Hi Tiego, 

I hear your concern about using a deprecated version of graph-tool. Unfortunately, I found out that nothing on CentOS7 meet the pre-requisite of graph-tool-2.16, not even the GCC compiler. And after many hours of reading Linux textbook and browsing the internet, we simply did not manage to build graph-tool-2.16 from source. And that's why we opted for graph-tool-2.8 as a far from perfect solution. 

I wonder if you have any recommendation or general comments for us non-CS trained researchers installing graph-tool-2.16 on CentOS7? Much appreciated,

Yu 

On Wed, Jul 6, 2016 at 3:00 AM, <graph-tool-request@skewed.de> wrote:
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Today's Topics:

   1. Re: Installation error: graph_triangulation.Io (Yu Zheng)
   2. Re: Installation error: graph_triangulation.Io
      (Tiago de Paula Peixoto)
   3. Simple node access runtime (killver)


----------------------------------------------------------------------

Message: 1
Date: Tue, 5 Jul 2016 14:01:25 -0700
From: Yu Zheng <yz2235@stanford.edu>
To: graph-tool@skewed.de
Subject: Re: [graph-tool] Installation error: graph_triangulation.Io
Message-ID:
        <CAKaJjmXNrzXRywDfRXvGyg27o_voUagJxx1u5sBgbMm_bZGtWg@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Tiego,

Thank you so much for helping us out! You were right, CGAL were not
properly configured on the server.

Instead of building everything from source on CentOS7, I built
graph-tool-2.8 instead of the latest release, following the step-by-step
directions here:
https://gist.github.com/sbonner0/2138f2e3e2b249df51c765e1656f9d48. I hope
this link will help others in similar situations.

Much obliged,
Yu

On Wed, Jun 29, 2016 at 3:00 AM, <graph-tool-request@skewed.de> wrote:

> Send graph-tool mailing list submissions to
>         graph-tool@skewed.de
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://lists.skewed.de/mailman/listinfo/graph-tool
> or, via email, send a message with subject or body 'help' to
>         graph-tool-request@skewed.de
>
> You can reach the person managing the list at
>         graph-tool-owner@skewed.de
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of graph-tool digest..."
>
>
> Today's Topics:
>
>    1. Re: Installation error: graph_triangulation.Io
>       (Tiago de Paula Peixoto)
>    2. Re: Installation error: graph_triangulation.Io
>       (Tiago de Paula Peixoto)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 28 Jun 2016 18:43:00 +0200
> From: Tiago de Paula Peixoto <tiago@skewed.de>
> To: Main discussion list for the graph-tool project
>         <graph-tool@skewed.de>
> Subject: Re: [graph-tool] Installation error: graph_triangulation.Io
> Message-ID: <a116a57c-3de4-32bc-f666-7ff9b4e3933f@skewed.de>
> Content-Type: text/plain; charset="utf-8"
>
> On 28.06.2016 18:38, Yu Zheng wrote:
> > CGAL version: 4.9
>
> This might be some incompatibility with version 4.9. I will investigate.
>
> In the mean time, you may downgrade to version 4.8, which should solve
> the problem.
>
> Best,
> Tiago
>
> --
> Tiago de Paula Peixoto <tiago@skewed.de>
>
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>
> Message: 2
> Date: Tue, 28 Jun 2016 22:45:22 +0200
> From: Tiago de Paula Peixoto <tiago@skewed.de>
> To: Main discussion list for the graph-tool project
>         <graph-tool@skewed.de>
> Subject: Re: [graph-tool] Installation error: graph_triangulation.Io
> Message-ID: <5dd77621-7395-a364-98f0-17305e9fff0c@skewed.de>
> Content-Type: text/plain; charset="utf-8"
>
>
> On 28.06.2016 18:38, Yu Zheng wrote:
> > CGAL version: 4.9
>
> I verified, and such a CGAL version simply does not exist. The latest
> version is 4.8.1, which works fine with graph-tool. You can verify here:
>
>        https://github.com/CGAL/cgal/releases
>
> Please check the _actual_ version of CGAL you have installed.
>
> Best,
> Tiago
>
> --
> Tiago de Paula Peixoto <tiago@skewed.de>
>
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Message: 2
Date: Tue, 5 Jul 2016 23:04:52 +0200
From: Tiago de Paula Peixoto <tiago@skewed.de>
To: Main discussion list for the graph-tool project
        <graph-tool@skewed.de>
Subject: Re: [graph-tool] Installation error: graph_triangulation.Io
Message-ID: <623f66ca-fc31-c02d-69f4-9b346de6660d@skewed.de>
Content-Type: text/plain; charset="utf-8"

On 05.07.2016 23:01, Yu Zheng wrote:
> Instead of building everything from source on CentOS7, I built
> graph-tool-2.8 instead of the latest release, following the
> step-by-step directions here:
> https://gist.github.com/sbonner0/2138f2e3e2b249df51c765e1656f9d48. I
> hope this link will help others in similar situations.

This is a _very_ outdated release! Many bugs have been fixed and many
features have been added since then.

Note also that if you encounter problems with old releases, I will not
be able to help.

Best,
Tiago

--
Tiago de Paula Peixoto <tiago@skewed.de>

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------------------------------

Message: 3
Date: Wed, 6 Jul 2016 00:46:00 -0700 (MST)
From: killver <killver@gmail.com>
To: graph-tool@skewed.de
Subject: [graph-tool] Simple node access runtime
Message-ID: <1467791160938-4026645.post@n3.nabble.com>
Content-Type: text/plain; charset=UTF-8

I am currently implementing an existing networkx implementation in graph-tool
and observed that the new implementation runs slower than the networkx one.
I then found out that a simple node access is already slower. So I have the
exact same undirected graph with 1000 nodes and avg. degree of 2 in nx and
gt, and then run:

def select(g):
    for i in range(1000):
        n = g.vertex(0)

def select_nx(g):
    for i in range(1000):
        n = g.nodes(0)

%time select(gt)
CPU times: user 75.6 ms, sys: 69 ?s, total: 75.6 ms
Wall time: 72.6 ms

%time select_nx(g)
CPU times: user 3.82 ms, sys: 0 ns, total: 3.82 ms
Wall time: 3.46 ms

So I am wondering whether this is to be expected and that I can only see the
drastic runtime improvements when working with calculations like shortest
paths etc.



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