[R-sig-hpc] libRblas.so => not found problem
jgrn at illinois.edu
Thu Apr 5 23:27:24 CEST 2012
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!
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:
>> 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)
> 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.
>> 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
>> R-sig-hpc mailing list
>> R-sig-hpc at r-project.org
Jonathan A. Greenberg, PhD
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007
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