RStudio
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The Research Computing Team
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, history, debugging and workspace management. To learn more about RStudio, click here.
Starting a RStudio server session
RStudio server session can be started on cheaha, by using command rserver.
[ravi89@login001 ~]$ rserver Waiting for RStudio server to start ... SSH port forwarding from laptop ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu Connection string for local browser http://localhost:8700 Authorization info for Rstudio Username: ravi89 Password: ................ [ravi89@login001 ~]$
Accessing the created RStudio session
Once RStudio session has started after running rserver command, it would give you the information you need to connect to it.
Here are the steps to connect to it, based on the information that it sends:
Port forwarding
SSH port forwarding from laptop ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu
If you are on a Mac/Linux system, start a new tab/terminal on your mac and copy the ssh line mentioned under SSH port forwarding from laptop which in the example above would be ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu . On a Windows system, you can set up port forwarding on your system, using the methods defined here.
Local Browser Connection
Connection string for local browser http://localhost:8700
Now, start up a web browser of your choice, Google Chrome, Firefox, Safari etc. , and go to the link mentioned under Connection string for local browser , which in the above example would be http://localhost:8700
Authorization Info
Authorization info for Rstudio Username: ravi89 Password: ................
Each RStudio server session is secured with a random temporary password, which can be found under Authorization info for Rstudio . Use this info to login to Rstudio server, on your web browser.
Setting your own password
You can setup your own password for accessing RStudio session, by setting environment variable RSTUDIO_PASSWORD . You can set an environment variable using the followng command on cheaha, before starting rserver
[ravi89@login001 ~]$ export RSTUDIO_PASSWORD=asdfghjkl [ravi89@login001 ~]$ rserver Waiting for RStudio server to start ............. SSH port forwarding from laptop ssh -L 8742:c0076:8742 ravi89@cheaha.rc.uab.edu Connection string for local browser http://localhost:8742 Authorization info for Rstudio Username: ravi89 Password: asdfghjkl [ravi89@login001 ~]$
Default parameters
If you use rserver without any additional parameters, it would start with the following default parameters
Partition: Short Time: 12:00:00 mem-per-cpu: 1024 cpus-per-task: 2
Setting parameters
You can set your own parameters with rserver like time, partition etc.
Example:
rserver --time=05:00:00 --partition=short --mem-per-cpu=4096
List of parameters that you can set up with rserver:
Parallel run options:
-a, --array=indexes job array index values
-A, --account=name charge job to specified account
--bb=<spec> burst buffer specifications
--bbf=<file_name> burst buffer specification file
--begin=time defer job until HH:MM MM/DD/YY
--comment=name arbitrary comment
--cpu-freq=min[-max[:gov]] requested cpu frequency (and governor)
-c, --cpus-per-task=ncpus number of cpus required per task
-d, --dependency=type:jobid defer job until condition on jobid is satisfied
--deadline=time remove the job if no ending possible before
this deadline (start > (deadline - time[-min]))
--delay-boot=mins delay boot for desired node features
-D, --workdir=directory set working directory for batch script
-e, --error=err file for batch script's standard error
--export[=names] specify environment variables to export
--export-file=file|fd specify environment variables file or file
descriptor to export
--get-user-env load environment from local cluster
--gid=group_id group ID to run job as (user root only)
--gres=list required generic resources
--gres-flags=opts flags related to GRES management
-H, --hold submit job in held state
--ignore-pbs Ignore #PBS options in the batch script
-i, --input=in file for batch script's standard input
-I, --immediate exit if resources are not immediately available
--jobid=id run under already allocated job
-J, --job-name=jobname name of job
-k, --no-kill do not kill job on node failure
-L, --licenses=names required license, comma separated
-M, --clusters=names Comma separated list of clusters to issue
commands to. Default is current cluster.
Name of 'all' will submit to run on all clusters.
NOTE: SlurmDBD must up.
-m, --distribution=type distribution method for processes to nodes
(type = block|cyclic|arbitrary)
--mail-type=type notify on state change: BEGIN, END, FAIL or ALL
--mail-user=user who to send email notification for job state
changes
--mcs-label=mcs mcs label if mcs plugin mcs/group is used
-n, --ntasks=ntasks number of tasks to run
--nice[=value] decrease scheduling priority by value
--no-requeue if set, do not permit the job to be requeued
--ntasks-per-node=n number of tasks to invoke on each node
-N, --nodes=N number of nodes on which to run (N = min[-max])
-o, --output=out file for batch script's standard output
-O, --overcommit overcommit resources
-p, --partition=partition partition requested
--parsable outputs only the jobid and cluster name (if present),
separated by semicolon, only on successful submission.
--power=flags power management options
--priority=value set the priority of the job to value
--profile=value enable acct_gather_profile for detailed data
value is all or none or any combination of
energy, lustre, network or task
--propagate[=rlimits] propagate all [or specific list of] rlimits
--qos=qos quality of service
-Q, --quiet quiet mode (suppress informational messages)
--reboot reboot compute nodes before starting job
--requeue if set, permit the job to be requeued
-s, --oversubscribe over subscribe resources with other jobs
-S, --core-spec=cores count of reserved cores
--signal=[B:]num[@time] send signal when time limit within time seconds
--spread-job spread job across as many nodes as possible
--switches=max-switches{@max-time-to-wait}
Optimum switches and max time to wait for optimum
--thread-spec=threads count of reserved threads
-t, --time=minutes time limit
--time-min=minutes minimum time limit (if distinct)
--uid=user_id user ID to run job as (user root only)
--use-min-nodes if a range of node counts is given, prefer the
smaller count
-v, --verbose verbose mode (multiple -v's increase verbosity)
-W, --wait wait for completion of submitted job
--wckey=wckey wckey to run job under
--wrap[=command string] wrap command string in a sh script and submit
Constraint options:
--contiguous demand a contiguous range of nodes
-C, --constraint=list specify a list of constraints
-F, --nodefile=filename request a specific list of hosts
--mem=MB minimum amount of real memory
--mincpus=n minimum number of logical processors (threads)
per node
--reservation=name allocate resources from named reservation
--tmp=MB minimum amount of temporary disk
-w, --nodelist=hosts... request a specific list of hosts
-x, --exclude=hosts... exclude a specific list of hosts
Consumable resources related options:
--exclusive[=user] allocate nodes in exclusive mode when
cpu consumable resource is enabled
--exclusive[=mcs] allocate nodes in exclusive mode when
cpu consumable resource is enabled
and mcs plugin is enabled
--mem-per-cpu=MB maximum amount of real memory per allocated
cpu required by the job.
--mem >= --mem-per-cpu if --mem is specified.
Affinity/Multi-core options: (when the task/affinity plugin is enabled)
-B --extra-node-info=S[:C[:T]] Expands to:
--sockets-per-node=S number of sockets per node to allocate
--cores-per-socket=C number of cores per socket to allocate
--threads-per-core=T number of threads per core to allocate
each field can be 'min' or wildcard '*'
total cpus requested = (N x S x C x T)
--ntasks-per-core=n number of tasks to invoke on each core
--ntasks-per-socket=n number of tasks to invoke on each socket