similar to: R-SIG-Debian Digest, Vol 58, Issue 3

Hello. I am a Linux neophyte and know almost nothing ?about compiling, so I would appreciate any help and advice y'all would care to offer. I am trying to compile the 64 bit version of R using a tuned ATLAS and LAPACK (ATLAS 3.9.24). I am running Ubunto 10.04 LTS (through wubi, FWIW). The ATLAS and LAPACK files (atlas.so, f77blas.so, lapack.so, and cblas.so) are sitting in the folder

So, tried again from scratch. Again, CentOS 5.3, which is essentially RHEL 5.3. ./configure --with-blas="-L/opt/acml4.3.0/gfortran64/lib -lacml" In config.log, get things like configure:37199: checking for dgemm_ in -L/opt/acml4.3.0/gfortran64/lib -lacml configure:37230: gcc -std=gnu99 -o conftest -g -O2 -I/usr/local/include -L/usr/local/lib64 conftest.c

Hello. I know almost nothing about Linux, so I apologize if the answer to this is obvious. I am trying to compile R with ATLAS (successfully compiled 3.9.24 on Ubuntu 10.04 64 bit). I configured with: ./configure --enable-R-shlib --enable-BLAS-shlib --with-blas="-L/usr/local/atlas/lib -lf77blas -latlas" --with-lapack="-L/usr/local/atlaslib -llapack -lcblas" --with-x and I

Hello. I know almost nothing about Linux, so I apologize if the answer to this is obvious. I am trying to compile R with ATLAS (successfully compiled 3.9.24 on Ubuntu 10.04 64 bit). I configured with: ./configure --enable-R-shlib --enable-BLAS-shlib --with-blas="-L/usr/local/atlas/lib -lf77blas -latlas" --with-lapack="-L/usr/local/atlaslib -llapack -lcblas" --with-x and I

Thanks Dirk.? That is what I thought, and sessionInfo() returns: Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3 LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3 locale: ?[1] LC_CTYPE=en_US.UTF-8?????? LC_NUMERIC=C ?[3] LC_TIME=en_US.UTF-8??????? LC_COLLATE=en_US.UTF-8 ?[5] LC_MONETARY=en_US.UTF-8??? LC_MESSAGES=en_US.UTF-8 ?[7]

Hi, everybody. I notice debian packages for Ubuntu on CRAN are missing "libRblas.so" and I'm trying to find out why. Why do I care? We are working in an hpc project in a CentOS Linux cluster. That led me to the question of "which BLAS is fastest?" Dirk E referred me this morning to the R admin manual. The standard R compilation creates a shared blas library libRblas.so

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,

I'm trying to build R-alpha using the ATLAS libraries as described in the R-admin manual, section A.3.1.1 (BLAS) and A.3.2 (LAPACK). I built ATLAS with LAPACK as described in the ATLAS documentation, and the ATLAS version is the latest, 3.9.10. The platform is openSUSE 11.1 x86_64 with GCC 4.3.2. "configure" is finding the ATLAS BLAS all right, but it is not finding the ATLAS

Dear R-help, Has anyone tried linking R against the Intel Math Kernel Library on (obviously) Intel architecture? Since MKL claimed to provide optimized BLAS and Lapack, I thought it might be possible to compile R against it w/o too much trouble. My first naive try under Linux (Mandrake 7.1), using R-patched dated Jan. 4, 2002: ./configure --with-blas=/usr/local/intel/mkl/LIB/libmkli32_p3.a

Hi, I tried to compile R with openblas on a ubuntu 12.04 machine. I have to say that I normally use the package system and that I have no experience with compiling R. I did the following: ./configure --enable-BLAS-shlib --enable-R-shlib LIBnn=lib --with-blas="-L/usr/lib/openblas-base/ -lopenblas" --enable-memory-profiling --with-x=yes go the output: R is now configured for

On Fri, Sep 4, 2015 at 5:58 PM, Martyn Plummer <plummerm at iarc.fr> wrote: > On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote: >> On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury <arnaud.gaboury at gmail.com> wrote: >> > After a few days of reading and headache, I finally gave a try at >> > building R from source with Intel MKL and ICC. Documentation

Julia Programming Language uses also OpenBlas, and it is actively maintained with bugs being fixed as I have checked it out: http://www.openblas.net/Changelog.txt So I still see it ok to be included as an options(...) feature (by default off, just for safety), over other Blas libraries. R could not use Intel MKL for legal reasons (I think), because as long that R ships with GPL libraries,

Thank you, Brad (and others), >>>>> Brad Bell on Mon, 4 Feb 2019 07:21:18 -0700 writes: > I get the failure message. To be specific: adcomp.git> R CMD BATCH --quiet test_nlminb.R adcomp.git> cat test_nlminb.Rout >> f <- function(x) sum( log(diff(x)^2+.01) + (x[1]-1)^2 ) >> opt <- nlminb(rep(0, 10), f, lower=-1, upper=3) >>

Do those issues still arise when OpenBLAS is compiled with USE_OPENMP=1 ? Keith > On Jan 9, 2018, at 6:03 PM, Benjamin Tyner <btyner at gmail.com> wrote: > > Please pardon my ignorance, but doesn't OpenBLAS still not always play nicely with multi-threaded OpenMP? (for example, don't race conditions sometimes crop up)? If so, it might be nice to have the ability to

On Sat, 2015-09-05 at 11:53 +0200, arnaud gaboury wrote: > On Fri, Sep 4, 2015 at 5:58 PM, Martyn Plummer <plummerm at iarc.fr> wrote: > > On Wed, 2015-09-02 at 20:49 +0200, arnaud gaboury wrote: > >> On Wed, Sep 2, 2015 at 7:35 PM, arnaud gaboury <arnaud.gaboury at gmail.com> wrote: > >> > After a few days of reading and headache, I finally gave a try at

Check if libopenblas is linked against libomp or libgomp. I?d be curious to see any errors that arise when an OpenMP version of OpenBLAS is linked with R. Keith > On Jan 9, 2018, at 11:01 PM, Benjamin Tyner <btyner at gmail.com> wrote: > > I didn't do the compile; is there a way to check whether that was used? If not, I'll inquire with our sysadmin and report back.

Hi, I'm trying to follow the R-admin instructions for using MKL10 as the external BLAS compiling R-2.6.2 under Linux on a RH EL head node of a cluster. The configure process seems to have problems when it checks for dgemm in the BLAS. I'm using configure as: ./configure CC=icc F77=ifort --with-lapack="$MKL" --with-blas="$MKL" where $MKL is defined as in R-admin

On 22 September 2018 at 16:08, Steve Gutreuter wrote: | R 3.5.1 is installed under Linux Mint 19 from binaries r-base and | r-base-dev from ubuntu bionic-cran35.? Mysteriously, packages using | libRblas cannot be compiled.? I get: libRblas.so: cannot open shared | object file: No such file or directory.? And indeed, I find no libRblas.so. | | Any ideas about how to fix this? What does

On Jan 10, 2018 8:24 PM, "Benjamin Tyner" <btyner at gmail.com> wrote: Thanks Keith. We checked, and indeed libopenblas is not linked against libomp nor libgomp. We suspect this is because we used conda to install R and OpenBLAS. So I guess we should be barking up the conda tree instead? What are you barking about? I don't understand what you are trying to accomplish. By

Please pardon my ignorance, but doesn't OpenBLAS still not always play nicely with multi-threaded OpenMP? (for example, don't race conditions sometimes crop up)? If so, it might be nice to have the ability to temporarily disable multi-threaded OpenMP (effectively: omp_set_num_threads(1)) for the duration of operations using OpenBLAS. Regards Ben > Julia using OpenBLAS is *very*