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 <[email protected]>: > 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, <[email protected]> wrote: > >> Send graph-tool mailing list submissions to >> [email protected] >> >> 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 >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> 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 <[email protected]> >> To: [email protected] >> Subject: Re: [graph-tool] Installation error: graph_triangulation.Io >> Message-ID: >> < >> cakajjmxnrzxrywdfrxvgyg27o_vouagjxx1u5sbgbmm_bzg...@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, <[email protected]> wrote: >> >> > Send graph-tool mailing list submissions to >> > [email protected] >> > >> > 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 >> > [email protected] >> > >> > You can reach the person managing the list at >> > [email protected] >> > >> > 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 <[email protected]> >> > To: Main discussion list for the graph-tool project >> > <[email protected]> >> > Subject: Re: [graph-tool] Installation error: graph_triangulation.Io >> > Message-ID: <[email protected]> >> > 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 <[email protected]> >> > >> > -------------- next part -------------- >> > A non-text attachment was scrubbed... >> > Name: signature.asc >> > Type: application/pgp-signature >> > Size: 819 bytes >> > Desc: OpenPGP digital signature >> > URL: < >> > >> https://lists.skewed.de/pipermail/graph-tool/attachments/20160628/4ac8ee73/attachment-0001.asc >> > > >> > >> > ------------------------------ >> > >> > Message: 2 >> > Date: Tue, 28 Jun 2016 22:45:22 +0200 >> > From: Tiago de Paula Peixoto <[email protected]> >> > To: Main discussion list for the graph-tool project >> > <[email protected]> >> > Subject: Re: [graph-tool] Installation error: graph_triangulation.Io >> > Message-ID: <[email protected]> >> > 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 <[email protected]> >> > >> > -------------- next part -------------- >> > A non-text attachment was scrubbed... >> > Name: signature.asc >> > Type: application/pgp-signature >> > Size: 819 bytes >> > Desc: OpenPGP digital signature >> > URL: < >> > >> https://lists.skewed.de/pipermail/graph-tool/attachments/20160628/3ba4cb18/attachment-0001.asc >> > > >> > >> > ------------------------------ >> > >> > Subject: Digest Footer >> > >> > _______________________________________________ >> > graph-tool mailing list >> > [email protected] >> > https://lists.skewed.de/mailman/listinfo/graph-tool >> > >> > >> > ------------------------------ >> > >> > End of graph-tool Digest, Vol 101, Issue 15 >> > ******************************************* >> > >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> https://lists.skewed.de/pipermail/graph-tool/attachments/20160705/c8b0873a/attachment-0001.html >> > >> >> ------------------------------ >> >> Message: 2 >> Date: Tue, 5 Jul 2016 23:04:52 +0200 >> From: Tiago de Paula Peixoto <[email protected]> >> To: Main discussion list for the graph-tool project >> <[email protected]> >> Subject: Re: [graph-tool] Installation error: graph_triangulation.Io >> Message-ID: <[email protected]> >> 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 <[email protected]> >> >> -------------- next part -------------- >> A non-text attachment was scrubbed... >> Name: signature.asc >> Type: application/pgp-signature >> Size: 819 bytes >> Desc: OpenPGP digital signature >> URL: < >> https://lists.skewed.de/pipermail/graph-tool/attachments/20160705/d8327959/attachment-0001.asc >> > >> >> ------------------------------ >> >> Message: 3 >> Date: Wed, 6 Jul 2016 00:46:00 -0700 (MST) >> From: killver <[email protected]> >> To: [email protected] >> Subject: [graph-tool] Simple node access runtime >> Message-ID: <[email protected]> >> 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 >> >> _______________________________________________ >> graph-tool mailing list >> [email protected] >> https://lists.skewed.de/mailman/listinfo/graph-tool >> >> >> ------------------------------ >> >> End of graph-tool Digest, Vol 102, Issue 4 >> ****************************************** >> > > > _______________________________________________ > graph-tool mailing list > [email protected] > https://lists.skewed.de/mailman/listinfo/graph-tool > >
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