Thank you so much, Frank! All the best for your research. And thank you so much for the step-by-step guide!
If I had a choice, I would not use CentOS 7. Unfortunately, this is not up to me. On Wed, Jul 6, 2016 at 2:05 PM, <[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: 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 <[email protected]> > To: Main discussion list for the graph-tool project > <[email protected]> > Subject: Re: [graph-tool] Best Practice for Installing graph-tool-2.16 > on CentOS 7 for Non-Tech Sophisticated Researcher > Message-ID: <[email protected]> > 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 <[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/20160706/0bbb6625/attachment-0001.asc > > > > ------------------------------ > > Message: 2 > Date: Wed, 6 Jul 2016 22:31:41 +0200 > From: Frank Takes <[email protected]> > To: Main discussion list for the graph-tool project > <[email protected]> > Subject: Re: [graph-tool] Best Practice for Installing graph-tool-2.16 > on CentOS 7 for Non-Tech Sophisticated Researcher > Message-ID: > <CAOUtDX89h0EP= > [email protected]> > Content-Type: text/plain; charset="utf-8" > > 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 > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > https://lists.skewed.de/pipermail/graph-tool/attachments/20160706/ee759616/attachment.html > > > > ------------------------------ > > 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 6 > ****************************************** >
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