can't get graphviz work on mac

Question

can't get graphviz work on mac

pfllo opened this issue 9 years ago · comments

When I try to use "graph.dot" on mac, it gives following error:

Warning: Could not load "/usr/local/Cellar/graphviz/2.38.0/lib/graphviz/libgvplugin_dot_layout.6.dylib" - file not found
Error: Layout type: "dot" not recognized. Use one of: circo dot fdp neato nop nop1 nop2 osage patchwork sfdp twopi
/Users/luo123n/torch/install/bin/luajit: ...s/luo123n/torch/install/share/lua/5.1/graph/graphviz.lua:135: graphviz layout failed
stack traceback:
    [C]: in function 'assert'
    ...s/luo123n/torch/install/share/lua/5.1/graph/graphviz.lua:135: in function 'graphvizFile'
    ...s/luo123n/torch/install/share/lua/5.1/graph/graphviz.lua:162: in function 'dot'
    test.lua:23: in main chunk
    [C]: in function 'dofile'
    ...123n/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:131: in main chunk
    [C]: at 0x010e387330

I can find similar issues using google, but there seems no solution yet.

Sebastian Bodenstein · Answer 1 · Sat Aug 08 2015 02:53:12 GMT+0800 (China Standard Time)

I get exactly the same error on two separate Mac's.

Hugh Perkins · Answer 2 · Sat Aug 08 2015 09:51:02 GMT+0800 (China Standard Time)

I originally thought this might be similar to #59 , but on closer inspection looks like you are missing a dependency of one of the dylibs imported, plausibly a dependency of libgvc.so . It seems that actually this dll is being loaded ok, since you get as far as line 135 of graphviz.lua before crashing, so maybe you have an older version of gvc, or a newer version, or you're missing a plugin called something like 'dot_layout'?

Hugh Perkins · Answer 3 · Sat Aug 08 2015 09:52:53 GMT+0800 (China Standard Time)

By the way, on linux ubuntu, I have no such plugin/.so, and graphviz works for me. Just in case it is useful, here is some output from a couple of diag commands:

user@pear:~/git/nngraph$ ldd /usr/lib/libgvc.so.6
    linux-vdso.so.1 =>  (0x00007fff5c3dd000)
    libltdl.so.7 => /usr/lib/x86_64-linux-gnu/libltdl.so.7 (0x00007f4af5bb8000)
    libcdt.so.5 => /usr/lib/libcdt.so.5 (0x00007f4af59b1000)
    libcgraph.so.6 => /usr/lib/libcgraph.so.6 (0x00007f4af579a000)
    libpathplan.so.4 => /usr/lib/libpathplan.so.4 (0x00007f4af5592000)
    libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f4af5368000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f4af514e000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f4af4e48000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f4af4a83000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f4af487e000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f4af6082000)
user@pear:~/git/nngraph$ ldd /usr/lib/libcgraph.so.6
    linux-vdso.so.1 =>  (0x00007fff653f9000)
    libcdt.so.5 => /usr/lib/libcdt.so.5 (0x00007f5aedc65000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f5aed8a0000)
    /lib64/ld-linux-x86-64.so.2 (0x00007f5aee0a7000)
user@pear:~/git/nngraph$ ls /usr/lib/*dot*
ls: cannot access /usr/lib/*dot*: No such file or directory

vid28 · Answer 4 · Fri Aug 14 2015 15:10:24 GMT+0800 (China Standard Time)

hi
I have the same error.
Did you find a solution ?

But for answer hughperkins :

$ otool -L /usr/local/lib/libgvc.6.dylib
/usr/local/lib/libgvc.6.dylib:
/usr/local/lib/libgvc.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libxdot.4.dylib (compatibility version 5.0.0, current version 5.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libcdt.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libcgraph.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libpathplan.4.dylib (compatibility version 5.0.0, current version 5.0.0)
/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 7.2.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)

$ otool -L /usr/local/lib/libcgraph.6.dylib
/usr/local/lib/libcgraph.6.dylib:
/usr/local/lib/libcgraph.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libcdt.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)

So I don't inderstand why it's doesn't works :/

Hugh Perkins · Answer 5 · Fri Aug 14 2015 16:06:35 GMT+0800 (China Standard Time)

well, to be fair, you really odnt have this file: libgvplugin_dot_layout.6.dylib do you have some way of asking your package manager which package contains this file?

vid28 · Answer 6 · Fri Aug 14 2015 16:11:42 GMT+0800 (China Standard Time)

this file is on the path referenced by the error :
/usr/local/Cellar/graphviz/2.38.0/lib/graphviz/libgvplugin_dot_layout.6.dylib

I don't know if It respond to you question

vid28 · Answer 7 · Fri Aug 14 2015 16:12:38 GMT+0800 (China Standard Time)

the file exist at this path, I check it

Andrew Ortman · Answer 8 · Sun Aug 16 2015 08:44:43 GMT+0800 (China Standard Time)

I'm also seeing this issue -

Andrews-MacBook-Pro:graphviz andrewortman$ otool -L /usr/local/Cellar/graphviz/2.38.0/lib/graphviz/libgvplugin_dot_layout.6.dylib
/usr/local/Cellar/graphviz/2.38.0/lib/graphviz/libgvplugin_dot_layout.6.dylib:
/usr/local/lib/graphviz/libgvplugin_dot_layout.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libgvc.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libxdot.4.dylib (compatibility version 5.0.0, current version 5.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libcgraph.6.dylib (compatibility version 7.0.0, current version 7.0.0)
/usr/local/Cellar/graphviz/2.38.0/lib/libpathplan.4.dylib (compatibility version 5.0.0, current version 5.0.0)
/usr/lib/libexpat.1.dylib (compatibility version 7.0.0, current version 7.2.0)
/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.5)
/usr/local/Cellar/graphviz/2.38.0/lib/libcdt.5.dylib (compatibility version 6.0.0, current version 6.0.0)
/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1213.0.0)

Andrew Ortman · Answer 9 · Sun Aug 16 2015 08:54:47 GMT+0800 (China Standard Time)

I just got this to work by uninstalling the brew version of graphviz and install 0.26 from graphviz's site:
www.graphviz.org/Download_macos.php

I'm using Mac OSX Yosemite, if that provides additional context

Hope that helps

W.P. McNeill · Answer 10 · Sat Aug 22 2015 06:18:31 GMT+0800 (China Standard Time)

I see the same thing, but I do have /usr/local/Cellar/graphviz/2.38.0/lib/graphviz/libgvplugin_dot_layout.6.dylib on my system. (Mac 10.10.5, graphviz installed via Homebrew.)

BersaKAIN · Answer 11 · Wed Sep 02 2015 04:37:18 GMT+0800 (China Standard Time)

it seems installing using brew will make a link

-r--r--r--  1 yiranzhang  admin   139K Aug 31 22:14 libgvplugin_dot_layout.6.dylib
lrwxr-xr-x  1 yiranzhang  admin    30B Oct 22  2014 libgvplugin_dot_layout.dylib ->libgvplugin_dot_layout.6.dylib

so that file we are looking for has only write permission. And there is another link to the file thats accessable.

koray kavukcuoglu · Answer 12 · Mon Sep 14 2015 18:03:28 GMT+0800 (China Standard Time)

If this is still a problem, please reopen the issue.

Sina Afrooze · Answer 13 · Sat Nov 07 2015 12:31:59 GMT+0800 (China Standard Time)

Is there actually a resolution to this issue?

Tingfan Wu · Answer 14 · Sun Dec 06 2015 19:21:08 GMT+0800 (China Standard Time)

Here's a workaround works for me. It appears somehow libgvplugin_dot_layout.6.dylib" fails to load its dependency libgvc.dylib so I preload it using

DYLD_INSERT_LIBRARIES=/usr/local/opt/graphviz/lib/libgvc.6.dylib qlua ./test_nngraph.lua

Alternatively,
or one can change torch/install/share/lua/5.1/graph/graphviz.lua, replacing this one

   graphvizOk, graphviz = pcall(function() return ffi.load('libgvc') end)

with

   graphvizOk, graphviz = pcall(function() return ffi.load('libgvc', true) end)

to achieve same effect. Hope this give hints to find the root cause.

Soumith Chintala · Answer 15 · Mon Dec 07 2015 02:21:10 GMT+0800 (China Standard Time)

reinstalling the graph package should fix the issue permanently.

luarocks install graph

Sina Afrooze · Answer 16 · Tue Dec 08 2015 03:27:41 GMT+0800 (China Standard Time)

Reinstalling the graph package using @soumith recommendation works. Thanks! I didn't try the solution recommended by @0wu.

heldev · Answer 17 · Sat Jun 15 2019 09:25:02 GMT+0800 (China Standard Time)

I had the same issue as @wpm had (just a different version and macOS 10.14.5).

bash-3.2$ sfdp -v
sfdp - graphviz version 2.40.1 (20161225.0304)
libdir = "/usr/local/Cellar/graphviz/2.40.1/lib/graphviz"
Warning: Could not load "/usr/local/Cellar/graphviz/2.40.1/lib/graphviz/libgvplugin_neato_layout.6.dylib" - file not found
There is no layout engine support for "sfdp"
Use one of: circo dot fdp neato nop nop1 nop2 osage patchwork sfdp twopi

Then I did this to get the reason why the lib can't be loaded:

bash-3.2$ DYLD_INSERT_LIBRARIES=/usr/local/opt/graphviz/lib/graphviz/libgvplugin_neato_layout.6.dylib sfdp -v
dyld: Library not loaded: /usr/local/opt/gettext/lib/libintl.8.dylib
  Referenced from: /usr/local/opt/graphviz/lib/graphviz/libgvplugin_neato_layout.6.dylib
  Reason: image not found
Segmentation fault: 11

A finally fixed the issue by brew link --force gettext