Re: [igraph] ARPACK error in igraph 0.6

[Gábor Csárdi]

Paul,

thanks for the useful tips.

R igraph 0.6 uses the same BLAS/LAPACK as R uses, and we want to keep
it this way. (Unless the BLAS in R turns out to be really bad.)

As for the problem, we would need a bit more info to see whether this
is just ARPACK failing, or something that we can repair.

Best,
Gabor

On Thu, Nov 24, 2011 at 12:34 AM, Paul Johnson <address@hidden> wrote:
> On Tue, Nov 15, 2011 at 6:22 PM, Leo Alekseyev <address@hidden> wrote:
>> I am trying to compute the page rank of a graph with ~50,000 vertices
>> and 300,000 edges.  I'm using the R interface to the latest nightly of
>> igraph (igraph_nightly_0.6-2591-20111110).  I keep running into the
>> following error:
>>
>> At arpack.c:961 : ARPACK error, The Schur form computed by LAPACK
>> routine dlahqr could not be reordered by LAPACK routine dtrsen.
>>
> I'm sorry if I am telling you something you already know.
>
> R is delivered with only a basic BLAS setup, and one can set it up to
> use an enhanced shared library implementation of BLAS, such as ATLAS,
> GOTOblas2 (now the openblas package), or the Intel MKL (packaged for
> Ubuntu's version of R).  This can  be done either by re-compiling R to
> tell it explicitly where the BLAS is located or by configuring R to
> use a shared BLAS that can be substituted at runtime.
> From what I can tell, this can be frustrating for Windows users, but
> it is easy on Linux/Unix/Mac.
>
> I am a little unsure which particular LAPACK routines get replaced, I
> think not all shared BLAS libraries will be identical.  I'm no expert
> on that part. But if you read, for example here:
>
> http://software.intel.com/en-us/articles/intel-mkl
>
> It appears that even if your particular LAPACK function is not
> replaced, it may work better because it is built on the better version
> of BLAS.
>
> Depending on which version of Linux you run, it may be more or less
> easy to switch the BLAS implementation you rely on.   I am sure there
> are substantial performance differences to be had by changing this.
>
> The first time I did this, I was following the instructions in the
> R-admin manual, and that describes one approach.  Dirk Eddelbuettel
> helped me figure out quite a few details, he's the packager for Ubuntu
> and Debian. If you run Ubuntu, I think it is quite easy to use the
> Intel MKL because r-revolution is a package that is designed to drop
> in the new BLAS where R will find it (as I recall, that R is compiled
> so that R looks in the ld load path.
>
> The devel headers for building R can be the same, the only part that
> changes is the location of the shared BLAS library. I'm running Debian
> now, for example, and the shared library name that programs look for
> is
>
> libblas.so
>
> but that ends up at ATLAS through a series of links,
>
>  libblas.so -> libblas.so.3gf
>
> /usr/lib/libblas.so.3gf -> /etc/alternatives/libblas.so.3gf
> /etc/alternatives/libblas.so.3gf -> /usr/lib/atlas-base/atlas/libblas.so.3gf
>
> Well, I can feel myself getting carried away. The point is, if your
> BLAS/LAPACK routine crashes, try swapping out your BLAS, it may make
> you happy.
>
> PJ
>
> --
> Paul E. Johnson
> Professor, Political Science
> 1541 Lilac Lane, Room 504
> University of Kansas
>
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-- 
Gabor Csardi <address@hidden>     MTA KFKI RMKI