[R-sig-hpc] libRblas.so => not found problem

[Jonathan Greenberg]

Follow-up below:

On Thu, Apr 5, 2012 at 11:58 AM, Dirk Eddelbuettel <edd at debian.org> wrote:
>
> On 5 April 2012 at 11:32, Jonathan Greenberg wrote:
> | r-sig-hpc'ers:
> |
> | I'm banging my head against a wall with this.  I recently updated R to 2.15 via:
> |
> | ./configure --prefix=/pathtoinstall/ --enable-R-shlib --enable-BLAS-shlib
> | make
> | make install
> |
> | I noticed that I wasn't getting a multithreaded response on, e.g.:
> | a = matrix(rnorm(5000*5000), 5000, 5000)
> | b = matrix(rnorm(5000*5000), 5000, 5000)
> | c = a%*%b
> |
> | [This used to light up all 12 cores on our system, now it only lights
> | up one and takes MUCH longer].
> |
> | I have an update-alternatives set up for /pathto/R/lib/libRblas.so (I
> | backed up the installed one to libRblas.so_bak) where I have a few
> | flavors of BLAS I've been playing with (including one that USED to
> | work, an alpha of OpenBLAS).  I also have the most recent OpenBLAS and
> | Intel MKL.  The update-alternatives IS working.
> |
> | When I ldd R I see I no longer have a link to libRblas.so:
> |  ldd /pathto/R/bin/exec/R
> |         linux-vdso.so.1 =>  (0x00007fffd4a9e000)
> |         libR.so => not found
> |         libRblas.so => not found
>
> I think that means that R chose to build its own BLAS as your configure call
> did not lead to all required headers.
>
> Do 'locate libRblas.so' -- it exists, and /usr/bin/R sets variables to find
> it.
>
> I suspect your problem really is with your local compilation.

Ah hah -- ok, where in the configure script can I point it towards my
local BLAS libraries?  I presume the --prefix isn't cutting it...
> | Nothing I do seems to re-link this, and even downgrading back to R
> | 2.14.2 hasn't fixed this.  I even removed the /pathto/R directory to
> | attempt a "clean" install.   FYI: I am on a system that MUST have R
> | compiled from scratch, so I can't use any pre-existing binaries.
>
> Why?
> It all works.  If you can't use them, maybe you want to at least study their
> build recipes. The debian/ directory is in the sources after all.  But it
> seems silly that you want to reinvent the use of update-alternatives etc.

I'm on a supercomputer which loads its entire base system and a small
subset of modules into main memory.  An optimized R is not one of
these modules that the admins have deigned to install.  All remaining
programs MUST be compiled by the end users, hence I can't use apt-get
(I've heard tales of non-root users getting this to work, but I was
not able to ever figure this out -- compiling from scratch was a lot
easier).  I will look at your build recipes to see if I can parse it.
It seems like I might just need to point the configure script towards
my "local" libraries, although I'm not quite sure how to do that...

--j


-- 
Jonathan A. Greenberg, PhD
Assistant Professor
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
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