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

Jonathan Greenberg jgrn at illinois.edu
Thu Apr 5 18:32:15 CEST 2012


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 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)

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.


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

More information about the R-sig-hpc mailing list