Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision		 Previous revision
habrok:examples:r [2023/03/21 13:15] – adminhabrok:examples:r [2023/03/22 13:29] (current) – [Multiple nodes] fokke
Line 26: Line 26:
 #SBATCH --mem=1000 #SBATCH --mem=1000
  
-ml R/3.4.4-foss-2018a-X11-20180131+module purge 
 +module load R/4.2.1-foss-2022a
 Rscript R_example1.R Rscript R_example1.R
 </code> </code>
Line 72: Line 73:
 #SBATCH --mem=10GB #SBATCH --mem=10GB
  
-module load R/3.4.4-foss-2018a-X11-20180131+module purge 
 +module load R/4.2.1-foss-2022a
  
 Rscript parallel.R Rscript parallel.R
 </code> </code>
  
-The file containing the R code is named ''%%parallel.R%%''. Note that the package ''%%parallel%%'' and ''%%snow%%'' are used but others might be available as well. If necessary additional packages have to be installed, see [[peregrine:software_environment:installation_of_extra_applications_or_libraries#r|this page]].+The file containing the R code is named ''%%parallel.R%%''. Note that the package ''%%parallel%%'' and ''%%snow%%'' are used but others might be available as well. If necessary additional packages have to be installed, see [[habrok:software_environment:installation_of_extra_applications_or_libraries#r|this page]].
  
 <code r parallel.R> <code r parallel.R>
Line 140: Line 142:
 #SBATCH --mem=10GB #SBATCH --mem=10GB
  
-module load R/3.4.4-foss-2018a-X11-20180131+module purge 
 +module load R/4.2.1-foss-2022a
  
 srun ${EBROOTR}/lib64/R/library/snow/RMPISNOW < parallel.R srun ${EBROOTR}/lib64/R/library/snow/RMPISNOW < parallel.R
Line 147: Line 150:
 ==== GPU ==== ==== GPU ====
  
-In order to let R use the GPUs of the Peregrine cluster, we first have install the R library ''gpuR''. Unfortunately, this library has been removed from CRAN, and we will need to install it from GitHub. To do this, we first start an interactive job on one of the GPU nodes with an NVidia V100 GPU. You can similarly install it from a node with an NVidia K40 GPU, but we have fewer of those. This is how you start an interactive job from the command line on the login node:+In order to let R use the GPUs of the Hábrók cluster, we first have install the R library ''gpuR''. Unfortunately, this library has been removed from CRAN, and we will need to install it from GitHub. To do this, we first start an interactive job on one of the GPU nodes with an NVidia V100 GPU. You can similarly install it from a node with an NVidia K40 GPU, but we have fewer of those. This is how you start an interactive job from the command line on the login node:
 <code bash> <code bash>
 srun --time=00:30:00 --partition=gpushort --gres=gpu:v100:1 --cpus-per-task=12 --pty bash -i srun --time=00:30:00 --partition=gpushort --gres=gpu:v100:1 --cpus-per-task=12 --pty bash -i
Line 217: Line 220:
 Now the packages will be available for any job that you run. Note that you do have to do this again once you switch to a completely different R version. Now the packages will be available for any job that you run. Note that you do have to do this again once you switch to a completely different R version.
  
-===== Login node limits =====+==== Login node limits ====
  
 Note that if you are trying to install something on the login node, you may run into certain limits that prevent you from using too much memory on the login node. See [[:habrok:additional_information:faq#i_am_running_something_on_the_login_node_and_the_process_gets_killed_why_does_this_happen|this]] question in the FAQ for more information. Note that if you are trying to install something on the login node, you may run into certain limits that prevent you from using too much memory on the login node. See [[:habrok:additional_information:faq#i_am_running_something_on_the_login_node_and_the_process_gets_killed_why_does_this_happen|this]] question in the FAQ for more information.