461.777729] pps pps1: PPS_FETCH
[324461.777738] pps pps1: timeout 3.000000000
[324462.135996] pps pps0: PPS event at 1720510288.350782081
[324462.136044] pps pps0: capture assert seq #316856
[324462.777316] pps pps1: PPS event at 1720510288.992116614
[324462.777329] pps pps1: capture assert seq #323668
[324462.777735] pps pps1: PPS_FETCH
[324462.777747] pps pps1: timeout 3.000000000
[324462.778526] pps pps1: PPS_FETCH
[324462.778537] pps pps1: timeout 3.000000000
[324463.159970] pps pps0: PPS event at 1720510289.374785732
[324463.160011] pps pps0: capture assert seq #316857
[324463.777305] pps pps1: PPS event at 1720510289.992137187
[324463.777317] pps pps1: capture assert seq #323669
[324463.777698] pps pps1: PPS_FETCH
[324463.777709] pps pps1: timeout 3.000000000
[324463.780135] pps pps1: PPS_FETCH
[324463.780147] pps pps1: timeout 3.000000000
[324463.832040] pps pps2: PPS_FETCH
[324463.832054] pps pps2: timeout 3.000000000
[324464.183946] pps pps0: PPS event at 1720510290.398792519
[324464.183958] pps pps0: capture assert seq #316858
[324464.777297] pps pps1: PPS event at 1720510290.992156928
[324464.777310] pps pps1: capture assert seq #323670
[324464.777441] pps pps1: PPS_FETCH
[324464.777499] pps pps1: timeout 3.000000000
[324464.777946] pps pps1: PPS_FETCH
[324464.777956] pps pps1: timeout 3.000000000
[324465.207912] pps pps0: PPS event at 1720510291.422787241
[324465.207925] pps pps0: capture assert seq #316859
[324465.777284] pps pps1: PPS event at 1720510291.992292304
[324465.777297] pps pps1: capture assert seq #323671
[324465.777418] pps pps1: PPS_FETCH
[324465.777429] pps pps1: timeout 3.000000000
[324465.777887] pps pps1: PPS_FETCH
[324465.777898] pps pps1: timeout 3.000000000
[324466.231639] pps pps0: PPS event at 1720510292.446791442
[324466.231682] pps pps0: capture assert seq #316860
[324466.777273] pps pps1: PPS event at 1720510292.992587664
[324466.777287] pps pps1: capture assert seq #323672
[324466.777406] pps pps1: PPS_FETCH
[324466.777416] pps pps1: timeout 3.000000000
[324466.777874] pps pps1: PPS_FETCH
[324466.777884] pps pps1: timeout 3.000000000
[324466.903502] pps pps2: PPS_FETCH
[324466.903516] pps pps2: timeout 3.000000000
[324467.255323] pps pps0: PPS event at 1720510293.470787902
[324467.255370] pps pps0: capture assert seq #316861
[324467.777261] pps pps1: PPS event at 1720510293.992882928
[324467.777272] pps pps1: capture assert seq #323673
[324467.777428] pps pps1: PPS_FETCH
[324467.777439] pps pps1: timeout 3.000000000
[324467.777608] pps pps1: PPS_FETCH
[324467.777618] pps pps1: timeout 3.000000000
[324468.279009] pps pps0: PPS event at 1720510294.494789228
[324468.279055] pps pps0: capture assert seq #316862
[324468.777249] pps pps1: PPS event at 1720510294.993179504
[324468.777261] pps pps1: capture assert seq #323674
[324468.777397] pps pps1: PPS_FETCH
[324468.777415] pps pps1: timeout 3.000000000
[324468.777671] pps pps1: PPS_FETCH
[324468.777681] pps pps1: timeout 3.000000000
[324469.302697] pps pps0: PPS event at 1720510295.518792378
[324469.302745] pps pps0: capture assert seq #316863
[324469.777239] pps pps1: PPS event at 1720510295.993356650
[324469.777251] pps pps1: capture assert seq #323675
[324469.777400] pps pps1: PPS_FETCH
[324469.777412] pps pps1: timeout 3.000000000
[324469.777724] pps pps1: PPS_FETCH
[324469.777734] pps pps1: timeout 3.000000000
[324469.974716] pps pps2: PPS_FETCH
[324469.974731] pps pps2: timeout 3.000000000
[324470.326646] pps pps0: PPS event at 1720510296.542783228
[324470.326658] pps pps0: capture assert seq #316864
[324470.777226] pps pps1: PPS event at 1720510296.993373177
[324470.777239] pps pps1: capture assert seq #323676
[324470.777343] pps pps1: PPS_FETCH
[324470.777391] pps pps1: timeout 3.000000000
[324470.777653] pps pps1: PPS_FETCH
[324470.777663] pps pps1: timeout 3.000000000
[324471.350624] pps pps0: PPS event at 1720510297.566790156
[324471.350662] pps pps0: capture assert seq #316865
[324471.777216] pps pps1: PPS event at 1720510297.993392169
[324471.777232] pps pps1: capture assert seq #323677
[324471.777350] pps pps1: PPS_FETCH
[324471.777362] pps pps1: timeout 3.000000000
[324471.778049] pps pps1: PPS_FETCH
[324471.778060] pps pps1: timeout 3.000000000
[324472.374589] pps pps0: PPS event at 1720510298.590784188
[324472.374630] pps pps0: capture assert seq #316866
[324472.777205] pps pps1: PPS event at 1720510298.993409016
[324472.777219] pps pps1: capture assert seq #323678
[324472.777339] pps pps1: PPS_FETCH
[324472.777354] pps pps1: timeout 3.000000000
[324472.778136] pps pps1: PPS_FETCH
[324472.778148] pps pps1: timeout 3.000000000
[324473.046618] pps pps2: PPS_FETCH
[324473.046632] pps pps2: timeout 3.000000000
[324473.398561] pps pps0: PPS event at 1720510299.614783794
[324473.398574] pps pps0: capture assert seq #316867
[324473.777194] pps pps1: PPS event at 1720510299.993426183
[324473.777207] pps pps1: capture assert seq #323679
[324473.777316] pps pps1: PPS_FETCH
[324473.777359] pps pps1: timeout 3.000000000
[324473.778324] pps pps1: PPS_FETCH
[324473.778336] pps pps1: timeout 3.000000000
[324474.422534] pps pps0: PPS event at 1720510300.638785053
[324474.422578] pps pps0: capture assert seq #316868
[324474.777182] pps pps1: PPS event at 1720510300.993441794
[324474.777194] pps pps1: capture assert seq #323680
[324474.777305] pps pps1: PPS_FETCH
[324474.777316] pps pps1: timeout 3.000000000
[324474.779096] pps pps1: PPS_FETCH
[324474.779113] pps pps1: timeout 3.000000000
[324475.446511] pps pps0: PPS event at 1720510301.662788039
[324475.446524] pps pps0: capture assert seq #316869
[324475.777183] pps pps1: PPS event at 1720510301.993465053
[324475.777197] pps pps1: capture assert seq #323681
[324475.777437] pps pps1: PPS_FETCH
[324475.777449] pps pps1: timeout 3.000000000
[324475.777559] pps pps1: PPS_FETCH
[324475.777569] pps pps1: timeout 3.000000000
[324476.118561] pps pps2: PPS_FETCH
[324476.118576] pps pps2: timeout 3.000000000
[324476.470489] pps pps0: PPS event at 1720510302.686795218
[324476.470501] pps pps0: capture assert seq #316870
[324476.777164] pps pps1: PPS event at 1720510302.993475639
[324476.777176] pps pps1: capture assert seq #323682
[324476.777333] pps pps1: PPS_FETCH
[324476.777344] pps pps1: timeout 3.000000000
[324476.777393] pps pps1: PPS_FETCH
[324476.777404] pps pps1: timeout 3.000000000
[324477.494472] pps pps0: PPS event at 1720510303.710805076
[324477.494484] pps pps0: capture assert seq #316871
[324477.777154] pps pps1: PPS event at 1720510303.993492036
[324477.777171] pps pps1: capture assert seq #323683
[324477.777301] pps pps1: PPS_FETCH
[324477.777308] pps pps1: PPS_FETCH
[324477.777316] pps pps1: timeout 3.000000000
[324477.777320] pps pps1: timeout 3.000000000
[324478.518420] pps pps0: PPS event at 1720510304.734782178
[324478.518433] pps pps0: capture assert seq #316872
[324478.777154] pps pps1: PPS event at 1720510304.993518647
[324478.777168] pps pps1: capture assert seq #323684
[324478.777305] pps pps1: PPS_FETCH
[324478.777316] pps pps1: timeout 3.000000000
[324478.777492] pps pps1: PPS_FETCH
[324478.777501] pps pps1: timeout 3.000000000
[324479.190463] pps pps2: PPS_FETCH
[324479.190478] pps pps2: timeout 3.000000000
[324479.542398] pps pps0: PPS event at 1720510305.758786641
[324479.542443] pps pps0: capture assert seq #316873
[324479.777131] pps pps1: PPS event at 1720510305.993521448
[324479.777143] pps pps1: capture assert seq #323685
[324479.777268] pps pps1: PPS_FETCH
[324479.777277] pps pps1: timeout 3.000000000
[324479.777467] pps pps1: PPS_FETCH
[324479.777477] pps pps1: timeout 3.000000000
[324480.566366] pps pps0: PPS event at 1720510306.782783264
[324480.566408] pps pps0: capture assert seq #316874
[324480.777117] pps pps1: PPS event at 1720510306.993538394
[324480.777129] pps pps1: capture assert seq #323686
[324480.777237] pps pps1: PPS_FETCH
[324480.777249] pps pps1: timeout 3.000000000
[324480.777678] pps pps1: PPS_FETCH
[324480.777688] pps pps1: timeout 3.000000000
[324481.590353] pps pps0: PPS event at 1720510307.806791447
[324481.590401] pps pps0: capture assert seq #316875
[324481.777110] pps pps1: PPS event at 1720510307.993546738
[324481.777123] pps pps1: capture assert seq #323687
[324481.777266] pps pps1: PPS_FETCH
[324481.777278] pps pps1: timeout 3.000000000
[324481.778592] pps pps1: PPS_FETCH
[324481.778605] pps pps1: timeout 3.000000000
[324482.614340] pps pps0: PPS event at 1720510308.830785014
[324482.614353] pps pps0: capture assert seq #316876
[324482.777097] pps pps1: PPS event at 1720510308.993544993
[324482.777110] pps pps1: capture assert seq #323688
[324482.777220] pps pps1: PPS_FETCH
[324482.777230] pps pps1: timeout 3.000000000
[324482.777660] pps pps1: PPS_FETCH
[324482.777671] pps pps1: timeout 3.000000000
[324483.638327] pps pps0: PPS event at 1720510309.854781109
[324483.638341] pps pps0: capture assert seq #316877
[324483.777093] pps pps1: PPS event at 1720510309.993544143
[324483.777105] pps pps1: capture assert seq #323689
[324483.777248] pps pps1: PPS_FETCH
[324483.777257] pps pps1: timeout 3.000000000
[324483.777409] pps pps1: PPS_FETCH
[324483.777417] pps pps1: timeout 3.000000000
[324484.662385] pps pps0: PPS event at 1720510310.878847124
[324484.662399] pps pps0: capture assert seq #316878
[324484.777077] pps pps1: PPS event at 1720510310.993535870
[324484.777089] pps pps1: capture assert seq #323690
[324484.777261] pps pps1: PPS_FETCH
[324484.777274] pps pps1: timeout 3.000000000
[324484.777392] pps pps1: PPS_FETCH
[324484.777403] pps pps1: timeout 3.000000000
[324485.686342] pps pps0: PPS event at 1720510311.902805459
[324485.686355] pps pps0: capture assert seq #316879
[324485.777066] pps pps1: PPS event at 1720510311.993526454
[324485.777077] pps pps1: capture assert seq #323691
[324485.777195] pps pps1: PPS_FETCH
[324485.777204] pps pps1: timeout 3.000000000
[324485.777315] pps pps1: PPS_FETCH
[324485.777322] pps pps1: timeout 3.000000000
[324486.710334] pps pps0: PPS event at 1720510312.926787108
[324486.710378] pps pps0: capture assert seq #316880
[324486.777056] pps pps1: PPS event at 1720510312.993508644
[324486.777068] pps pps1: capture assert seq #323692
[324486.777173] pps pps1: PPS_FETCH
[324486.777184] pps pps1: timeout 3.000000000
[324486.777201] pps pps1: PPS_FETCH
[324486.777215] pps pps1: timeout 3.000000000
[324487.734346] pps pps0: PPS event at 1720510313.950786516
[324487.734386] pps pps0: capture assert seq #316881
[324487.777044] pps pps1: PPS event at 1720510313.993486930
[324487.777055] pps pps1: capture assert seq #323693
[324487.777167] pps pps1: PPS_FETCH
[324487.777177] pps pps1: timeout 3.000000000
[324487.782772] pps pps1: PPS_FETCH
[324487.782783] pps pps1: timeout 3.000000000
[324488.758363] pps pps0: PPS event at 1720510314.974791940
[324488.758375] pps pps0: capture assert seq #316882
[324488.777032] pps pps1: PPS event at 1720510314.993461472
[324488.777043] pps pps1: capture assert seq #323694
[324488.777171] pps pps1: PPS_FETCH
[324488.777180] pps pps1: timeout 3.000000000
[324488.777356] pps pps1: PPS_FETCH
[324488.777366] pps pps1: timeout 3.000000000
[324489.777027] pps pps1: PPS event at 1720510315.993455716
[324489.777040] pps pps1: capture assert seq #323695
[324489.777145] pps pps1: PPS_FETCH
[324489.777156] pps pps1: timeout 3.000000000
[324489.778560] pps pps1: PPS_FETCH
[324489.778573] pps pps1: timeout 3.000000000
[324489.782346] pps pps0: PPS event at 1720510315.998788971
[324489.782356] pps pps0: capture assert seq #316883
[324490.777015] pps pps1: PPS event at 1720510316.993470427
[324490.777028] pps pps1: capture assert seq #323696
[324490.777139] pps pps1: PPS_FETCH
[324490.777149] pps pps1: timeout 3.000000000
[324490.782103] pps pps1: PPS_FETCH
[324490.782117] pps pps1: timeout 3.000000000
[324490.806338] pps pps0: PPS event at 1720510317.022790851
[324490.806389] pps pps0: capture assert seq #316884

I don’t need any errors from your dmesg.
Which PPS are you using for your Ublox ZED-F9P?

We don’t have this module to verify locally.
Have you also asked your vendor for the timestamp issue?

Yes I asked them here: https://portal.u-blox.com/s/feed/0D5Oj00000L3CvbKAF?t=1720560706277 but no helpful reply until now

Since you are using the devkit, could you also verify with the latest R35.5.0 for your Xavier NX devkit?

Ok, we will quickly check, but we have to check the device tree for the PPS support, do you have any idea for this?
My colleague has already started the jetpack 5.1, is it also ok?

Please refer to the following thread for this.
Device Tree Overlay for PPS Support on JP4.6.4 - #9 by KevinFFF
Enable PPS on Jetson Linux 35.3.1 for Xavier AGX
Enabling PPS on Xavier AGX

We would suggest using Jetpack 5.1.3(R35.5.0) in case missing any fixes.