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rinstallationredhatatlasopenblas
Bas
Bas

Reputation: 1076

Attempting to run R with Atlas/OpenBLAS on redhat

For two days I've been trying to install Openblas/atlas with Lapack and use it in R. it's driving me crazy. I'm at a point where I can't even think anymore.

My server uses:
Red Hat Enterprise Linux Server release 6.6 (Santiago)

Here is what I've installed so far:

[root@tpdb05 atlas]# yum install atlas.x86_64 blas.x86_64 lapack.x86_64 Loaded plugins: product-id, refresh-packagekit, rhnplugin, security, subscription-manager
    Setting up Install Process
    Package atlas-3.8.4-2.el6.x86_64 already installed and latest version
    Package blas-3.2.1-4.el6.x86_64 already installed and latest version
    Package lapack-3.2.1-4.el6.x86_64 already installed and latest version
[root@tpdb05 ruser]#


yum install lapack.i686
    Installed:
    lapack.i686 0:3.2.1-4.el6

    Dependency Installed:
    blas.i686 0:3.2.1-4.el6                          glibc.i686 0:2.12-1.166.el6_7.3        libgfortran.i686 0:4.4.7-16.el6
    nss-softokn-freebl.i686 0:3.14.3-23.el6_7

    Dependency Updated:
    glibc.x86_64 0:2.12-1.166.el6_7.3         glibc-common.x86_64 0:2.12-1.166.el6_7.3    glibc-devel.x86_64 0:2.12-1.166.el6_7.3
    glibc-headers.x86_64 0:2.12-1.166.el6_7.3 nss-softokn-freebl.x86_64 0:3.14.3-23.el6_7


yum install atlas.i686
    Installed:
        atlas.i686 0:3.8.4-2.el6

[root@tpdb05 SRPMS]# yum install rpm-build
    Installed:
    rpm-build.x86_64 0:4.8.0-47.el6

    Dependency Installed:
    redhat-rpm-config.noarch 0:9.0.3-44.el6

    Dependency Updated:
    rpm.x86_64 0:4.8.0-47.el6             rpm-libs.x86_64 0:4.8.0-47.el6             rpm-python.x86_64 0:4.8.0-47.el6

[root@tpdb05 SRPMS]# yum install atlas-c++-devel.x86_64
    Installed:
      atlas-c++-devel.x86_64 0:0.6.1-1.el5.rf

    Dependency Installed:
      atlas-c++.x86_64 0:0.6.1-1.el5.rf

several sources I've tried without success: 1 2 3

The R manual mentions the following:

The usual way to specify ATLAS will be via
--with-blas="-lf77blas -latlas"

However I have no clue where to use this command. While installing R? I'm pretty sure it should be possible to simply swap between libraries..

How do I get R to use the atlas/openblas/lapack libraries?

Upvotes: 5

Views: 1018

Answers (0)

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