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Today's Topics:
1. Re: Best Practice for Installing graph-tool-2.16 on CentOS 7
for Non-Tech Sophisticated Researcher (Tiago de Paula Peixoto)
2. Re: Best Practice for Installing graph-tool-2.16 on CentOS 7
for Non-Tech Sophisticated Researcher (Frank Takes)
----------------------------------------------------------------------
Message: 1
Date: Wed, 6 Jul 2016 19:30:35 +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] Best Practice for Installing graph-tool-2.16
on CentOS 7 for Non-Tech Sophisticated Researcher
Message-ID: <ed1693d4-2490-80e0-7871-fd3dc09d2756@skewed.de>
Content-Type: text/plain; charset="utf-8"
On 06.07.2016 19:28, Yu Zheng wrote:
> 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,
Don't use CentOS 7, I guess...
--
Tiago de Paula Peixoto <tiago@skewed.de>
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Message: 2
Date: Wed, 6 Jul 2016 22:31:41 +0200
From: Frank Takes <ftakes@liacs.nl>
To: Main discussion list for the graph-tool project
<graph-tool@skewed.de>
Subject: Re: [graph-tool] Best Practice for Installing graph-tool-2.16
on CentOS 7 for Non-Tech Sophisticated Researcher
Message-ID:
<CAOUtDX89h0EP=KvaC9S741D61JR9BncX8Rpkq9QUB2PTP4JPWQ@mail.gmail.com>
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Hello Yu,
CentOS is not meant as an operating system with the latest packages.
It is rather meant as a stable server operating system.
However, you can install the devtoolset-4 SCL which does provide more
recent packages, see for example
https://www.softwarecollections.org/en/scls/rhscl/devtoolset-4/
At my university, I have Graph-Tool running on a large number of CentOS 7
servers.
For installation, I use the steps as described below this e-mail.
Good luck!
Kind regards,
Frank
---
=================================
Installing graph-tool on CentOS (6.)7
=================================
Introduction:
=============
This document briefly describes how graph-tool, a package for network
analysis, can be installed on a freshly installed CentOS (6.)7 server.
It relies both on python and on a number of C++ packages, and it will be
installed with OpenMP support for parallel computation.
See https://graph-tool.skewed.de/ for more details on the package.
Note that for yum install and make install, sudo/root-rights are needed.
Installation steps:
===================
- yum-install devtoolset-4, which brings GCC compiler version 5, and enable
it by typing:
scl enable devtoolset-4 bash
Or permanently use this SCL by adding to your ~/.bashrc file the line:
source /opt/rh/devtoolset-4/enable
Depending on which Python version you want graph-tool to talk to, you may
also want to install an SCL of Python 2.7 or 3.4.
- yum install bzip2-devel zlib-devel expat-devel mpfr-devel (mpfr is needed
for CGAL)
- pip install scipy numpy matplotlib
- optional: yum install cairo-devel cairomm sparsehash-devel graphviz-devel
- to avoid confusion and extra steps later on, remove the old boost version
using:
yum remove boost148*
In theory, I guess that maybe you could also leave the old version as is,
and only install boost in the devtoolset-4 SCL, but I don't know how that
works.
- download boost >= 1.6 from http://www.boost.org/ and then install using:
./bootstrap.sh
./b2 install --prefix=/opt/rh/devtoolset-4/root/usr/local
If next * is whatever in the next step graph-tool complains about missing
from boost, such as iostreams or coroutine, run:
./b2 install --prefix=/opt/rh/devtoolset-4/root/usr/local --with-*
- download CGAL from the website http://www.cgal.org/ and install using:
cmake .
make
make install
- download graph-tool from the website https://graph-tool.skewed.de/ and
install using:
./configure --enable-openmp
make
Configure with --disable-cairo or --disable-sparsehash if you skipped those
optional installs.
Other parameters allow one to set for example the python version.
Done.
---
2016-07-06 19:28 GMT+02:00 Yu Zheng <yz2235@stanford.edu>:
> 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:
>
>> 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 (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>
>> >
>> > -------------- next part --------------
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>> >
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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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>> >
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>> > >
>> >
>> > ------------------------------
>> >
>> > Subject: Digest Footer
>> >
>> > _______________________________________________
>> > graph-tool mailing list
>> > graph-tool@skewed.de
>> > https://lists.skewed.de/mailman/listinfo/graph-tool
>> >
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>> >
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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.
>>
>>
>>
>> --
>> View this message in context:
>> http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/Simple-node-access-runtime-tp4026645.html
>> Sent from the Main discussion list for the graph-tool project mailing
>> list archive at Nabble.com.
>>
>>
>> ------------------------------
>>
>> Subject: Digest Footer
>>
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>> graph-tool@skewed.de
>> https://lists.skewed.de/mailman/listinfo/graph-tool
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>>
>
>
> _______________________________________________
> graph-tool mailing list
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