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changes.mady.by.user Abigail Smith (Unlicensed)

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changes.mady.by.user Simon Alexander

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Code Block
[]$ module spider r
----------------------------
  r:
----------------------------
     Versions:
        r/3.4.4
        r/3.5.0-py27
        r/3.5.0
        r/3.5.1s
        r/3.5.2-py27
        r/3.5.2
        r/3.5.3-py27
        r/3.5.3
        r/3.6.1-intel
        r/3.6.1-py27
        r/3.6.1
        r/4.0.0-py27
        r/4.0.2-intel
        r/4.0.2-py27
----------------------------
  For detailed information about a specific "r" module (including how to load the modules) use the module's full name.
  For example:
     $ module spider r/34.60.12-py27
----------------------------


[]$ module spider r/3.5.1s
----------------------------
  r: r/3.5.1s
----------------------------
    You will need to load all module(s) on any one of the lines below before the "r/3.5.1s" module is available to load.
      singularity/2.5.2
      singularity/3.1.1


[]$ module spider r/3.6.1
----------------------------
  r: r/3.6.1
----------------------------
    You will need to load all module(s) on any one of the lines below before the "r/3.6.1" module is available to load.
      swset/2018.05  gcc/7.3.0

module load gcc/7.3.0 r/3.6.1

...

R Package: RStan

R and Intel/MKL

We have a version of r3versions of r (3.6.1/4.0.2) built with the Intel compiler and related MKL (Maths Kernel Library) that follows a request relating to Improving R Performance by installing optimized BLAS/LAPACK libraries.
To use:

Code Block
languagebash
[]$ module load r/34.60.12-intel

[]$ R
R version 34.60.12 (20192020-0706-0522) -- "ActionTaking ofOff the ToesAgain"
Copyright (C) 20192020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
...

> sessionInfo()
R version 34.60.12 (20192020-0706-0522)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Storage

Matrix products: default
BLAS/LAPACK: /pfs/tsfs1/apps/el7-x86_64/u/intel/18.0.1/intel-mkl/2018.2.199-pti6y2y/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin/libmkl_rt.so
...

  • The Intel built version is dependent on the following modules core:

    swset/2018.05

    • intel/18.0.1

    • intel-mkl/2018.2.199

    • readline/7.0

    • bzip2/1.0.6

    • xz/5.2.4

    • curl/7.60.0

    • jdk/8u172-b11

    • The module load r/3.6.1-intel line will automatically load these modules for you.

    • The readline, bzip2, xz and curl libraries are all versions that have also been built using the intel compiler.

...

    • The module load r/*.*.*-intel line will automatically load these modules for you.

Installing Packages to Use with Intel Version

Info

  • The packages that you have installed for the standard versions of R will not work for the Intel version since they are built with different compilers. This means you will need to re-install the packages that you use.

  • If you potentially want to use both versions then you will need to create a second folder to install the Intel versions into.

  • This has been tested with R.3.6.1 intel version - a similar approach should apply for 4.0

On Teton, R packages are typically installed into:

...