{"type":"doc","content":[{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":66.66},"content":[{"type":"paragraph","content":[{"text":"This section provide additional information on different aspects of using R on ALICE and SHARK.","type":"text"}]},{"type":"paragraph","content":[{"text":"For a basic example of submitting an R job on both cluster, please see ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37027982"}},{"text":" ","type":"text"}]},{"type":"paragraph","content":[{"text":"For background information on installing R packages yourself, please see ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37749400"}}]},{"type":"paragraph","content":[{"text":"For further reading, check out some of the references here: ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37749488/References+and+further+reading#R"}},{"text":" ","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":33.33},"content":[{"type":"extension","attrs":{"layout":"default","extensionType":"com.atlassian.confluence.macro.core","extensionKey":"toc","parameters":{"macroParams":{"minLevel":{"value":"1"},"maxLevel":{"value":"7"},"exclude":{"value":"Contents"}},"macroMetadata":{"macroId":{"value":"310da701-8328-4cbc-8fa0-bbee80bc6d1c"},"schemaVersion":{"value":"1"},"title":"Table of Contents"}},"localId":"3f897b79-4ad4-471f-948f-3d2aa7063710"}}]}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Running an R script on the command line","type":"text"}]},{"type":"paragraph","content":[{"text":"There are several ways to launch an R script on the command line:","type":"text"}]},{"type":"orderedList","attrs":{"order":1},"content":[{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"Rscript yourfile.R","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"R CMD BATCH yourfile.R","type":"text","marks":[{"type":"code"}]}]}]},{"type":"listItem","content":[{"type":"paragraph","content":[{"text":"R --no-save < yourfile.R","type":"text","marks":[{"type":"code"}]}]}]}]},{"type":"paragraph","content":[{"text":"The first approach (i.e. using the Rscript command) redirects the output into stdout. The second approach (i.e. using the R CMD BATCH command) redirects its output into a file (in case yourfile.Rout). A third approach is to redirect the input of the file yourfile.R to the R executable. Note that in the latter approach you must specify one of the following flags: ","type":"text"},{"text":"--save","type":"text","marks":[{"type":"code"}]},{"text":", ","type":"text"},{"text":"--no-save","type":"text","marks":[{"type":"code"}]},{"text":" or ","type":"text"},{"text":"--vanilla","type":"text","marks":[{"type":"code"}]},{"text":". Careful with using the option ","type":"text"},{"text":"--vanilla","type":"text","marks":[{"type":"code"}]},{"text":", because it will also tell R to not read your user profile and environment.","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Using R with OpenMPI","type":"text"}]},{"type":"paragraph","content":[{"text":"In addition to the examples for running R in parallel in ","type":"text"},{"type":"inlineCard","attrs":{"url":"https://pubappslu.atlassian.net/wiki/spaces/HPCWIKI/pages/37027982"}},{"text":" , we provide here a basic HelloWorld example for using with OpenMPI","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"The R script","type":"text"}]},{"type":"paragraph","content":[{"text":"We will use the following R script and saved in a file called ","type":"text"},{"text":"test_r_mpi.R","type":"text","marks":[{"type":"code"}]}]},{"type":"codeBlock","attrs":{"language":"r"},"content":[{"text":"library(Rmpi)\n\nid <- mpi.comm.rank(comm = 0)\nnp <- mpi.comm.size(comm = 0)\nhostname <- mpi.get.processor.name()\n\nmsg <- sprintf(\"Hello world from process %03d of %03d, on host %s\\n\", id, np, hostname)\ncat(msg)\n\nmpi.barrier(comm = 0)\nmpi.finalize()","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"The Slurm batch file","type":"text"}]},{"type":"paragraph","content":[{"text":"Now, we need a Slurm batch file to run the R script as a batch job which we call ","type":"text"},{"text":"test_r_mpi.slurm","type":"text","marks":[{"type":"code"}]},{"text":":","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n\n#SBATCH --job-name=test_r_mpi # Job name\n#SBATCH --output=%x_%j.out # Output file name\n#SBATCH --partition=testing # Partition\n#SBATCH --time=00:05:00 # Time limit\n#SBATCH --nodes=2 # Number of nodes\n#SBATCH --ntasks-per-node=4 # MPI processes per node\n\nmodule purge\nmodule load slurm\nmodule add R/4.0.5-foss-2020b\n\nsrun Rscript test_r_mpi.R","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"#!/bin/bash\n\n#SBATCH --job-name=test_r_mpi # Job name\n#SBATCH --output=%x_%j.out # Output file name\n#SBATCH --partition=short # Partition\n#SBATCH --time=00:05:00 # Time limit\n#SBATCH --nodes=2 # Number of nodes\n#SBATCH --ntasks-per-node=4 # MPI processes per node\n\nmodule purge\nmodule load slurm\nmodule add statistical/R/4.1.2/gcc.8.3.1\nmodule add library/mpi/openmpi/4.1.1/gcc-8.3.1\n\nsrun Rscript test_r_mpi.R","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"After running the job above, Slurm will have created a file called ","type":"text"},{"text":"test_r_mpi_.out","type":"text","marks":[{"type":"code"}]},{"text":" whose content will look something like this","type":"text"}]},{"type":"codeBlock","content":[{"text":"[me@ ]$ cat test_r_mpi_.out \nHello world from process 000 of 008, on host res-hpc-gpu01\nHello world from process 001 of 008, on host res-hpc-gpu01\nHello world from process 002 of 008, on host res-hpc-gpu01\nHello world from process 003 of 008, on host res-hpc-gpu01\nHello world from process 004 of 008, on host res-hpc-gpu02\nHello world from process 005 of 008, on host res-hpc-gpu02\nHello world from process 006 of 008, on host res-hpc-gpu02\nHello world from process 007 of 008, on host res-hpc-gpu02","type":"text"}]},{"type":"heading","attrs":{"level":1},"content":[{"text":"Running R interactively","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"You can start to run R interactively, just as an exercise and test. The recommended way is to run R in batch mode.","type":"text"}]}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@nodelogin02 ~]$ salloc --ntasks 1 --mem=1G --time=00:05:00 --partition=testing\nsalloc: Pending job allocation 656147\nsalloc: job 656147 queued and waiting for resources\nsalloc: job 656147 has been allocated resources\nsalloc: Granted job allocation 656147\nsalloc: Waiting for resource configuration\nsalloc: Nodes nodelogin01 are ready for job\n[me@nodelogin02 ~]$ ssh nodelogin01\nLast login: Tue Aug 9 15:35:06 2022 from p-cfer-016105.infra.leidenuniv.nl\n[me@nodelogin01 ~]$ module load R/4.0.5-foss-2020b\n[me@nodelogin01 ~]$ R\n\nR version 4.0.5 (2021-03-31) -- \"Shake and Throw\"\nCopyright (C) 2021 The R Foundation for Statistical Computing\nPlatform: x86_64-pc-linux-gnu (64-bit)\n\nR is free software and comes with ABSOLUTELY NO WARRANTY.\nYou are welcome to redistribute it under certain conditions.\nType 'license()' or 'licence()' for distribution details.\n\n Natural language support but running in an English locale\n\nR is a collaborative project with many contributors.\nType 'contributors()' for more information and\n'citation()' on how to cite R or R packages in publications.\n\nType 'demo()' for some demos, 'help()' for on-line help, or\n'help.start()' for an HTML browser interface to help.\nType 'q()' to quit R.\n\n[Previously saved workspace restored]\n\n> q()\nSave workspace image? [y/n/c]: n\n[me@nodelogin01 ~]$ exit\nlogout\nConnection to nodelogin01 closed.\n[me@nodelogin02 ~]$ exit\nexit\nsalloc: Relinquishing job allocation 656147\nsalloc: Job allocation 656147 has been revoked.","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"[me@res-hpc-lo02 ~]$ salloc --ntasks 1 --mem=1G --time=00:05:00 --partition=short\nsalloc: Granted job allocation 11441259\nsalloc: Waiting for resource configuration\nsalloc: Nodes res-hpc-gpu09 are ready for job\n[me@res-hpc-gpu09 ~]$ module load statistical/R/4.1.2/gcc.8.3.1\n[me@res-hpc-gpu09 ~]$ R\n\nR version 4.1.2 (2021-11-01) -- \"Bird Hippie\"\nCopyright (C) 2021 The R Foundation for Statistical Computing\nPlatform: x86_64-pc-linux-gnu (64-bit)\n\nR is free software and comes with ABSOLUTELY NO WARRANTY.\nYou are welcome to redistribute it under certain conditions.\nType 'license()' or 'licence()' for distribution details.\n\n Natural language support but running in an English locale\n\nR is a collaborative project with many contributors.\nType 'contributors()' for more information and\n'citation()' on how to cite R or R packages in publications.\n\nType 'demo()' for some demos, 'help()' for on-line help, or\n'help.start()' for an HTML browser interface to help.\nType 'q()' to quit R.\n\n> q()\nSave workspace image? [y/n/c]: n\n[me@res-hpc-gpu09 ~]$ exit\nexit\nsalloc: Relinquishing job allocation 11441259\nsalloc: Job allocation 11441259 has been revoked.","type":"text"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":1},"content":[{"text":"RStudio","type":"text"}]},{"type":"paragraph","content":[{"text":"RStudio is an Integrated Development Environment (IDE) for R. It includes a console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, debugging, history and workspace management. For more information see RStudio webpage.","type":"text"}]},{"type":"paragraph","content":[{"text":"RStudio is installed on both clusters and can be invoked on a login node as follows:","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":" module load R/4.4.0-gfbf-2023a\n module load RStudio-Desktop/2024.04.2+764\n rstudio","type":"text"}]},{"type":"paragraph","content":[{"text":"Note that you also need to load a version of R. Here, we are loading R/4.4.0","type":"text"}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"module load statistical/RStudio/1.3.959/gcc-8.3.1\nrstudio","type":"text"}]},{"type":"paragraph","content":[{"text":"Note that you also need to load a version of R","type":"text"}]}]}]},{"type":"rule"},{"type":"paragraph","content":[{"text":"RStudio cannot be executed from a slurm job submitted with sbatch, but you can use it by running an interactive job.","type":"text"}]},{"type":"heading","attrs":{"level":2},"content":[{"text":"Interactive jobs for RStudio","type":"text"}]},{"type":"paragraph","content":[{"text":"Interactive jobs can be submitted to queue by using the Slurm command ","type":"text"},{"text":"salloc","type":"text","marks":[{"type":"code"}]},{"text":" which takes the same options as slurm batch files.","type":"text"}]},{"type":"paragraph","content":[{"text":"Since interactive jobs also go into the queue, it can take some time until your job runs depending on the load on the cluster. Therefore, it is best to submit the interactive job from a screen or tmux session.","type":"text"}]},{"type":"paragraph","content":[{"text":"Here is an example of a ","type":"text"},{"text":"salloc","type":"text","marks":[{"type":"code"}]},{"text":" command","type":"text"}]},{"type":"codeBlock","content":[{"text":" salloc --ntasks=1 --cpus-per-task=1 --mem-per-cpu=10GB --partition= --time=00:05:00 --x11","type":"text"}]},{"type":"paragraph","content":[{"text":"where ","type":"text"},{"text":"","type":"text","marks":[{"type":"code"}]},{"text":" needs be replaced by a valid partition. The option ","type":"text"},{"text":"--x11","type":"text","marks":[{"type":"code"}]},{"text":" is important for forwarding x11 from the compute node on which the job is running. The job uses a rather short running time because it is intended for testing how to launch RStudio.","type":"text"}]},{"type":"paragraph","content":[{"text":"Note that the above command will already log you into the compute node that was assigned to you.","type":"text"}]},{"type":"paragraph","content":[{"text":"Once your interactive is running, you can launch RStudio in the following way:","type":"text"}]},{"type":"layoutSection","content":[{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"ALICE","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"module load R/4.4.0-gfbf-2023a\nmodule load RStudio-Desktop/2024.04.2+764\nexport XDG_RUNTIME_DIR=/tmp/runtime-$USER\nrstudio","type":"text"}]},{"type":"paragraph","content":[{"text":"Please note that you can safely ignore the following error message when starting rstudio: ","type":"text"},{"text":"Failed to connect to the bus:","type":"text","marks":[{"type":"code"}]}]}]},{"type":"layoutColumn","attrs":{"width":50.0},"content":[{"type":"rule"},{"type":"paragraph","content":[{"text":"SHARK","type":"text","marks":[{"type":"strong"}]}]},{"type":"codeBlock","content":[{"text":"module purge\nmodule add statistical/RStudio/1.3.959/gcc-8.3.1\nrstudio","type":"text"}]}]}]},{"type":"rule"},{"type":"heading","attrs":{"level":2},"content":[{"text":"RStudio on the OOD (OpenOnDemand portal)","type":"text"}]},{"type":"panel","attrs":{"panelType":"warning"},"content":[{"type":"paragraph","content":[{"text":"OOD is only available to SHARK users.","type":"text"}]}]},{"type":"paragraph","content":[{"text":"You can also start an RStudio server on the OOD portal","type":"text"}]}],"version":1}

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