Re: [graph-tool] Best Practice for Installing graph-tool-2.16 on CentOS 7 for Non-Tech Sophisticated Researcher
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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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)
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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:
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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)
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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>
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>
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)
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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)
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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>
participants (3)
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Frank Takes -
Tiago de Paula Peixoto -
Yu Zheng