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

[Dirk Eddelbuettel]

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.

|         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.

Why?

| Thoughts?

It just works for all of us. I push new packages into Debian when R Core
releases them; I use the same packages also on a bunch of Ubuntu machines
where they are ready thanks to Michael's builds a day later.  

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.

Dirk

 
| --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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