search for: blas

Hi Tomas, Thanks for your reply. I find your response curious, however. Surely the identical() test is simply incorrect when catering for possibly different BLAS implementations? Or is it the case that conformant BLAS implementations all produce bit-identical results, which seems unlikely? (Sorry, I am unfamiliar with the BLAS spec.) Although whatever the answer to this theoretical question, the CentOS 7 external BLAS library evidently doesn't produc...

...rom the process: error message, and info from configure output, in that order. I appreciate that someone can guide me (technically in-sophisticated) through this process. Again, thanks for your help. Michael Niu (1). Output from make make[3]: Entering directory `/R/R-2.4.1/src/extra/blas' make[4]: Entering directory `/R/R-2.4.1/src/extra/blas' g77 -D__NO_MATH_INLINES -fpic -g -O2 -c blas.f -o blas.o blas.f:0: warning: -fpic ignored for target (all code is position independent) g77 -D__NO_MATH_INLINES -fpic -g -O2 -c cmplxblas.f -o cmplxblas.o cmplxblas.f:0: warning:...

In practical terms, failing tests are not preventing anyone from using an optimized BLAS/LAPACK implementation they trust. Building R with dynamically linked BLAS on Unix is supported, documented and easy for anyone who builds R from source. It is also how Debian/Ubuntu R packages are built by default, so R uses whichever BLAS is installed in the system and the user does not have t...

>>>>> Tomas Kalibera <tomas.kalibera at gmail.com> >>>>> on Fri, 5 Jan 2018 00:41:47 +0100 writes: > In practical terms, failing tests are not preventing anyone from using > an optimized BLAS/LAPACK implementation they trust. Building R with > dynamically linked BLAS on Unix is supported, documented and easy for > anyone who builds R from source. It is also how Debian/Ubuntu R packages > are built by default, so R uses whichever BLAS is installed in the >...

Dear list, What is the recommended incantation on Fedora 32 to swap out the openblas BLAS that the packaged (rpm) version of R-core installs for ATLAS? I'm running into some problems with some big models I want to fit using the mgcv package, and openblas is apparently not thread safe and is causing problems. I have the following installed: $ dnf list installed | grep ^R R-co...

Dear Tom, The change in the Fedora RPM from using R's internal BLAS to external BLAS means the Fedora R binary now fails one of R's regression tests, specifically: tests/reg-BLAS.R. You can run this code by hand to verify the issue. As noted in the R administration and Installation Manual, "R relies on ISO/IEC 60559 compliance of an external BLAS. This ca...

Hi Tomas, Thanks for your answer. Indeed, I checked and my R-3.4.1 installed from the ubuntu repository use 'libopenblasp-r0.2.18.so' while my R-3.3.2 that I did compiled on my machine use 'libRblas.so' which explain the difference of behavior. I will use RhpcBLASctl to avoid issue when combining matrix product and other multi-threading package. Maybe this point regarding multi-threading with BLAS cou...

I believe that actually means configure was able to use the BLAS you specified (MKL in this case). You can scan through config.log to make sure. Andy > From: > > Fedora Core 3 > > I installed the Intel MLk, > > and tried : --with-blas="-lmkl -lguide -lpthread" > > and got : External libraries: readline, BLAS...

...of problems with one particular package named "Matrix_0.3-15.tar.gz" Where should I start? OK! I have successfully installed R version R-1.3.1 as well as a host of other packages (piece of cake). When I tried to install the Matrix package, I got an error message stating that the "BLAS library could not be found" I then downloaded a copy of the blas(blas.tgz) tar file from www.netlib.org/blas that contained nothing but function files. I created the library using Fortran (g77) and "ar". I called it "blas.a", moved it to the /usr/local/lib directory and...

...viewed as a bug or at least a strange behavior in R-3.4.1. I ask my question here (as recommended on https://www.r-project.org/bugs.html) since I am not member of the R's Bugzilla. When running 'R --vanilla' from the command line, the standard matrix product is by default based on BLAS and multi-threaded on all cores available on the machine, c.f. following examples: n=10000 p=1000 q=5000 A = matrix(runif(n*p),nrow=n, ncol=p) B = matrix(runif(p*q),nrow=p, ncol=q) C = A %*% B # multi-threaded matrix product However, the default behavior to use all available cores can be an is...

Hi, I saw on the mailing list and in the NEWS file that some unsafe math transformations were disabled for the reference BLAS implementation that is used in R. We have a set of performance tests for the OpenMx library, and some of the tests have a x3-10 slowdown in R 2.12.0 versus 2.11.1. When I copy the shared library libRblas.0.dylib from the 2.11.1 installation into the 2.12.0 installation, the slowdown goes away. I...

Dear developeRs, I'm trying to build R (2.7.1, on an x86_64 running Linux, but I believe I have observed this on x86 and with earlier versions of R as well) using external BLAS and LAPACK libraries _and_ generating libR.so, libRblas.so and libRlapack.so. Without --enable-BLAS-shlib, configure is able to find and use the external LAPACK library: ./configure \ --with-blas="-L/site/intel/cmkl/8.1/lib/em64t -lmkl -lvml -lguide -lpthread" \ --with-lapack="...

...ted for asking here. Apologies for the cross-posting! I'm on Ubuntu artful, and upgraded with 'apt'. Then ---------------------------------------------------------------- goran at M6800:~/src/R-3.4.3$ /usr/bin/R /usr/lib/R/bin/exec/R: symbol lookup error: /usr/lib/x86_64-linux-gnu/libblas.so.3: undefined symbol: sgemv_thread_n ---------------------------------------------------------------- Never seen this before. What can I do? G?ran Brostr?m

Hi Ista, Maybe a little comment in the 'matmult {base}' doc page or on the 'options {base}' in the field 'matprod' would be useful to remind users to be cautious regarding BLAS multi-threading? I understand why this is a BLAS related issue and not directly an R related issue. Nonetheless, my concern was for non-advanced R users, that may don't even know what BLAS is. For instance, I have a package on the CRAN that use 'mclapply' from the 'parallel'...

OS X 10.2 and higher comes standard with highly optimized versions of BLAS and Lapack in /Systems/Library/Frameworks/vecLib.framework. It seems that even for double precision they do much better. See http://sthmac.magnet.fsu.edu/benchmarks/ I am not sure how these numbers would look on G3 Macs, but obviously for double precision there is not much reliance on Altivec. S...

I am encountering segfaults when checking the lme4 package on an Athlon64 system if I use the acml blas. R was built as a 64-bit application using the GCC 4.0.3 compiler suite including gfortran. The version of acml is 3.5.0 gfortran64. I do not encounter the segfaults when I compile R with R's built-in BLAS. The errors occur in the first example in lme4 in a call to lmer. It looks like they w...

I'd like to build R using my optimized blas and lapack libraries. It seems know matter what I do, the configure script uses the blas supplied with the source. My blas and lapack libraries are in /usr/local/atlas/lib. How can I get configure to use these? [[alternative HTML version deleted]]

I have problems building R 2.11.1 with an external BLAS. I've tried several with several libraries: # ACML: export LD_LIBRARY_PATH=/site/VERSIONS/acml-3.6.0/gfortran64_int64/lib BLAS=--with-blas="-L/site/VERSIONS/acml-3.6.0/gfortran64_int64/lib -lacml" LAPACK=--with-lapack # MKL 11: BLAS=--with-blas="-L/site/VERSIONS/intel-11.1/mkl...

...rtran 77 compiler: g77 -g C++ compiler: g++ -g -O2 Fortran 90/95 compiler: g77 -g Obj-C compiler: Interfaces supported: X11 External libraries: readline Additional capabilities: PNG, JPEG, TIFF, iconv, MBCS, NLS Options enabled: shared BLAS, R profiling, Java Recommended packages: yes When I then run make, I get: make[3]: Entering directory `/usr/local/src/R-2.8.0/src/extra/blas' make[4]: Entering directory `/usr/local/src/R-2.8.0/src/extra/blas' g77 fPIC -g -c blas.f -o blas.o g77: cannot specify -o with -c or -S...

...owing all of the instructions in the various manuals, but clearly I am missing something. I have an Intel EM64T Dell with 2 dual-core Xeon processors running Red Hat EL5. I would like to build R 2.6.1 with lots of debugging and profiling options, and link it to the processor-specific Intel MKL blas. The problem is that after I compile R, and do R CMD config BLAS_LIBS, the response is -L/usr/local/lib64/R/lib -lRblas. This tells me that R is not linked to the Intel BLAS at all. My config.site file for R is: #! /bin/sh R_PAPERSIZE=letter CFLAGS="-g -O2 -p -pg" CPPFLAGS="-I/...