how to use neato with spline and avoid mutual edges overlapping?

Question

I have a directed graph with ~20 nodes that I need to have their positions fixed. So, I'm using neato to generate my svg file. The problem is that if I use the straight lines, I have edges overlapping some of the nodes. If a set -Gsplines=true -Gsep=1 the edges avoid the nodes nicely but them the mutual nodes (that is, nodes from a -> b and b -> a) are displayed on top of each other... Below is a piece of it, for example, where edges 9 -> 12 and 12 -> are completely overlapped. Does anyone know a way around this? I can go with the straight lines that crosses nodes, but if I can manage to avoid them and have the mutual edges displayed separately, would be ideal. Unfortunately, using plain dot is not an option since the fixed position of the nodes is imperative, since my final goal is to put this on top of a map (which I'm doing "by hand" with inkscape). Solutions in other languages (with examples, if possible), are also appreciated.

digraph {
7 [width=0.388723, shape=circle, style=filled,pos="-5.3642582,-2.953523!", color="#CCFFFF"];
9 [width=1.02852, shape=circle, style=filled,pos="-9.84668,4.0044438!", color="#CCFF00"];
12 [width=0.337023, shape=circle, style=filled,pos="-9.2490238,1.6804541!", color="#CC9933"];
13 [width=0.315507, shape=circle, style=filled,pos="-7.456055,0.035156!", color="#99FFCC"];
17 [width=0.164396, shape=circle, style=filled,pos="-7.2275394,1.8979026!", color="#33FF99"];

9 -> 7 [penwidth=0.644654, color="#CCFF00"];
9 -> 12 [penwidth=2.04003, color="#CCFF00"];
9 -> 13 [penwidth=1.10067, color="#CCFF00"];
9 -> 17 [penwidth=1.79226, color="#CCFF00"];
12 -> 9 [penwidth=0.5, color="#CC9933"];
12 -> 13 [penwidth=0.75431, color="#CC9933"];
12 -> 17 [penwidth=0.828487, color="#CC9933"];
13 -> 7 [penwidth=0.695661, color="#99FFCC"];
17 -> 13 [penwidth=1.78682, color="#33FF99"];
}

Answer 1

This may be a problem with a particular version of graphviz - here's the output I get with 2.28, and it doesn't display the problems you mentioned.

I added simply splines=true; sep=1; in the graph.

Answer 2

I've installed version 2.28 and got the same result as you for this sample of the data. Unfortunately, for the complete set it breaks down. Without the splines=true it works fine (with straight lines overlapping nodes, as usual). But when I set splines=true, sep=1 it does not generate the svg properly. Runnig it without -Tsvg, I get a memory related error that starts likes this:

 *** glibc detected *** neato: free(): invalid next size (normal): 0x0000000001e96c00  ***
 ======= Backtrace: =========
 /lib/x86_64-linux-gnu/libc.so.6(+0x7a6e6)[0x7f256f1856e6]
 /lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7f256f1899cc]
 /usr/local/lib/graphviz/libgvplugin_neato_layout.so.6(freeRouter+0x3e)[0x7f256aa0095e]
 /usr/local/lib/graphviz/libgvplugin_neato_layout.so.6(+0x19e59)[0x7f256a9eee59]
 /usr/local/lib/graphviz/libgvplugin_neato_layout.so.6(splineEdges+0x24d)[0x7f256a9ef3fd]
 /usr/local/lib/graphviz/libgvplugin_neato_layout.so.6(neato_layout+0x532)[0x7f256a9ea6e2]
 /usr/local/lib/libgvc.so.6(gvLayoutJobs+0x91)[0x7f256f6dae61]
 neato[0x400f3c]
 /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f256f12c30d]
 neato[0x400fad]
 ======= Memory map: ========

The complete graph is this one:

digraph {
 graph [size="16.68,8.55",resolution="72",bgcolor=transparent];
 1 [width=      0.10000000 shape=circle, style=filled,pos="     13.39800000,     -2.34524000!" color="#FFFFFF"];
 2 [width=      0.59517100 shape=circle, style=filled,pos="      1.70387000,      2.39732000!" color="#FFFFCC"];
 3 [width=      1.02015000 shape=circle, style=filled,pos="      0.71950000,      4.79922000!" color="#FF6600"];
 4 [width=      0.42447300 shape=circle, style=filled,pos="      4.54980430,      2.96880530!" color="#FFFF66"];
 5 [width=      0.86597700 shape=circle, style=filled,pos="      3.76904280,      5.57271100!" color="#FFCCCC"];
 6 [width=      1.51677000 shape=circle, style=filled,pos="     11.65283190,      3.98422860!" color="#FFCC33"];
 7 [width=      0.38872300 shape=circle, style=filled,pos="     -5.36425820,     -2.95352300!" color="#CCFFFF"];
 8 [width=      0.18210900 shape=circle, style=filled,pos="      7.01074180,      4.85747900!" color="#CCFF99"];
 9 [width=      1.02852000 shape=circle, style=filled,pos="     -9.84668000,      4.00444380!" color="#CCFF00"];
10 [width=      0.78439800 shape=circle, style=filled,pos="      0.15527310,      0.75367640!" color="#CCFFFF"];
11 [width=      0.58314700 shape=circle, style=filled,pos="      3.67089810,     -0.14061090!" color="#CC99FF"];
12 [width=      0.33702300 shape=circle, style=filled,pos="     -9.24902380,      1.68045410!" color="#CC9933"];
13 [width=      0.31550700 shape=circle, style=filled,pos="     -7.45605500,      0.03515600!" color="#99FFCC"];
14 [width=      2.10000000 shape=circle, style=filled,pos="      7.83691370,      2.19430460!" color="#99FF66"];
15 [width=      1.35638000 shape=circle, style=filled,pos="     11.44042930,      0.19332270!" color="#CC3399"];
16 [width=      0.37155900 shape=circle, style=filled,pos="      2.31738250,     -2.19430460!" color="#33FFFF"];
17 [width=      0.16439600 shape=circle, style=filled,pos="     -7.22753940,      1.89790260!" color="#33FF99"];
 1 ->   6[arrowshape=vee,penwidth=      0.76772236, color="#FFFFFF"];
 1 ->   7[arrowshape=vee,penwidth=      0.50000000, color="#FFFFFF"];
 1 ->  15[arrowshape=vee,penwidth=      0.57695912, color="#FFFFFF"];
 2 ->   3[arrowshape=vee,penwidth=      0.71351528, color="#FFFFCC"];
 2 ->   7[arrowshape=vee,penwidth=      0.98261125, color="#FFFFCC"];
 2 ->  10[arrowshape=vee,penwidth=      2.98429611, color="#FFFFCC"];
 3 ->   2[arrowshape=vee,penwidth=      3.10970125, color="#FF6600"];
 3 ->   4[arrowshape=vee,penwidth=      2.19246934, color="#FF6600"];
 3 ->   5[arrowshape=vee,penwidth=      3.48380699, color="#FF6600"];
 3 ->   8[arrowshape=vee,penwidth=      2.56421761, color="#FF6600"];
 3 ->   9[arrowshape=vee,penwidth=      0.86576911, color="#FF6600"];
 3 ->  10[arrowshape=vee,penwidth=      3.08433716, color="#FF6600"];
 3 ->  16[arrowshape=vee,penwidth=      1.50759938, color="#FF6600"];
 3 ->  17[arrowshape=vee,penwidth=      2.42768450, color="#FF6600"];
 4 ->   2[arrowshape=vee,penwidth=      3.52409026, color="#FFFF66"];
 4 ->   3[arrowshape=vee,penwidth=      1.16680621, color="#FFFF66"];
 4 ->   8[arrowshape=vee,penwidth=      2.83247875, color="#FFFF66"];
 4 ->  11[arrowshape=vee,penwidth=      3.18186134, color="#FFFF66"];
 4 ->  14[arrowshape=vee,penwidth=      3.71014548, color="#FFFF66"];
 4 ->  15[arrowshape=vee,penwidth=      1.33899072, color="#FFFF66"];
 5 ->   3[arrowshape=vee,penwidth=      0.83007122, color="#FFCCCC"];
 5 ->   8[arrowshape=vee,penwidth=      5.11512052, color="#FFCCCC"];
 6 ->   1[arrowshape=vee,penwidth=      1.05435052, color="#FFCC33"];
 6 ->   8[arrowshape=vee,penwidth=      2.17017566, color="#FFCC33"];
 6 ->  15[arrowshape=vee,penwidth=      1.78042048, color="#FFCC33"];
 7 ->  13[arrowshape=vee,penwidth=      1.70638297, color="#CCFFFF"];
 8 ->   5[arrowshape=vee,penwidth=      3.21975483, color="#CCFF99"];
 9 ->  12[arrowshape=vee,penwidth=      2.47722286, color="#CCFF00"];
 9 ->  13[arrowshape=vee,penwidth=      1.41201772, color="#CCFF00"];
 9 ->  17[arrowshape=vee,penwidth=      2.31502497, color="#CCFF00"];
10 ->   2[arrowshape=vee,penwidth=      1.44435627, color="#CCFFFF"];
10 ->   7[arrowshape=vee,penwidth=      1.03121586, color="#CCFFFF"];
10 ->  16[arrowshape=vee,penwidth=      1.50003087, color="#CCFFFF"];
11 ->  10[arrowshape=vee,penwidth=      1.72840183, color="#CC99FF"];
11 ->  16[arrowshape=vee,penwidth=      2.13382591, color="#CC99FF"];
12 ->   9[arrowshape=vee,penwidth=      0.73349271, color="#CC9933"];
12 ->  13[arrowshape=vee,penwidth=      1.50699757, color="#CC9933"];
13 ->   7[arrowshape=vee,penwidth=      1.39745583, color="#99FFCC"];
13 ->  17[arrowshape=vee,penwidth=      1.13347078, color="#99FFCC"];
14 ->   4[arrowshape=vee,penwidth=      1.30211157, color="#99FF66"];
14 ->   5[arrowshape=vee,penwidth=      1.00132679, color="#99FF66"];
15 ->   1[arrowshape=vee,penwidth=      1.32443039, color="#CC3399"];
15 ->   4[arrowshape=vee,penwidth=      1.63346112, color="#CC3399"];
15 ->   6[arrowshape=vee,penwidth=      2.27386028, color="#CC3399"];
15 ->  14[arrowshape=vee,penwidth=      2.67493819, color="#CC3399"];
16 ->  10[arrowshape=vee,penwidth=      3.33223069, color="#33FFFF"];
16 ->  11[arrowshape=vee,penwidth=      3.32587861, color="#33FFFF"];
17 ->   3[arrowshape=vee,penwidth=      0.88032271, color="#33FF99"];
17 ->   9[arrowshape=vee,penwidth=      0.56000418, color="#33FF99"];
17 ->  13[arrowshape=vee,penwidth=      2.95412645, color="#33FF99"];
}