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On Shaheen we recommend using Cray’s R installation for intercalatively using via R’s CLI or preferably batch processing of R scripts.
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R interactive shell on compute node
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Here, as an example, I install readxl package. Please note that this will ultimately be installed in the directory pointed to by R_LIBS variable set earlier. If you don’t set the variable, R will try to install it in the root directory of R and it will fail due to permissions issue.
Passing compiler configuration FLAGs
Sometime R requires extra help to get directions where include headers and dynamic libraries are located. This is usually needed in the configure step of C , C++, or Fortran codes. For example, the following is a package that depends on NetCDF and requires headers information where they are. These flags can be listed in a file /scratch/$USER/.R/Makevars and R will honor them when compiling the package.
The following steps are executed in an interactive session on Shaheen compute node
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srun -n 1 -c 32 -t 0:30:0 -p debug --pty bash
module swap PrgEnv-cray PrgEnv-gnu
module load cray-netcdf
module load cray-R |
Create the Makevars if it doesn’t already exist:
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mkdir -p /scratch/$USER/.R/Makevars |
The contents of Makevars can be:
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CC=cc
CXX=CC
FC=ftn
CFLAGS=-I/opt/cray/pe/netcdf/4.7.4.4/GNU/8.2/include
LDFLAGS=-L/opt/cray/pe/netcdf/4.7.4.4/GNU/8.2/lib |
Now we can call the package installer either in a R interactive session or with R CMD INSTALL command line interface.
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shaima0d@nid00008:/lustre/scratch/project/k01/exclude/shaima0d/tickets/48534> R
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-suse-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> install.packages('ncdf4')
Installing package into '/lustre/scratch/project/k01/exclude/shaima0d/tickets/48534/libs'
(as 'lib' is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors
1: 0-Cloud [https]
2: Australia (Canberra) [https]
....
77: Uruguay [https]
78: (other mirrors)
Selection: 1
trying URL 'https://cloud.r-project.org/src/contrib/ncdf4_1.21.tar.gz'
Content type 'application/x-gzip' length 127380 bytes (124 KB)
==================================================
downloaded 124 KB
* installing *source* package 'ncdf4' ...
** package 'ncdf4' successfully unpacked and MD5 sums checked
** using staged installation
configure.ac: starting
checking for nc-config... yes
Using nc-config: nc-config
Output of nc-config --all:
This netCDF 4.7.4 has been built with the following features:
--cc -> cc
--cflags -> -DpgiFortran
--libs ->
--static -> -lhdf5_hl -lhdf5 -lm -lz -ldl
--has-c++ -> no
--cxx ->
--has-c++4 -> yes
--cxx4 -> CC
--cxx4flags -> -DpgiFortran
--cxx4libs ->
--has-fortran -> yes
--fc -> ftn
--fflags ->
--flibs ->
--has-f90 ->
--has-f03 -> yes
--has-dap -> no
--has-dap2 -> no
--has-dap4 -> no
--has-nc2 -> yes
--has-nc4 -> yes
--has-hdf5 -> yes
--has-hdf4 -> no
--has-logging -> no
--has-pnetcdf -> no
--has-szlib -> no
--has-cdf5 -> yes
--has-parallel4 -> no
--has-parallel -> no
--prefix -> /opt/cray/pe/netcdf/4.7.4.4/GNU/8.2
--includedir -> /opt/cray/pe/netcdf/4.7.4.4/GNU/8.2/include
--libdir -> /opt/cray/pe/netcdf/4.7.4.4/gnu/8.2/lib
--version -> netCDF 4.7.4
---
netcdf.m4: about to set rpath, here is source string: ><
netcdf.m4: final rpath:
Netcdf library version: netCDF 4.7.4
Netcdf library has version 4 interface present: yes
Netcdf library was compiled with C compiler: cc
configure: creating ./config.status
config.status: creating src/Makevars
********************** Results of ncdf4 package configure *******************
netCDF v4 CPP flags = -DpgiFortran
netCDF v4 LD flags =
netCDF v4 runtime path =
netCDF C compiler used = cc
R C compiler used = cc -I/opt/cray/pe/netcdf/4.7.4.4/GNU/8.2/include
******************************************************************************
** libs
cc -I"/opt/R/4.1.1.0/lib64/R/include" -DNDEBUG -DpgiFortran -I/usr/local/include -fpic -I/opt/cray/pe/netcdf/4.7.4.4/GNU/8.2/include -c ncdf.c -o ncdf.o
cc -Wl,-rpath,/opt/cray/pe/gcc-libs -shared -L/usr/local/lib64 -o ncdf4.so ncdf.o
installing to /lustre/scratch/project/k01/exclude/shaima0d/tickets/48534/libs/00LOCK-ncdf4/00new/ncdf4/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ncdf4)
The downloaded source packages are in
'/tmp/RtmpdVkhKP/downloaded_packages' |
Using R packages
For using the installed package, please set the R_LIBS variable before you call the R package:
...