search for: openblas

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. In any case, my suggestion was motivated by the fact that some parts of R use OpenMP while others do not, in the hope that the former could have their OpenBLAS omelet without breaking the OpenMP eggs, so to speak. On 01/09/2018 06:41 PM, Keith O'Hara wrote: > 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: >>...

Dear List, I am trying to build R on Fedora against a threaded openblas installed from Fedora's yum repos, or alternatively swap out libRblas.so with a threaded openblas built locally. I have installed $ yum list installed | grep openblas openblas.x86_64 0.2.11-1.fc20 @updates openblas-devel.x86_64 0.2.11-1.fc20...

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. Reg...

Hello, I thought that I should try openblas when building a CRAN package containing lots of old (twentieth century) C-code with frequent calls to blas and lapack routines. I have the following options on my Ubuntu 20.04 machine: Selection Path Priority Status --------------------------------------------...

Hello, macosx 10.13.6, Rdevel r76458 I'm trying to compile against openblas to reproduce an error on the CRAN check page (my package is clean under winbuilder and all but one of the checks). I've downloaded and installed openblas 0.3.7 but I am not 100% sure that it is being used by R. Using ./configure --with-blas="-lopenblas" Then running R to discover...

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...

On Wed, 8 May 2019 at 04:52, Peter Langfelder <peter.langfelder at gmail.com> wrote: > > (CCing the R-devel list, maybe someone will have a better answer.) > > To be honest, I don't know how to. I wasn't able to configure R to use > OpenBLAS using the configure script and options on my Linux Fedora system. > I configure it without external BLAS, then replace the libRblas.dylib (.so > in my case) with a link to the OpenBLAS dynamic link library. R on Fedora uses openblas by default since Fedora 23. In fact, there's a specific...

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? By the way, I also noticed on my home machine (Ubuntu), /usr/lib/libopenblas.so.0 is also not linked against those, for what...

I’ve installed R 3.1 with the latest Fedora rpm (R-3.1.0-5.el6.x86_64.rpm) and I run into some issues with openblas. I’ve documented this with an open question on stack overflow here: http://stackoverflow.com/questions/24158372/openblas-r-3-1-and-fedora-centos-dist Basically before 3.1 I had 3.02 and I was able to install and use openblas following the instruction from official CRAN documentation, symlinking t...

Of course, even a simpler trick is to launch R as follows: LD_PRELOAD=/lib64/atlas/libsatlas.so.3 R and then the symbols in libsatlas take precedence over libopenblas. Or a mix between both alternatives, i.e., setting LD_PRELOAD=/path/to/some/link R and then change that link to point to openblas, atlas... Whatever suits you best. I?aki On Wed, 27 May 2020 at 11:00, I?aki Ucar <iucar at fedoraproject.org> wrote: > > Hi Gavin, > > On Wed, 27...

...un-time", so any user-friendly implementation for R would have to compile ATLAS for 1-16 threads to allow the user to switch at run-time. This might dramatically affect install times. - MKL seems like it's been outright rejected in the past based on not being "free-enough". - OpenBLAS causes crashes. Has anyone tried ExBLAS for use with R? On Sun, Dec 17, 2017 at 1:03 PM, Peter Langfelder < peter.langfelder at gmail.com> wrote: > I would be very cautious about OpenBLAS in particular... from time to > time I get complains from users that compiled code calculations...

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),...

Multi-threaded Math Libraries (Trough OpenBlas), taking into account that today's laptops have a minimum of 2-4 cores, are an important topic, and in my opinion, shall be included in R for the general interest. I think that the way to go would be to create a configuration setting in R's options(OpenBlas= TRUE|FALSE) which enables or di...

I?m not really familiar with conda, but if they?re being packaged together then an omp build might be more appropriate. Perhaps another point for Juan?s list: whether OpenBLAS is the right choice to pair with. The library itself hasn?t produced optimized kernels for any of the Intel *Lake chips yet; might be worth considering its near- and long-term future (vs something else). Keith > On Jan 10, 2018, at 8:24 PM, Benjamin Tyner <btyner at gmail.com> wrote: &gt...

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 whethe...

Dear colleagues, The *ropenblas* <https://prdm0.github.io/ropenblas/> is a package designed to facilitate the linking of the library *OpenBLAS* <https://www.openblas.net/> with the language *R* <https://www.r-project.org/>. The package, which works only for Linux systems, will automatically download the latest s...

Dear colleagues, The *ropenblas* <https://prdm0.github.io/ropenblas/> is a package designed to facilitate the linking of the library *OpenBLAS* <https://www.openblas.net/> with the language *R* <https://www.r-project.org/>. The package, which works only for Linux systems, will automatically download the latest s...

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 the way, I also noticed on my home mac...

...e next step (i.e. forum) for debugging the race condition? On 01/11/2018 07:56 AM, Ista Zahn wrote: > > > On Jan 10, 2018 8:24 PM, "Benjamin Tyner" <btyner at gmail.com > <mailto: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 > accompli...

...+ 13836 2.5 0.2 441664 52024 pts/1 Sl+ 06:44 0:00 /usr/lib/R/bin/exec/R user+ 13932 0.0 0.0 8900 660 pts/2 S+ 06:45 0:00 grep exec/R user at user:~$ lsof -p 13836 | grep 'blas\|lapack' R 13836 user mem REG 8,1 33562376 3961750 /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 R 13836 user mem REG 8,1 27200552 3961749 /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 user at user:~$ ls -l /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 -rw-r--r-- 1 root root 27200552 Jun 2 06:55 /usr/lib/x86_64-linux-gnu/openblas-pthrea...