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 > ****************************************** >
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