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

[Simon Urbanek]

On Apr 5, 2012, at 12:32 PM, 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
>        libgomp.so.1 => /usr/lib64/libgomp.so.1 (0x00007f6b80bf4000)
>        libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f6b809d8000)
>        libc.so.6 => /lib64/libc.so.6 (0x00007f6b80649000)
>        librt.so.1 => /lib64/librt.so.1 (0x00007f6b80441000)
>        /lib64/ld-linux-x86-64.so.2 (0x00007f6b80e01000)
> 

The above is meaningless - use "R CMD ldd" to get the actual paths.

You can override the locations using LD_LIBRARY_PATH but I'd stay away form that as it tends to mess other things up (if you don't know what you're doing).


> Nothing I do seems to re-link this,

You don't want to re-link anything - it's already linked with shared BLAS support as you can see above.

Cheers,
Simon


> 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.
> Thoughts?
> 
> --j
> 
> -- 
> Jonathan A. Greenberg, PhD
> Assistant Professor
> Department of Geography and Geographic Information Science
> University of Illinois at Urbana-Champaign
> 607 South Mathews Avenue, MC 150
> Urbana, IL 61801
> Phone: 415-763-5476
> AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
> http://www.geog.illinois.edu/people/JonathanGreenberg.html
> 
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