search for: libopenbla

...linux-gnu/openblas-pthread/liblapack.so.3 while before when `solve` was not working it was: Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 so it seems the issue is with the Ubuntu package `libopenblas0-pthread` and has nothing to do with R. I don't know why openblas-pthread was the default BLAS on my system. Thank you for your help. Best, Sam

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-core.x86_64

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...

Has anyone succeeded in getting a parallel BLAS, such as Goto's BLAS, installed on a machine running Ubuntu 11.10? I currently have the libatlas3gf-base package installed on a machine with an AMD Athlon X4 processor. I tried to install the libopenblas-base and libopenblas-dev packages but there seemed to be a glich related to having both libopenblas and libatlas3gf installed so that when I tried to recompile R it failed to start because one of the ATL symbols from Atlas was undefined. Is it worthwhile making a custom version of Atlas? Every t...

Hello, the following is a part of a question asked on R-help. I realized that it is better suited 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:

...a good alternative. Cheers G On Wed, 27 May 2020 at 03:20, I?aki Ucar <iucar at fedoraproject.org> wrote: > > 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> w...

...was a proposal [1], but it was never pushed forward due to some issues and lack of time. There's a simple hack you can do though. Since recently, R in Fedora no longer uses openblas-Rblas and links against system openblas, as you can see here: $ ldd /usr/lib64/R/bin/exec/R | grep blas libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f8fff849000) So one simple trick to override that is something along these lines: $ mkdir ~/blas $ ln -s /lib64/atlas/libsatlas.so.3 ~/blas/libopenblas.so.0 $ LD_LIBRARY_PATH=~/blas ldd /usr/lib64/R/bin/exec/R | grep blas libopenblas.so.0 =>...

...as-pthread/liblapack.so.3 | | while before when `solve` was not working it was: | | Matrix products: default | BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 | LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 | | so it seems the issue is with the Ubuntu package `libopenblas0-pthread` | and has nothing to do with R. I don't know why openblas-pthread was the | default BLAS on my system. That is most helpful! It could potentially affect lots of other users too. And on the aforementioned rocker/r-ubuntu:20.04 image, if upgrade to libopenblas-dev I get it too:...

...t bud:~$ COLUMNS=70 dpkg -l | grep blas > ii libblas-common 3.7.0-1 amd64 Dependency package for all BLAS i > ii libblas-dev 3.7.0-1 amd64 Basic Linear Algebra Subroutines > ii libblas3 3.7.0-1 amd64 Basic Linear Algebra Reference im > ii libopenblas-ba 0.2.19-2 amd64 Optimized BLAS (linear algebra) l > edd at bud:~$ > > At work: > ........ at .....:~$ COLUMNS=70 dpkg -l | grep blas > ii libblas-common 3.7.0-1 amd64 Dependency package for all BLAS i > ii libblas-dev 3.7.0-1 amd64 Basic...

...Selection: 3 Process R exited abnormally with code 70 at Tue Dec 11 10:36:51 2012 I double-checked /etc/alternatives and as you can see it does now point to openbas pauljohn at pjlap-124:alternatives$ ls -la libblas.* lrwxrwxrwx 1 root root 36 Dec 11 10:34 libblas.a -> /usr/lib/openblas-base/libopenblas.a lrwxrwxrwx 1 root root 37 Dec 11 10:34 libblas.so -> /usr/lib/openblas-base/libopenblas.so lrwxrwxrwx 1 root root 39 Dec 11 10:34 libblas.so.3 -> /usr/lib/openblas-base/libopenblas.so.0 lrwxrwxrwx 1 root root 39 Dec 11 10:34 libblas.so.3gf -> /usr/lib/openblas-base/libopenblas.so.0 --...

...> a ?crit : > > Salut Adrien, > > It appears to be a bad OpenMP and and OpenBLAS interaction you can (for > now) > avoid) by replacing the 'pthread' variant of OpenBLAS with the OpenMP > version > (see the thread for details). Doing > > sudo apt install libopenblas-openmp-dev > sudo apt remove libopenblas-pthread-dev > This works! Thank's a lot! should do -- make sure you do the second step too to ensure that the pthread > variant is remove as it would rank higher. Check via `R -s -e > 'sessionInfo()'` > and look closely at the...

...). However, at home (ubuntu 17.10): goran at M6800:~$ dpkg -l | grep blas ii libblas-dev:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra Subroutines 3, static library ii libblas3:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra Reference implementations, shared library ii libopenblas-base:amd64 0.2.20+ds-4 amd64 Optimized BLAS (linear algebra) library (shared library) and it worked before upgrade but not after. Seems to be missing 'libblas-common'. So I try to install: goran at M6800:~$ sudo apt install libblas-common [sudo] password for goran: Reading pac...

...t home (ubuntu 17.10): | | goran at M6800:~$ dpkg -l | grep blas | ii libblas-dev:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra | Subroutines 3, static library | ii libblas3:amd64 3.7.1-3ubuntu2 amd64 Basic Linear Algebra | Reference implementations, shared library | ii libopenblas-base:amd64 0.2.20+ds-4 amd64 Optimized BLAS | (linear algebra) library (shared library) | | and it worked before upgrade but not after. Seems to be missing | 'libblas-common'. Maybe. Maybe not. Did you check packages.ubuntu.com (or another source) to see if it still exists? P...

...(with its paid licencing) and the need to build my own R package is really worth. Do anyone have some realistic point of view/advice? Then, in case I gave up with the Intel stuff, I am confused between the Lapack package and Openblas one. I know first one will provide liblas.so.3 when second one libopenblas.so. Am i right to say I only need one blas library and the openBlas one is the one to get? Can I use instead the openmp version of openblas, or shall I installed both? here again, I am a litle confused. As for the liblapack.so.3, I will get it from the Fedora lapack package. last, what is the cor...

...o? At home: edd at bud:~$ COLUMNS=70 dpkg -l | grep blas ii libblas-common 3.7.0-1 amd64 Dependency package for all BLAS i ii libblas-dev 3.7.0-1 amd64 Basic Linear Algebra Subroutines ii libblas3 3.7.0-1 amd64 Basic Linear Algebra Reference im ii libopenblas-ba 0.2.19-2 amd64 Optimized BLAS (linear algebra) l edd at bud:~$ At work: ........ at .....:~$ COLUMNS=70 dpkg -l | grep blas ii libblas-common 3.7.0-1 amd64 Dependency package for all BLAS i ii libblas-dev 3.7.0-1 amd64 Basic Linear Algebra Subroutines i...

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 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

Dear all, I am estimating a mixed-model in Ubuntu Raring (13.04¸ amd64), with the code: fm0 <- lme(rt ~ run + group * stim * cond, random=list( subj=pdSymm(~ 1 + run), subj=pdSymm(~ 0 + stim)), data=mydat1) When I check the approximate variance-covariance matrix, I get: > fm0$apVar [1] "Non-positive definite

I have upgraded R (from 3.6 to 4.0) and RStudio (from 1.1 to 1.2.5) a few days ago, and Ubuntu from 18.04 to 20.04 yesterday. Since then, R sometimes never terminates when executing certain commands: ivreg (from package AER), summary (of a logit regression) and logitmfx (from package mfx). Sometimes these commands run fine, but most of the time I have to kill the process because R won't

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 ma...