Problem installing MKL on Linux

[Jason Hoeksema]

I am having trouble successfully installing MKL Math Libraries. My computer is a Zareason Limbo 6250a (with 8-core AMD processor), running Ubuntu 12.04 LTS.

I have installed Revolution R Open, have upgraded to version 3.2.0, and am attempting to perform data analyses in RStudio, fitting mixed meta-analysis models with the rma.mv function from the metafor package. I have large datasets, and my analyses involve matrix algebra, so I would like to use multiple cores during model fitting.

However, when I go to install MKL it is not recognizing the R version correctly. Here is the error I'm getting in the Linux terminal when I try to install MKL:
Error in print(Revo.version) : object 'Revo.version' not found
Execution halted
Error: Revolution R Open was detected; however, it is not the correct version.
This utility is for version 3.2.0 only.  Exiting now.........

However, when I check the version of R in RStudio, using R.Version(), it returns the following:

$platform
[1] "x86_64-unknown-linux-gnu"

$arch
[1] "x86_64"

$os
[1] "linux-gnu"

$system
[1] "x86_64, linux-gnu"

$status
[1] ""

$major
[1] "3"

$minor
[1] "2.0"

$year
[1] "2015"

$month
[1] "04"

$day
[1] "16"

$`svn rev`
[1] "68180"

$language
[1] "R"

$version.string
[1] "R version 3.2.0 (2015-04-16)"

$nickname
[1] "Full of Ingredients"


One caveat is that I am a relatively new Linux user.
Thanks for any help or suggestions.
Jason

[Andrie de Vries]

I am making a guess here: it seems you are using RStudio Server as opposed to RStudio Desktop.

RStudio Server will only recognize a single installation of R. I am guessing that you installed R before installing RRO, and RStudio server is still pointing to R.

To fix this, you have two options:

1. Reconfigure RStudio Server (instructions at https://support.rstudio.com/hc/en-us/articles/200552316-Configuring-the-Server)

2. Install and use RStudio desktop - this allows you easily select the version of R you want to use.

I hope this helps

Andrie

[Jason Hoeksema]

Andrie,

Thank you, but I believe I am running the Desktop version of RStudio. I am not accessing it remotely. Also, upon start-up, I see a message saying the Revolution R open 3.2.0 is the version being used in RStudio.

Jason

--

Dr. Jason D. Hoeksema, Associate Professor
Department of Biology
University of Mississippi
phone: 662-915-1275
http://www.olemiss.edu/depts/biology/hoeksema/index.html

[Andrie de Vries]

Hi, Jason

 

OK, in that case it seems that somehow you have a confused system. You say you get the RRO startup message, but that Revo.version isn’t available.

 

I don’t know how that came about.

 

I suggest you install RRO-3.2.1 from scratch.  It is available now (since a few hours ago) at https://mran.revolutionanalytics.com/download/

 

I suggest you uninstall your current version of RRO, then install RRO-3.2.1 followed by the matching MKL installer.

 

Good luck.

 

Andrie

[Jason Hoeksema]

OK, thank you--I will try that.

[terry leitch]

Same issue. Tried to remove MKL but get this:

Error : .onLoad failed in loadNamespace() for 'RevoUtilsMath', details:

  call: fun(libname, pkgname)

  error: To use RevoUtilsMath you must first install the MKL Math Library.

 Visit http://mran.revolutionanalytics.com/download.

 If you have previously installed the MKL Math Library,

remove it and then re-install.

Error: package or namespace load failed for ‘RevoUtilsMath’

Execution halted

Error: Revolution R Open was detected; however, it is not the correct version.

This utility is for version 3.2.2 only.  Exiting now.........

Cannot uninstall MKL or install it. I've uninstalled RRO 3.2.2 and installed it several times, no joy. Command line R is rro 3.2.2 and rsever.conf points to same version. NOt sure what to do here, stuck in loop..

[Dwayne Paschall]

I'll add a second data point here. Same configuration. Same attempted fix. Same outcome (can't uninstall MKL, can't install over current version). Also have a directory of packages in my user directory that I install new R packages into. Another Windows 7 user had a similar difficulty. Not sure how to get around it so that I can get back to faster processing with the MKL lib installed (and working). Thanks.

[Josée Martens]

Hi Terry and Dwayne,

If the uninstall script doesn’t work, a workaround is to perform all of its steps by hand:

 

        rm $LIB_PATH/libmkl*

        rm $LIB_PATH/libiomp5.so

        rm $LIB_PATH/libRblas.so

        rm $LIB_PATH/libRlapack.so

        mv $LIB_PATH/libRblas.so.keep $LIB_PATH/libRblas.so

        mv $LIB_PATH/libRlapack.so.keep $LIB_PATH/libRlapack.so

        ## remove env variables from Rprofile.site

        sed -i -e '/MKL_INTERFACE_LAYER/d' $ETC_PATH/Rprofile.site

        sed -i -e '/MKL_THREADING_LAYER/d' $ETC_PATH/Rprofile.site

        echo "remove.packages('RevoUtilsMath')" | $R_PATH -q --no-save > mkl_log.txt 2>&1

 

($LIB_PATH is typically /usr/lib64/RRO-3.2.2/R-3.2.2/lib/R/lib—it’s the path to R shared libraries.)

Please let us know how that goes.

Also please let us know if you've upgraded from a previous version of RRO.

Thanks,

Josée