graph-tool can't find Graphviz renderer

graph-tool
1

Hello!

I've got graphviz installed with python and python27 bindings.
However, when I do:

graph_draw(ug, vprops={"label": ug.vertex_index},
output="two-nodes.pdf", layout="fdp")

I get the following error:

graph G {
  graph [outputorder=edgesfirst, mode=major, overlap=true, ratio=fill,
size="5.905512,5.905512", start=3019255687130444316];
  node [label="\N", shape=circle, width="0.105", height="0.105",
style=filled, color="#2e3436", fillcolor="#a40000"];
  edge [arrowsize="0.3", color="#2e3436", penwidth="1.0"];
  graph [bb="0,0,425,425"];
  0 [label=0, width="0.47", height="0.47", pos="330,101"];
  1 [label=1, width="0.47", height="0.47", pos="93,324"];
  0 -- 1 [pos="318,113 277,152 147,274 106,312"];
}
Error: renderer for pdf is unavailable
Out[8]: <PropertyMap object with key type 'Vertex' and value type
'vector<double>', for Graph 0x5ff3f90, at 0x6001290>

At the same time, if I save the above dot expression as test1.dot and
run the following command from the command line:

$ dot -Tpng test1.dot -o graph1.png

I get a beautiful graph1.png.

Graphviz is installed in a non-standard location as I don't have admin
rights. However, the graphviz folder is in LD_LIBRARY_PATH and gv.py
is in PYTHONPATH.
Would very much appreciate your advice on what else graph-tool might
need to find the libraries and/or how to test it better.

Many thanks,
Mikhail

2

PS. Sorry for an inconsistent example!
In fact, both of these work:

$ dot -Tpng test1.dot -o graph1.png
$ dot -Tpdf test1.dot -o graph1.pdf

while none of those do:

graph_draw(ug, vprops={"label": ug.vertex_index},
output="two-nodes.png", layout="fdp")
graph_draw(ug, vprops={"label": ug.vertex_index},
output="two-nodes.pdf", layout="fdp")

so it's not format-dependent.

Many thanks,
Mikhail

3

Hi,

PS. Sorry for an inconsistent example!
In fact, both of these work:

dot \-Tpng test1\.dot \-o graph1\.png dot -Tpdf test1.dot -o graph1.pdf

while none of those do:

graph_draw(ug, vprops={"label": ug.vertex_index},
output="two-nodes.png", layout="fdp")
graph_draw(ug, vprops={"label": ug.vertex_index},
output="two-nodes.pdf", layout="fdp")

so it's not format-dependent.

I cannot reproduce this... Are you sure your command line examples use
the same graphviz installation which is available to graph-tool?

graph-tool just passes the format choice down to the graphviz
library. If it complains it does not understand the format, it means it
was not enabled during compilation.

Check again your LD_LIBRARY_PATH and PYTHON_PATH to make sure they are
pointing to the correct places.

Cheers,
Tiago

4

I've now managed to resolve this. Was due to multiple libgvc versions
present in the system.
My solution, which unfortunately isn't elegant, was to hardcode the
library name into draw/__init__.py instead of using
ctypes.util.find_library.
The problem with find_library is that it doesn't consult
LD_LIBRARY_PATH, making the search algorithm rather inflexible.

libgv = ctypes.CDLL("libgvc.so.6.0.0")
# libname = ctypes.util.find_library("gvc")
# if libname is None:
# raise OSError()
# libgv = ctypes.CDLL(libname)

Best,
Mikhail

5

There should be a way to fix this in a more robust fashion... Could you
perhaps open a ticket, so that I don't forget?

Cheers,
Tiago

6

It's been 4 years since the original post, but I ran into this problem today.
I'm in ubuntu 14.04. Originally I installed graphviz through the ubuntu
repos with `apt-get` and `graphviz_draw` worked fine with pdf's. I removed
my installation of graphviz and built from source and I get the same error
mentioned above. The fix works, although its in 'graphviz_draw.py' not
'__init__.py'.