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

[Jonathan Greenberg]

Simon:

I think you located my problem.  I had set the LD_LIBRARY_PATH for
some other reason, and had compiled the new version of openblas when I
had gotten R 2.15.  openblas was what had apparently not compiled
properly (not R), so R was only using one core.  I removed the
LD_LIBRARY_PATH reference, recompiled/reinstalled openblas, and voila,
I'm back in business.

Just in case someone was wondering about your ldd suggestion, the full
command you want to use to check it is:

R CMD ldd /pathto/R/bin/exec/R

(I was trying to figure out the second part of that statement)

Now, back to coding.  Thanks!

--j

On Thu, Apr 5, 2012 at 1:02 PM, Simon Urbanek
<simon.urbanek at r-project.org> wrote:
>
> 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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>>
>>
>



-- 
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