Uncalled for pauses during print?

Does anyone notice little pauses during printing that don't seem to have an obvious explanation in the slicing?
I first noticed it when printing a part with a relatively large perimeter. The hotend had a start point on each layer where it would pause and that was all perfectly clear in the slicer. Some retraction there too. But then about half way around the perimeter the hotend would pause perceptibly, before carrying on its way. In the final print there was a sort of diagonal raised vertical line corresponding to those moments where it would just hang and ooze.
Anyone notice something similar?
Was wondering if it's perhaps a combination of events  such as a long straight in which the extruder has time to accelerate to full speed (only 40mm/s in my case) combined with plenty of microsteps to generate  that sort of overload the processor with calculations such that it needs to pause and gather itself?

I have seen exactly that behaviour with files generated by Cura. It was inserting very short nonextruding gcode segments between extruding segments.

Hmm Looking though my S3d .gcode don't see any of that. But the layers of the aforementioned part are quite (surprisingly!) easy to read in the code so will pick up the print tomorrow, count the layers and identify the offending regions precisely.

Perhaps it's the point at which it is switching between the external and the internal perimeter? If so, using pressure advance may help.

I am experiencing the same problem. I'm new to duet, I installed mine last Sunday and after setting up everything my first print was the "Yet Another Duet WiFi Mount" for the e3d BigBox.
I was very astonished about how smooth the movements are but in every circular movement there was a significant pause.
This leads to big globs. I am using a volcano hotend with big nozzles and PETG which is a combination in which getting the oozing under control is very hard (I tested pressure control only once, I have not dialed it in yet)Looking at the gcode I think you are right, it is the perimeter switch:
G1 X65.300 Y67.544 E0.0789 G1 X66.573 Y66.203 E0.0797 G1 X67.890 Y64.889 E0.0802 ; inner perimeter G1 X67.491 Y64.474 F6000 G1 X70.170 Y61.999 E0.1572 F1395 G1 X73.037 Y59.606 E0.1610 G1 X73.307 Y59.386 E0.0150
This is done by S3D, going from the outer to the inner perimeter using a small nonextruding movement perpendicular to the previous path. Marlin just "thumps" over these bits but it looks like Duet is coming to a near or full stop.
My jerk setting on Marlin was 8mm/s and on Duet 10mm/s. 
I'm on a volcano and PETG as well. What nozzle? I did pressure advance @ 0.1, seems to help a little, but S3d is being painful on it.
(1.2mm nozzle was comically bad 0.8 works great)My prints tend to just "thump" over it as well. I'll check some individual settings if you want.

I tested it with a 0.8 nozzle and pressure advance coefficient of S0.05
Getting the nozzle to stop oozing would require a retraction of at least 34mm so preassure advance can't really solve the problem. 
Pressure advance of 0.05 is rather low, You probably need more unless you have a direct (i.e. nonBowden) extruder.

I have a directdrive Titan extruder. I'll try a higher value.
Does that mean the duet will stop movement when switching from an extruding move to a nonextruding move? 
Yes, because the extruder has to stop completely.

First of all, I'll admit I don't know what "pressure advance" is in S3d. Don't find this parameter anywhere?
Not sure this is going to interest anyone but here follows the details. Am puzzled.
The part in question is a casing, a shell. It's nominally 1mm thick and most of it (though some of the sloping areas have gap fill) is just a single perimeter (so two 0.48mm walls) thick.
The printer origin is “bottom left” and the start point for each layer (as fixed in F360) is “top left” on the part.
It’s normal that there’s a “scar” corresponding to the start points but there are some other scars (see various photos) that are not so easily explained.
In particular I’d like to concentrate on the one that is “bottom right” because I remember that, during printing, the extruder would actually come to a STOP at that point (for say half a second) on each layer. The close up photo reveals that this scar has a strange weave structure. In the gcode I can see nothing to “create” it.
Somewhat arbitrarily picked Layer 40 as one for analysis.
The extruder starts “top left”, moves to “top right”, then “bottom right”, then "bottom left”,
then it starts moving back to “bottom right” and then, on it’s way to “top right” we get the pause and the scar.
Have put what I think is the relevant region in bold. There seems nothing odd?
X and Y seem to increase together in a way that is consistent with going around a corner. Don’t see anything to create a weave. And if there were, don’t see anything to justify coming to a standstill and then a PAUSE.
My wild guess was something to do with Microstep overload. But really, have no idea.
Photos include a close up of the scar, photos of start point (top left) corner and corner in question (bottom right), the slicing set to Layer 40, also zoomed on the corner in question (nothing to see, just two perimeters). Sorry not clearer… tricky for imbeciles like me to post in a forum with no image management
; Layer 40, Z = 6
; inner perimeter
; inner perimeter
; inner perimeter
; inner perimeter
; inner perimeter
; inner perimeter
; inner perimeter
; outer perimeter
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G1 X78.786 Y130.215 E3.8799
G1 E1.6000 F2700
; Layer 41, Z = 6.15 
Are you printing from SD card or over USB?

Sorry for the long post, trying to answer questions before they are asked. I just switched from Smoothie to Duet Wifi and am having pauses then jumps that ruin a print. The first couple of layers are silky smooth (amazingly so compared to Smoothie and Ramps) then on some arcs it pauses then jumps forward leaving a space without extrusion and then over extrudes at the point it starts extruding again. I am using Firmware Version: 1.17e (20170210). The gcode file is sliced by Slic3r1.3.0master322 and in the areas the jerking happens I do not see any non extrusion moves. Gcode Simulator v1.3 is not showing a jerk in the areas it is happening. There was no jerking in the same gcode file with Smoothie, except I was using 1.8 steppers which I changed for 0.9 at the same time I installed the Duet Wifi and Panel Due. I am using a 24V 17A supply, I am using a 200W bed and the standard E3D V6 heater, same as before. I had the same problem trying to print the finger wrench digit spanner from Thingiverse https://www.thingiverse.com/thing:947423 .
(Highlight in blue to show area it is happening)
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G1 X21.134 Y1.629 F12000.000[/c][c]; Communication and general
M111 S0 ; Debug off
M550 K250 ; Machine name and Netbios name (can be anything you like)
M551 XXXXXXXXX ; Machine password (used for FTP)
;*** If you have more than one Duet on your network, they must all have different MAC addresses, so change the last digits
M540 P0xBE:0xEF:0xDE:0xAD:0xFE:0xEF ; MAC Address
;*** Wifi Networking
M552 P192.168.1.100 S1 ; Set Static IP and Enable WiFiM555 P2 ; Set output to look like Marlin
M575 P1 B57600 S1 ; Comms parameters for PanelDue
G21 ; Work in millimetres
G90 ; Send absolute coordinates…
M83 ; ...but relative extruder moves; Axis and motor configuration
M569 P0 S1 ; Drive 0
M569 P1 S1 ; Drive 1
M569 P2 S1 ; Drive 2
M569 P3 S1 ; Drive 3
M569 P4 S1 ; Drive 4
M574 X2 Y2 Z2 S1 ; set endstop configuration (all endstops at high end, active high)
;M574 E0 S1 ; set FSR controller active lowM665 R168.23 L288.02 B110 H237.997 X0.223 Y0.059 Z0.00 ; delta radius, diagonal rod length, printable radius and homed height
M666 X0.31 Y0.35 Z0.04 ; endstop adjustments
M350 X16 Y16 Z16 E16 I1 ;Stepper mode (I1 only works with 16)
M92 X160 Y160 Z160 ; Set axis steps/mm
M906 X1000 Y1000 Z1000 E500 ; Set motor currents (mA)
M201 X1000 Y1000 Z1000 E1000 ; Accelerations (mm/s^2)
M203 X20000 Y20000 Z20000 E3600 ; Maximum speeds (mm/min)
M566 X1200 Y1200 Z1200 E1200 ; Maximum instant speed changes mm/minute; Fans
M106 P1 T50 S255 H1 ; hotend heatsink FAN1
M106 P2 T50 S35 H1 ; extruder motor FAN2; Thermistors
M305 P0 T100000 B3950 R4700 ;L54 H97 ; Put your own H and/or L values here to set the bed thermistor ADC correction
M305 P1 T100000 B4388 R4700 ;L54 H97 ; Put your own H and/or L values here to set the first nozzle thermistor ADC correction
M570 S180 ; Hot end may be a little slow to heat up so allow it 180 seconds; PID
; Bed
M301 H0 P1 ; negative P means use bangbang control
; Heater 1
;M301 H1 P60 I1 D125 T1.0 S1 W300 B30
M307 H1 A419.8 C158.4 D4.4 B0; Tool definitions
M563 P0 D0 H1 ; Define tool 0
G10 P0 S0 R0 ; Set tool 0 operating and standby temperatures
M92 E1385 ; Set extruder steps per mm; Z probe and compensation definition
;*** If you have a switch instead of an IR probe, change P1 to P4 in the following M558 command
M558 P4 X0 Y0 Z0 H3 I1 ; Z probe is a switch and is not used for homing any axes
G31 X0 Y0 Z0.1 P500 ; lower Z # = more smooshed higher Z # = less smooshed;*** If you are using axis compensation, put the figures in the following command
M556 S78 X0 Y0 Z0 ; Axis compensation hereM208 S1 Z0.2 ; set minimum Z
;
T0 ; select first hot end[/c] 
The gcode moves you posted are all nonextruding moves, because there is no E parameter on them. The jerkiness is because they are highspeed moves (F12000 is 200mm/sec) and very short  some are less than 0.04mm long  so you have hit the limit at which the firmware can process moves. Looks like a slicer bug to me.

Me… I was printing from the SD on the Duet after uploading file via web interface.

The gcode moves you posted are all nonextruding moves, because there is no E parameter on them. The jerkiness is because they are highspeed moves (F12000 is 200mm/sec) and very short  some are less than 0.04mm long  so you have hit the limit at which the firmware can process moves. Looks like a slicer bug to me.
How stupid of me not to notice that, and thank you for being nice about it. I will drop my travel from 200 to 100 to account for the steppers and mesh the files again less dense. I have another thing going on but will start a thread about it instead of continuing here.

A small correction: I should have said "you have hit the limit at which the firmware can process gcodes". It's somewhere between 1000 and 2000 gcodes/sec. There is probably scope to increase it, however it doesn't seem to be a limiting factor during normal printing.

Hello, I have some strange pause also during printing but the speed is not so hight. For me it seem appear arround G92 E0. My slicer is S3D.
[[language]] G1 X62.782 Y81.493 E8.0561 G1 X62.809 Y81.520 E8.0575 G1 X62.915 Y81.626 F2074 G92 E0 G1 E4.5000 F3600 G1 Z0.340 F3000 G1 X63.007 Y76.626 F4500 G1 Z0.240 F3000 G1 E0.0000 F3600 G92 E0 G1 X63.207 Y76.826 E0.0102 F2074 G1 X63.772 Y76.826 E0.0306 G1 X63.572 Y76.626 E0.0408 G1 X64.138 Y76.626 E0.0613
SOLVED : After looking deeper, the pause was only because the retraction speed is higher than in my config file.

On the offchance, just tried taking the code for "layer 40" from the 3rd March 14:58hrs post above, added some startup code and ran it on the printer (a BigBox).
The layer is printed "in the air" at Z = 6mm, and pause is perceptible when the extruder reaches the 4 o'clock position (as it passes in both directions).
Still have no idea why?
G90 M83 M106 S0 M140 S85 M190 S85 M104 S230 T0 M109 S230 T0 ;BigBox Printer Start Script Begin ;M117 Home. ;Autohome G28 ;M117 Print Starting. ;Dock G1 X70 Y200 F3000 G1 Y240 ;M117 Prime Extruder T0 ;Select Extruder 0 G92 E0 ;Reset E G1 E10 F200 ;Extruder 10mm G92 E0 ;Reset E ;M117 Undock against fresh part of nozzlewiper G1 X80 Y240 F3000 G1 X80 Y200 F3000 ;BigBox Printer Start Script End G1 E1.6000 F2700 G1 Z0.150 F360 ; Layer 1, Z = 0.15 T0 ; tool H0.150 W0.600 ; Layer 40, Z = 6 ; inner perimeter ; inner perimeter ; inner perimeter ; inner perimeter ; inner perimeter ; inner perimeter ; inner perimeter ; outer perimeter G1 X78.786 Y130.215 F4500 G1 Z6.000 F360 G1 E1.6000 F2700 G1 X78.080 Y130.185 E0.0201 F1800 G1 X77.345 Y130.097 E0.0210 G1 X76.588 Y129.952 E0.0219 G1 X75.814 Y129.750 E0.0227 G1 X75.329 Y129.596 E0.0145 G1 X74.843 Y129.420 E0.0147 G1 X74.359 Y129.224 E0.0149 G1 X73.879 Y129.006 E0.0150 G1 X73.405 Y128.768 E0.0151 G1 X72.940 Y128.510 E0.0151 G1 X72.485 Y128.231 E0.0152 G1 X72.043 Y127.934 E0.0151 G1 X71.616 Y127.617 E0.0151 G1 X71.206 Y127.282 E0.0151 G1 X70.815 Y126.928 E0.0150 G1 X70.444 Y126.556 E0.0149 G1 X70.097 Y126.166 E0.0149 G1 X69.774 Y125.764 E0.0147 G1 X69.476 Y125.352 E0.0145 G1 X69.200 Y124.930 E0.0143 G1 X69.085 Y124.740 E0.0063 G1 X69.766 Y124.740 E0.0194 G1 X70.160 Y125.294 E0.0193 G1 X70.532 Y125.752 E0.0168 G1 X70.936 Y126.190 E0.0169 G1 X71.370 Y126.608 E0.0171 G1 X71.831 Y127.004 E0.0173 G1 X72.316 Y127.375 E0.0174 G1 X72.822 Y127.721 E0.0174 G1 X73.345 Y128.040 E0.0174 G1 X73.884 Y128.329 E0.0174 G1 X74.434 Y128.588 E0.0173 G1 X74.992 Y128.813 E0.0171 G1 X75.553 Y129.006 E0.0169 G1 X76.114 Y129.168 E0.0166 G1 X76.670 Y129.298 E0.0162 G1 X77.219 Y129.398 E0.0159 G1 X77.756 Y129.468 E0.0154 G1 X78.278 Y129.510 E0.0149 G1 X78.778 Y129.524 E0.0142 G1 X215.167 Y129.524 E3.8785 G1 X215.667 Y129.510 E0.0142 G1 X216.189 Y129.468 E0.0149 G1 X216.726 Y129.397 E0.0154 G1 X217.275 Y129.297 E0.0159 G1 X217.831 Y129.167 E0.0162 G1 X218.392 Y129.006 E0.0166 G1 X218.953 Y128.813 E0.0169 G1 X219.511 Y128.588 E0.0171 G1 X220.061 Y128.330 E0.0173 G1 X220.600 Y128.040 E0.0174 G1 X221.124 Y127.722 E0.0174 G1 X221.629 Y127.376 E0.0174 G1 X222.114 Y127.004 E0.0174 G1 X222.575 Y126.608 E0.0173 G1 X223.009 Y126.190 E0.0171 G1 X223.413 Y125.752 E0.0169 G1 X223.785 Y125.295 E0.0167 G1 X224.126 Y124.824 E0.0165 G1 X224.437 Y124.342 E0.0163 G1 X224.719 Y123.852 E0.0161 G1 X224.971 Y123.358 E0.0158 G1 X225.194 Y122.863 E0.0154 G1 X225.389 Y122.371 E0.0150 G1 X225.555 Y121.886 E0.0146 G1 X225.693 Y121.410 E0.0141 G1 X225.807 Y120.946 E0.0136 G1 X225.966 Y120.077 E0.0251 G1 X226.049 Y119.292 E0.0225 G1 X226.073 Y118.619 E0.0192 G1 X226.073 Y81.381 E1.0589 G1 X226.049 Y80.710 E0.0191 G1 X226.015 Y80.325 E0.0110 G1 X225.896 Y79.496 E0.0238 G1 X225.694 Y78.592 E0.0264 G1 X225.555 Y78.114 E0.0141 G1 X225.389 Y77.629 E0.0146 G1 X225.194 Y77.137 E0.0150 G1 X224.971 Y76.642 E0.0154 G1 X224.719 Y76.148 E0.0158 G1 X224.437 Y75.658 E0.0161 G1 X224.126 Y75.176 E0.0163 G1 X223.785 Y74.705 E0.0165 G1 X223.413 Y74.248 E0.0167 G1 X223.009 Y73.810 E0.0169 G1 X222.575 Y73.392 E0.0171 G1 X222.114 Y72.996 E0.0173 G1 X221.629 Y72.625 E0.0174 G1 X221.123 Y72.279 E0.0174 G1 X220.600 Y71.960 E0.0174 G1 X220.061 Y71.671 E0.0174 G1 X219.511 Y71.412 E0.0173 G1 X218.953 Y71.187 E0.0171 G1 X218.392 Y70.994 E0.0169 G1 X217.831 Y70.832 E0.0166 G1 X217.275 Y70.702 E0.0162 G1 X216.726 Y70.602 E0.0159 G1 X216.189 Y70.532 E0.0154 G1 X215.667 Y70.490 E0.0149 G1 X215.167 Y70.476 E0.0142 G1 X78.778 Y70.476 E3.8785 G1 X78.278 Y70.490 E0.0142 G1 X77.756 Y70.532 E0.0149 G1 X77.218 Y70.603 E0.0154 G1 X76.670 Y70.703 E0.0159 G1 X76.114 Y70.833 E0.0162 G1 X75.553 Y70.994 E0.0166 G1 X74.992 Y71.187 E0.0169 G1 X74.434 Y71.412 E0.0171 G1 X73.884 Y71.670 E0.0173 G1 X73.345 Y71.960 E0.0174 G1 X72.821 Y72.278 E0.0174 G1 X72.316 Y72.624 E0.0174 G1 X71.831 Y72.996 E0.0174 G1 X71.370 Y73.392 E0.0173 G1 X70.934 Y73.811 E0.0172 G1 X70.536 Y74.260 E0.0171 G1 X69.757 Y74.260 E0.0222 G1 X69.776 Y74.233 E0.0009 G1 X70.164 Y73.755 E0.0175 G1 X70.590 Y73.293 E0.0179 G1 X71.047 Y72.858 E0.0180 G1 X71.533 Y72.448 E0.0181 G1 X72.043 Y72.066 E0.0181 G1 X72.575 Y71.711 E0.0182 G1 X73.125 Y71.385 E0.0182 G1 X73.688 Y71.087 E0.0181 G1 X74.262 Y70.818 E0.0180 G1 X74.843 Y70.579 E0.0178 G1 X75.427 Y70.371 E0.0176 G1 X76.010 Y70.194 E0.0173 G1 X76.588 Y70.048 E0.0170 G1 X77.158 Y69.933 E0.0165 G1 X77.716 Y69.851 E0.0160 G1 X78.258 Y69.802 E0.0155 G1 X78.785 Y69.785 E0.0150 G1 X215.222 Y69.785 E3.8799 G1 X215.749 Y69.801 E0.0150 G1 X216.292 Y69.849 E0.0155 G1 X216.850 Y69.930 E0.0160 G1 X217.420 Y70.044 E0.0165 G1 X217.997 Y70.188 E0.0169 G1 X218.579 Y70.365 E0.0173 G1 X219.162 Y70.572 E0.0176 G1 X219.741 Y70.809 E0.0178 G1 X220.314 Y71.076 E0.0180 G1 X220.876 Y71.372 E0.0181 G1 X221.423 Y71.697 E0.0181 G1 X221.953 Y72.050 E0.0181 G1 X222.461 Y72.430 E0.0181 G1 X222.945 Y72.837 E0.0180 G1 X223.399 Y73.270 E0.0179 G1 X223.823 Y73.730 E0.0178 G1 X224.210 Y74.208 E0.0175 G1 X224.562 Y74.702 E0.0173 G1 X224.882 Y75.207 E0.0170 G1 X225.170 Y75.720 E0.0167 G1 X225.428 Y76.238 E0.0165 G1 X225.657 Y76.757 E0.0161 G1 X225.857 Y77.275 E0.0158 G1 X226.031 Y77.788 E0.0154 G1 X226.179 Y78.291 E0.0149 G1 X226.303 Y78.781 E0.0144 G1 X226.485 Y79.717 E0.0271 G1 X226.585 Y80.562 E0.0242 G1 X226.616 Y81.295 E0.0208 G1 X226.616 Y118.707 E1.0639 G1 X226.603 Y119.181 E0.0135 G1 X226.560 Y119.708 E0.0150 G1 X226.485 Y120.282 E0.0165 G1 X226.374 Y120.896 E0.0177 G1 X226.179 Y121.708 E0.0237 G1 X225.918 Y122.553 E0.0251 G1 X225.584 Y123.416 E0.0263 G1 X225.169 Y124.282 E0.0273 G1 X224.933 Y124.708 E0.0139 G1 X224.673 Y125.131 E0.0141 G1 X224.390 Y125.547 E0.0143 G1 X224.084 Y125.953 E0.0145 G1 X223.754 Y126.349 E0.0146 G1 X223.400 Y126.730 E0.0148 G1 X223.023 Y127.092 E0.0149 G1 X222.625 Y127.437 E0.0150 G1 X222.210 Y127.763 E0.0150 G1 X221.779 Y128.071 E0.0151 G1 X221.333 Y128.359 E0.0151 G1 X220.876 Y128.628 E0.0151 G1 X220.408 Y128.877 E0.0151 G1 X219.933 Y129.105 E0.0150 G1 X219.452 Y129.313 E0.0149 G1 X218.968 Y129.501 E0.0148 G1 X218.482 Y129.667 E0.0146 G1 X217.997 Y129.811 E0.0144 G1 X217.516 Y129.934 E0.0141 G1 X217.039 Y130.035 E0.0139 G1 X216.569 Y130.114 E0.0135 G1 X216.109 Y130.170 E0.0132 G1 X215.661 Y130.204 E0.0128 G1 X215.222 Y130.215 E0.0125 G1 X78.786 Y130.215 E3.8799 G1 E1.6000 F2700 ; Layer 41, Z = 6.15

A small correction: I should have said "you have hit the limit at which the firmware can process gcodes". It's somewhere between 1000 and 2000 gcodes/sec. There is probably scope to increase it, however it doesn't seem to be a limiting factor during normal printing.
Found what was going on. The gap fill speed was set to 0 in Slic3r.