Re: [igraph] Comparing large graphs

[Charles Novaes de Santana]

Thank you very much, Gábor! Now I could calculate the shortest_paths
for my graphs correctly. I run it for each vertex and stored the
resulted matrix (actually a vector) in a row of my "shortest-path
matrix" using rbind. It worked for both, large and small networks.
Like this:

#include<igraph.h>

int main(void){

        igraph_t g1;
        igraph_matrix_t l1,v1;
        igraph_vs_t vertices;
        int i,j,nverts,nedges;
        FILE *ifile1;

        ifile1=fopen("./network.net", "r");
        if (ifile1==0) {return 10;}
        igraph_read_graph_pajek(&g1, ifile1);
        fclose(ifile1);

        nverts = igraph_vcount(&g1);
        igraph_vs_all(&vertices);
        igraph_matrix_init(&l1,0,nverts );
        igraph_matrix_init(&v1,1,nverts );
        for(i=0;i<nverts;i++){
                
igraph_shortest_paths(&g1,&v1,igraph_vss_1(i),vertices,IGRAPH_ALL);
                igraph_matrix_rbind(&l1,&v1);
        }
        igraph_matrix_destroy(&l1);
        igraph_matrix_destroy(&v1);
        igraph_vs_destroy(&vertices);
        igraph_destroy(&g1);
        
        return;
}

Best,

Charles



On Thu, Dec 6, 2012 at 6:06 PM, Gábor Csárdi <address@hidden> wrote:
> I tried to run your code, but could not on your graph, because the graph is
> too big for my virtual machine. It works well on smaller graphs, though.
>
> If I just calculate the shortest paths from ta single source, i.e.
> igraph_shortest_paths(&g1,&l1,igraph_vss_1(0),vertices,IGRAPH_ALL);
> then it works well, too.
>
> This was on ubuntu 12.4 32 bit with gcc 4.6.3 and igraph 0.6.1. What is your
> igraph version, by the way?
>
> So I don't think inf is the problem. Could you double check that this code
> really fails?
>
> Gabor
>
>
> On Wed, Dec 5, 2012 at 4:17 PM, Charles Novaes de Santana
> <address@hidden> wrote:
>>
>> 32 bits :)
>>
>> On Wed, Dec 5, 2012 at 10:06 PM, Gábor Csárdi <address@hidden> wrote:
>> > PC, I guess. 64 bit or 32 bit?
>> >
>> > G.
>> >
>> >
>> > On Wed, Dec 5, 2012 at 4:04 PM, Charles Novaes de Santana
>> > <address@hidden> wrote:
>> >>
>> >> Sorry. I am using Gcc 4.6.3 on a Ubuntu 12.04.
>> >>
>> >> Thanks,
>> >>
>> >> Charles
>> >> On Wed, Dec 5, 2012 at 10:01 PM, Gábor Csárdi <address@hidden>
>> >> wrote:
>> >> > Charles,
>> >> >
>> >> > what is your platform? OS, OS version, C compiler version? Anything
>> >> > else
>> >> > that you might think is needed to reproduce this?
>> >> >
>> >> > G.
>> >> >
>> >> >
>> >> > On Wed, Dec 5, 2012 at 3:44 PM, Charles Novaes de Santana
>> >> > <address@hidden> wrote:
>> >> >>
>> >> >> Just to explay why I think my problem with the "infinity" values:
>> >> >>
>> >> >> Because I tryied to debug my program and I got the following
>> >> >> message:
>> >> >>
>> >> >> Program received signal SIGSEGV, Segmentation fault.
>> >> >> igraph_vector_fill (v=0xbffff6ac, e=inf) at vector.pmt:682
>> >> >> 682         *ptr = e;
>> >> >>
>> >> >> As the value received by function igraph_vector_fill is "e=inf" I
>> >> >> suppose it was my problem.
>> >> >>
>> >> >> Best,
>> >> >>
>> >> >> Charles
>> >> >>
>> >> >> On Wed, Dec 5, 2012 at 9:40 PM, Charles Novaes de Santana
>> >> >> <address@hidden> wrote:
>> >> >> > Thank you again, Tamás. You were absolutely right about my mistake
>> >> >> > in
>> >> >> > printing the matrix. I did a simple cast and my matrix operations
>> >> >> > worked fine.
>> >> >> >
>> >> >> > But I still have problems with the "infinity" given by the
>> >> >> > shortest_paths function. I did the function you suggested me (to
>> >> >> > replace all IGRAPH_INFINITY by zeros), but I have problems in the
>> >> >> > calculation of the shortest paths itself, before I have the
>> >> >> > opportunity to replace the "inifinity" by "zero".
>> >> >> >
>> >> >> > If you don't mind, I am sending attached to this message a small
>> >> >> > program with the part of my code where I got the error. And an
>> >> >> > example
>> >> >> > of a network I am studying. Maybe it is an error in the format of
>> >> >> > my
>> >> >> > network and I can not understand it yet. Or maybe it is because my
>> >> >> > network is very sparse.
>> >> >> >
>> >> >> > Thank you very much for your attention,
>> >> >> >
>> >> >> > Best,
>> >> >> >
>> >> >> > Charles
>> >> >> >
>> >> >> > /*SOURCE CODE*/
>> >> >> >
>> >> >> > #include<igraph.h>
>> >> >> >
>> >> >> > int main(void){
>> >> >> >         igraph_t g1;
>> >> >> >         igraph_matrix_t l1;
>> >> >> >         igraph_vs_t vertices;
>> >> >> >
>> >> >> >         int i,j;
>> >> >> >         FILE *ifile1;
>> >> >> >
>> >> >> > /*Reading the network*/
>> >> >> >         ifile1=fopen("./network.net", "r");
>> >> >> >         if (ifile1==0) {return 10;}
>> >> >> >         igraph_read_graph_pajek(&g1, ifile1);
>> >> >> >         fclose(ifile1);
>> >> >> >
>> >> >> > /*Initializing the matrix l1 and the vector of vertices*/
>> >> >> >
>> >> >> >         igraph_vs_all(&vertices);
>> >> >> >         igraph_matrix_init(&l1, 0, 0);
>> >> >> >
>> >> >> > /*Calculating the shortest paths*/
>> >> >> >
>> >> >> > igraph_shortest_paths(&g1,&l1,vertices,vertices,IGRAPH_ALL);
>> >> >> >
>> >> >> > /*Desconstructors*/
>> >> >> >         igraph_matrix_destroy(&l1);
>> >> >> >         igraph_vs_destroy(&vertices);
>> >> >> >         igraph_destroy(&g1);
>> >> >> >         return;
>> >> >> > }
>> >> >> >
>> >> >> >
>> >> >> >         igraph_matrix_destroy(&l1);
>> >> >> >         igraph_vs_destroy(&vertices);
>> >> >> >         igraph_destroy(&g1);
>> >> >> >
>> >> >> >
>> >> >> > On Wed, Dec 5, 2012 at 10:32 AM, Tamás Nepusz <address@hidden>
>> >> >> > wrote:
>> >> >> >>> First, I was wondering if Igraph considers IGRAPH_INFINITY as
>> >> >> >>> zero
>> >> >> >>> or
>> >> >> >>> as other value.
>> >> >> >> IGRAPH_INFINITY is infinity, period. It is there only to provide
>> >> >> >> us
>> >> >> >> with a sort-of-platform-independent way to refer to infinity.
>> >> >> >>
>> >> >> >>> I am working with shortest-paths matrices and I would
>> >> >> >>> like the distance between two vertices that can not reach each
>> >> >> >>> other
>> >> >> >>> to be zero.
>> >> >> >> Well, you have to check all the cells in the matrix and if a cell
>> >> >> >> is
>> >> >> >> equal to IGRAPH_INFINITY, you have to set it to  zero.
>> >> >> >>
>> >> >> >>> (I tryied to do "igraph_matrix_scale(matrix,1./2)" and it gave
>> >> >> >>> me a zero-matrix).
>> >> >> >> Theoretically it should work; there is no limitation on
>> >> >> >> igraph_matrix_scale to work on integer values only. I have just
>> >> >> >> tested it on
>> >> >> >> my machine and it worked for me, so I guess that the error is
>> >> >> >> somewhere
>> >> >> >> else; for instance, in the way you print the values.
>> >> >> >>
>> >> >> >> Cheers,
>> >> >> >> --
>> >> >> >> T.
>> >> >> >>
>> >> >> >>
>> >> >> >> _______________________________________________
>> >> >> >> igraph-help mailing list
>> >> >> >> address@hidden
>> >> >> >> https://lists.nongnu.org/mailman/listinfo/igraph-help
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Um axé! :)
>> >> >> >
>> >> >> > --
>> >> >> > Charles Novaes de Santana
>> >> >> > http://www.imedea.uib-csic.es/~charles
>> >> >> > PhD student - Global Change
>> >> >> > Laboratorio Internacional de Cambio Global
>> >> >> > Department of Global Change Research
>> >> >> > Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
>> >> >> > Calle Miquel Marques 21, 07190
>> >> >> > Esporles - Islas Baleares - España
>> >> >> >
>> >> >> > Office phone - +34 971 610 896
>> >> >> > Cell phone - +34 660 207 940
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >> Um axé! :)
>> >> >>
>> >> >> --
>> >> >> Charles Novaes de Santana
>> >> >> http://www.imedea.uib-csic.es/~charles
>> >> >> PhD student - Global Change
>> >> >> Laboratorio Internacional de Cambio Global
>> >> >> Department of Global Change Research
>> >> >> Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
>> >> >> Calle Miquel Marques 21, 07190
>> >> >> Esporles - Islas Baleares - España
>> >> >>
>> >> >> Office phone - +34 971 610 896
>> >> >> Cell phone - +34 660 207 940
>> >> >>
>> >> >> _______________________________________________
>> >> >> igraph-help mailing list
>> >> >> address@hidden
>> >> >> https://lists.nongnu.org/mailman/listinfo/igraph-help
>> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Gabor Csardi <address@hidden>     MTA KFKI RMKI
>> >> >
>> >> >
>> >> > _______________________________________________
>> >> > igraph-help mailing list
>> >> > address@hidden
>> >> > https://lists.nongnu.org/mailman/listinfo/igraph-help
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Um axé! :)
>> >>
>> >> --
>> >> Charles Novaes de Santana
>> >> http://www.imedea.uib-csic.es/~charles
>> >> PhD student - Global Change
>> >> Laboratorio Internacional de Cambio Global
>> >> Department of Global Change Research
>> >> Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
>> >> Calle Miquel Marques 21, 07190
>> >> Esporles - Islas Baleares - España
>> >>
>> >> Office phone - +34 971 610 896
>> >> Cell phone - +34 660 207 940
>> >>
>> >> _______________________________________________
>> >> igraph-help mailing list
>> >> address@hidden
>> >> https://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>> >
>> >
>> >
>> > --
>> > Gabor Csardi <address@hidden>     MTA KFKI RMKI
>> >
>> >
>> > _______________________________________________
>> > igraph-help mailing list
>> > address@hidden
>> > https://lists.nongnu.org/mailman/listinfo/igraph-help
>> >
>>
>>
>>
>> --
>> Um axé! :)
>>
>> --
>> Charles Novaes de Santana
>> http://www.imedea.uib-csic.es/~charles
>> PhD student - Global Change
>> Laboratorio Internacional de Cambio Global
>> Department of Global Change Research
>> Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
>> Calle Miquel Marques 21, 07190
>> Esporles - Islas Baleares - España
>>
>> Office phone - +34 971 610 896
>> Cell phone - +34 660 207 940
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> https://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
>
>
> --
> Gabor Csardi <address@hidden>     MTA KFKI RMKI
>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> https://lists.nongnu.org/mailman/listinfo/igraph-help
>



-- 
Um axé! :)

--
Charles Novaes de Santana
http://www.imedea.uib-csic.es/~charles
PhD student - Global Change
Laboratorio Internacional de Cambio Global
Department of Global Change Research
Instituto Mediterráneo de Estudios Avanzados(CSIC/UIB)
Calle Miquel Marques 21, 07190
Esporles - Islas Baleares - España

Office phone - +34 971 610 896
Cell phone - +34 660 207 940