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Commit 40931012 authored by Natalie Breidenbach's avatar Natalie Breidenbach
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Update data_analytics_with_r.md

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2 merge requests!938Automated merge from preview to main,!936Update to Five-Cluster-Operation
...@@ -6,7 +6,7 @@ classical statistical tests, time-series analysis, classification, etc.), machin ...@@ -6,7 +6,7 @@ classical statistical tests, time-series analysis, classification, etc.), machin
algorithms and graphical techniques. R is an integrated suite of software facilities for data algorithms and graphical techniques. R is an integrated suite of software facilities for data
manipulation, calculation and graphing. manipulation, calculation and graphing.
We recommend using the partitions Haswell and/or Romeo to work with R. For more details We recommend using the clusters Barnard and/or Romeo to work with R. For more details
see our [hardware documentation](../jobs_and_resources/hardware_overview.md). see our [hardware documentation](../jobs_and_resources/hardware_overview.md).
## R Console ## R Console
...@@ -14,14 +14,17 @@ see our [hardware documentation](../jobs_and_resources/hardware_overview.md). ...@@ -14,14 +14,17 @@ see our [hardware documentation](../jobs_and_resources/hardware_overview.md).
In the following example, the `srun` command is used to start an interactive job, so that the output In the following example, the `srun` command is used to start an interactive job, so that the output
is visible to the user. Please check the [Slurm page](../jobs_and_resources/slurm.md) for details. is visible to the user. Please check the [Slurm page](../jobs_and_resources/slurm.md) for details.
_The module environments /hiera, /scs5, /classic and /ml originated from the taurus system are momentarily under construction. The script will be updated after completion of the redesign accordingly_
```console ```console
marie@login$ srun --partition=haswell --ntasks=1 --nodes=1 --cpus-per-task=4 --mem-per-cpu=2541 --time=01:00:00 --pty bash marie@login.barnard$ srun --ntasks=1 --nodes=1 --cpus-per-task=4 --mem-per-cpu=2541 --time=01:00:00 --pty bash
marie@haswell$ module load modenv/scs5 marie@barnard$ module load modenv/scs5
marie@haswell$ module load R/3.6 marie@barnard$ module load R/3.6
[...] [...]
Module R/3.6.0-foss-2019a and 56 dependencies loaded. Module R/3.6.0-foss-2019a and 56 dependencies loaded.
marie@haswell$ which R marie@barnard$ which R
marie@haswell$ /sw/installed/R/3.6.0-foss-2019a/bin/R marie@barnard$ /sw/installed/R/3.6.0-foss-2019a/bin/R
``` ```
Using interactive sessions is recommended only for short test runs, while for larger runs batch jobs Using interactive sessions is recommended only for short test runs, while for larger runs batch jobs
...@@ -30,7 +33,7 @@ should be used. Examples can be found on the [Slurm page](../jobs_and_resources/ ...@@ -30,7 +33,7 @@ should be used. Examples can be found on the [Slurm page](../jobs_and_resources/
It is also possible to run `Rscript` command directly (after loading the module): It is also possible to run `Rscript` command directly (after loading the module):
```console ```console
marie@haswell$ Rscript </path/to/script/your_script.R> <param1> <param2> marie@barnard$ Rscript </path/to/script/your_script.R> <param1> <param2>
``` ```
## R in JupyterHub ## R in JupyterHub
...@@ -263,6 +266,9 @@ Submitting a multicore R job to Slurm is very similar to submitting an ...@@ -263,6 +266,9 @@ Submitting a multicore R job to Slurm is very similar to submitting an
[OpenMP Job](../jobs_and_resources/binding_and_distribution_of_tasks.md), [OpenMP Job](../jobs_and_resources/binding_and_distribution_of_tasks.md),
since both are running multicore jobs on a **single** node. Below is an example: since both are running multicore jobs on a **single** node. Below is an example:
_The module environments /hiera, /scs5, /classic and /ml originated from the taurus system are momentarily under construction. The script will be updated after completion of the redesign accordingly_
```Bash ```Bash
#!/bin/bash #!/bin/bash
#SBATCH --nodes=1 #SBATCH --nodes=1
......
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