R

There is a dedicated section here, https://cambridge-ceu.github.io/csd3/systems/languages.html#r.

9/5/2024 Update

There are three ceuadmin modules with the latest R 4.4.0.

Module	gcc version	Packages	R_LIBS⁺	Comments
4.4.0	6.5.0	R/	R:library:R-gcc11	also called ceuadmin/R/latest
4.4.0-gcc11	11.2.0	R-gcc11/	R-gcc11:library:R	Rfast, DRMR, etc.
4.4.0-icelake	8.5.0	R-icelake/	R-icelake:library:R

⁺ The library refers to the path of R recommended packages

The packages are at /rds/project/jmmh2/rds-jmmh2-public_databases/software

The latest versions on cclake and icelake are 4.2.2 and 4.3.3, respectively; they work with rstudio/1.1.383 and ceuadmin/rstudio/1.3.1093 on cclake and ceuadmin/rstudio/2023.09.2-508-icelake on icelake; to accommodate the available packages the R_LIBS environment variables are set in the module definition.

29/2/2024 Update

R 4.3.3 has become default on icelake.

Installed modules

From the console we check its availability with module avail R and see

------------------------------------------------------------- /usr/local/software/modulefiles --------------------------------------------------------------
R/3.4           R/3.5           R/3.6           R/4.0.3         R/4.0.5-icelake R/4.1.0-icelake
 

so we can proceed with

module load R/4.0.3
R
 

The second line calls /usr/local/Cluster-Apps/R/R.4.0.3/bin/R.

Compiling from source

To compile all the PDF documentations, load texlive.

module load gcc/6
module load pcre/8.38
module load texlive
wget https://cran.r-project.org/src/base/R-4/R-4.0.0.tar.gz
tar xvfz R-4.0.0.tar.gz
cd R-4.0.0
export prefix=/rds-d4/user/$USER/hpc-work
./configure --prefix=${prefix} \
            --with-pcre1 \
            --enable-R-shlib CPPFLAGS=-I${prefix}/include LDFLAGS=-L${prefix}/lib
make
make install
 

With this setup, R CMD check --as-cran for a CRAN package check can be run smoothly.

Package reinstallation could be done with update.packages(checkBuilt = TRUE, ask = FALSE).

Additional amemendments are necessary, e.g., package igraph 2.0.2 requires glpk/4.57 (see below).

libiconv

It may complain about libiconv.so.2,

… R: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directory

which can be installed as follows,

wget -qO- https://ftp.gnu.org/pub/gnu/libiconv/libiconv-1.16.tar.gz | tar xvfz -
cd libiconv-1.16
./configure --prefix=${HPC_WORK}
make
make install
 

We could also try from module avail libiconv.

4.2.2

The following script is used to generate ceuadmin/R/4.2.2

#!/usr/bin/bash

module load gcc/6 geos-3.6.2-gcc-5.4.0-vejexvy gettext-0.19.8.1-gcc-5.4.0-5iqkv5z pcre2-10.20-gcc-5.4.0-tcuhtrb texlive
export prefix=/usr/local/Cluster-Apps/ceuadmin/R/4.2.2
cd ${prefix}
export version=4.2.2
wget -qO- https://cran.r-project.org/src/base/R-${major}/R-${version}.tar.gz | \
tar xvfz -
cd R-${version}
export gcc6=/usr/local/software/master/gcc/6
export intl=/usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/gettext-0.19.8.1-5iqkv5zrractwd57vydu5czosgtrlwj2/
export HPC_WORK=/rds/user/jhz22/hpc-work
export include=${gcc6}/include:${intl}/include:${HPC_WORK}/include
export ldflags=${gcc6}/lib64:${gcc6}/lib:${intl}/lib:${HPC_WORK}/lib64:${HPC_WORK}/lib
./configure --prefix=${prefix} \
            --with-pcre2 \
            --enable-R-shlib CPPFLAGS=-I${include} LDFLAGS=-L${ldflags} LIBS=-ltinfo LIBS=-lintl
make
make install
 

4.3.3[-gcc11]

This is a lot messier,

#!/usr/bin/bash

module load gcc/6 geos-3.6.2-gcc-5.4.0-vejexvy gettext-0.19.8.1-gcc-5.4.0-5iqkv5z pcre2-10.20-gcc-5.4.0-tcuhtrb texlive
module load image-magick-7.0.5-9-gcc-5.4.0-d4lemcc
module load ceuadmin/glpk/4.57

export prefix=/rds-d4/user/$USER/hpc-work
export prefix=/rds/project/jmmh2/rds-jmmh2-public_databases/software
cd ${prefix}
export version=4.3.3
IFS=\. read major minor1 minor2 <<<${version}
wget -qO- https://cran.r-project.org/src/base/R-${major}/R-${version}.tar.gz | \
tar xvfz -
cd R-${version}
export gcc6=/usr/local/software/master/gcc/6
export intl=/usr/local/software/spack/spack-0.11.2/opt/spack/linux-rhel7-x86_64/gcc-5.4.0/gettext-0.19.8.1-5iqkv5zrractwd57vydu5czosgtrlwj2/
export HPC_WORK=/rds/user/jhz22/hpc-work
export include=${gcc6}/include:${intl}/include:${HPC_WORK}/include
export ldflags=${gcc6}/lib64:${gcc6}/lib:${intl}/lib:${HPC_WORK}/lib64:${HPC_WORK}/lib
./configure --prefix=${prefix} \
            --with-pcre2 \
            --enable-R-shlib CPPFLAGS=-I${include} LDFLAGS=-L${ldflags} LIBS=-ltinfo LIBS=-lintl
make
make install
ln -sf  ${prefix}/R-${version}/bin/R $HOME/bin/R
Rscript -e 'update.packages(checkBuilt=TRUE,ask=FALSE)'
 

Package DescTools 0.99.54 requires gcc/11 (there is problem with gcc/9 on CSD3) and to get around we also created ceuadmin/R/4.3.3-gcc11.

This is created under gcc/11 to enable package in the following list,

DescTools 0.99.54
Rfast 2.1.0
Rfast2 0.1.5.2
RcppTOML 0.2.2
rstanarm 2.32.1
rstan 2.32.6
StanHeaders 2.32.6
 

icelake

A module called ceuadmin/R/4.3.3-icelake is now available, whose definition is as follows,

#%Module -*- tcl -*-
##
## modulefile
##
proc ModulesHelp { } {

  puts stderr "\tR: a free software environment for statistical computing and graphics\n"
  puts stderr "\tInstalled under: /usr/local/Cluster-Apps/ceuadmin/R/4.3.3-icelake"
  puts stderr "\tHomepage: https://www.r-project.org/"

}

module-whatis "A free software environment for statistical computing and graphics."

module load gcc/8 texlive
module load geos-3.6.2-gcc-5.4.0-vejexvy libiconv/1.16/gcc/4miyzf3w gettext/0.21/gcc/qnrcglqo pcre2/10.36/gcc/sya23vzi
module load image-magick-7.0.5-9-gcc-5.4.0-d4lemcc libpng/1.6.37/intel/jfrl6z6c
module load readline/8.1/gcc/bgw44yb2 curl/7.79.0/gcc/75dxv7ac
module load ceuadmin/openssl/3.2.1-icelake ceuadmin/glpk/4.57 ceuadmin/icu/70.1 ceuadmin/nettle/2.7.1
module load ceuadmin/libssh/0.10.6-icelake ceuadmin/openssh/9.7p1-icelake

remove-path LD_LIBRARY_PATH /rds/user/jhz22/hpc-work/lib
remove-path LD_LIBRARY_PATH /rds/user/jhz22/hpc-work/lib64
remove-path LIBRARY_PATH /rds/user/jhz22/hpc-work/lib
remove-path LIBRARY_PATH /rds/user/jhz22/hpc-work/lib64

set               rds                   /rds/project/jmmh2/rds-jmmh2-public_databases/software
set               root                  /usr/local/Cluster-Apps/ceuadmin/R/4.3.3-icelake
prepend-path      PATH                  $root/bin
prepend-path      INCLUDE               $rds/lib64/R/include
prepend-path      MANPATH               $rds/share/man
prepend-path      LD_LIBRARY_PATH       $root/lib
setenv            R_LIBS                $rds/R-icelake:$rds/R:$root/library
 

26/3/2022 Update

module load R/4.1.0-icelake will enable R 4.1.0 from icelake.

As CSD3 often experiences problem from the login nodes, it is then desirable to use login-icelake.hpc.cam.ac.uk.

However, there will be complaints about availability of libreadline.so.6 and then libiccuuc.so.50 which can be got around with their installations.

error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory
...
error while loading shared libraries: libicuuc.so.50: cannot open shared object file: No such file or directory
...
error while loading shared libraries: libgnutls.so.28: cannot open shared object file: No such file or directory
...
libpng15.so.15: cannot open shared object file: No such file or directory
 

The setup below complies with ordinary login nodes.

wget -qO- --no-check-certificate https://ftp.gnu.org/pub/pub/gnu/readline/readline-6.3.tar.gz | tar xfvz -
cd readline-6.3/
./configure --prefix=${HPC_WORK} --enable-shared --with-curses
make
make install
 

where ncurses can be installed as follows (recent version actually is with libtinfo.so, e.g., LDFLAGS=-L$HPC_WORK/lib LIBS=-ltinfo),

wget -qO- https://invisible-mirror.net/archives/ncurses/current/ncurses.tar.gz | \
tar xfz -
cd ncurses-6.3-20221224/
./configure --prefix=$HPC_WORK --with-shared --enable-termcap
make
make install
 

while libicuuc.so.50 can be installed following similar procedure, their availability is as follows,

Finally, libgnutls.so.28¹ requires nettle-2.7.1.

module load autogen-5.18.12-gcc-5.4.0-jn2mr4n
module load gettext-0.19.8.1-gcc-5.4.0-zaldouz

cd ${HPC_WORK}
wget -qO- wget http://www.lysator.liu.se/~nisse/archive/nettle-2.7.1.tar.gz | \
tar xfvz -
cd nettle-2.7.1/
configure --prefix=$HPC_WORK --with-include-path=$HPC_WORK/include --with-lib-path=$HPC_WORK/lib:$HPC_WORK/lib64 --enable-mini-gmp
make
make install
wget --no-check-certificate https://www.gnupg.org/ftp/gcrypt/gnutls/v3.2/gnutls-3.2.21.tar.xz
tar xf gnutls-3.2.21.tar.xz
cd gnutls-3.2.21/
./configure --prefix=${HPC_WORK} --enable-shared --disable-non-suiteb-curves
make
make install
 

The libpng15.so can be made available from a standard GNU-ware installation as follows,

cd ${HPC_WORK}
wget -qO- https://sourceforge.net/projects/libpng/files/libpng15/1.5.30/libpng-1.5.30.tar.gz | \
tar xvfz -
cd libpng-1.5.30
./configure --prefix=$HPC_WORK
make
make install
 

nano editor

It is relatively easy to set up nano, but one has to use the usual login node,

module load gcc/6
wget -qO- --no-check-certificate https://nano-editor.org/dist/v6/nano-6.0.tar.gz | \
tar xfz -
cd nano-6.0
configure --prefix=${HPC_WORK}
make
make install
 

The executable thus obtained also runs under icelake.

alpine

We rather attemp to mirror efforts for nano,

wget -qO- wget https://alpine.x10host.com/alpine/release/src/alpine-2.25.tar.xz | \
tar Jxf -
cd alpine-2.25
configure
make
 

but pico, pilot and alpine obtained from the usual login node do not work, and we have to do these under icelake whose executables require TCL 8.6 under the usual login node where we amend them with

module load tcl-8.6.6-gcc-5.4.0-mongkp2

i.e., loading libtcl8.6.so. Take forward this idea, we could create two files,

#!/usr/bin/bash

export alpine=${HOME}/alpine-2.25
module load tcl-8.6.6-gcc-5.4.0-mongkp2
${alpine}/pico/pico $@
 

called pico.sh and

#!/usr/bin/bash

export alpine=${HOME}/alpine-2.25
module load tcl-8.6.6-gcc-5.4.0-mongkp2
${alpine}/pico/pilot $@
 

called pilot.sh, respectively. Then the two commands can be used both from the usual login nodes as well as icelake.

For alpine we get alpine/alpine: /usr/lib64/libcrypt.so.1: version XCRYPT_2.0' not found (required by alpine/alpine)`. Nevertheless we might compile two sets of executables under the usual login node and icelake, respectively.

Additional information is available from https://alpine.x10host.com/alpine/release/.

On CSD3, there is a more recent module nettle-3.4-gcc-5.4.0-2mdpaut. Moreover, with 3.5 there is also an option --with-included-unistring during configuration.

Version 3.7.8 requires libunistring (optionally –with-included-unistring), libidn2, libunbound, and trousers.
```
./configure --prefix=$HPC_WORK --with-included-unistring --with-nettle-mini --enable-ssl3-support \
            CFLAGS=-I$HPC_WORK/include LDFLAGS=-L$HPC_WORK/lib LIBS=-lunbound LIBS=-ltspi --enable-sha1-support --disable-guile
```
It is necessary to edit lib/pkcs11_privkey.c to make ck_rsa_pkcs_pss_params definition explicit. Then there is error with guile so we use –disable-guile. ↩