RStudio - Revision history

Wwarr@uab.edu at 22:00, 24 June 2021

2021-06-24T22:00:29Z

← Older revision		Revision as of 22:00, 24 June 2021
Line 200:		Line 200:

	</pre>		</pre>

			===Setting per-project package libraries===
			Please see the page on [[R#Per-Project_Package_Libraries\|R Per-Project Package Libraries]] for more information

	===Moving rstudio directory===		===Moving rstudio directory===

Wwarr@uab.edu: Added info on move/symlink rstudio dir to user data

2021-03-24T19:49:35Z

Added info on move/symlink rstudio dir to user data

← Older revision		Revision as of 19:49, 24 March 2021
Line 199:		Line 199:


			</pre>

			===Moving rstudio directory===
			As you accumulate rstudio packages, you may find that it is taking a lot of space in your $HOME directory, leading to issues with interactive sessions failing to start. The issue may be resolved by moving the directory and creating a shortcut to the new location in its place.

			How to: Move a pre-existing rstudio directory and create a symlink
			<pre>
			cd ~
			mv ~/.rstudio $USER_DATA/
			ln -s $USER_DATA/.rstudio .rstudio
	</pre>		</pre>

Ravi89@uab.edu: /* Local Browser Connection */ Removing the link for http://localhost:8700 as it is just an example

2018-03-07T17:35:21Z

Local Browser Connection: Removing the link for http://localhost:8700 as it is just an example

← Older revision		Revision as of 17:35, 7 March 2018
Line 38:		Line 38:
	http://localhost:8700		http://localhost:8700
	</pre>		</pre>
	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'		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 <nowiki>http://localhost:8700</nowiki>

	====Authorization Info====		====Authorization Info====

Ravi89@uab.edu: /* Default parameters */

2018-03-06T19:11:05Z

Default parameters

← Older revision		Revision as of 19:11, 6 March 2018
Line 71:		Line 71:
	If you use '''rserver''' without any additional parameters, it would start with the following default parameters		If you use '''rserver''' without any additional parameters, it would start with the following default parameters
	<pre>		<pre>
	Partition: ~~Express~~		Partition: Short
	Time: 02:00:00		Time: 12:00:00
	mem-per-cpu: 1024		mem-per-cpu: 1024
	~~ntasks~~: 1		cpus-per-task: 2
	</pre>		</pre>

Ravi89@uab.edu: /* Accessing the created RStudio session */ Adding a method to create your own passwords.

2018-03-05T20:53:49Z

Accessing the created RStudio session: Adding a method to create your own passwords.

@@ Line 26: / Line 26: @@
 Here are the steps to connect to it, based on the information that it sends:
 <pre>
 SSH port forwarding from laptop
@@ Line 32: / Line 33: @@
 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 [https://docs.uabgrid.uab.edu/wiki/Setting_Up_VNC_Session#Port-forwarding_from_Windows_Systems here].
 <pre>
 Connection string for local browser
@@ Line 38: / Line 40: @@
 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'
 <pre>
 Authorization info for Rstudio
@@ Line 44: / Line 47: @@
 </pre>
 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.
 ===Default parameters===

Ravi89@uab.edu: /* Accessing the created RStudio session */

2018-03-03T22:03:23Z

Accessing the created RStudio session

← Older revision		Revision as of 22:03, 3 March 2018
Line 30:		Line 30:
	ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu		ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu
	</pre>		</pre>
	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 above ~~example~~ would be '''ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu''' . ~~If you are on~~ a Windows system, you can set up port forwarding on your system, using the methods defined [https://docs.uabgrid.uab.edu/wiki/Setting_Up_VNC_Session#Port-forwarding_from_Windows_Systems here].		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 [https://docs.uabgrid.uab.edu/wiki/Setting_Up_VNC_Session#Port-forwarding_from_Windows_Systems here].

	<pre>		<pre>
Line 43:		Line 43:
	Password: ................		Password: ................
	</pre>		</pre>
	Each RStudio server session is secured with a random temporary password, which ~~you~~ can ~~find~~ under '''Authorization info for Rstudio''' . Use this info to login to Rstudio server, on your web browser.		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.

	===Default parameters===		===Default parameters===

Ravi89@uab.edu: Initial RStudio page.

2018-03-03T21:39:21Z

Initial RStudio page.

New page

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 [https://www.rstudio.com/ here].

===Starting a RStudio server session===
RStudio server session can be started on cheaha, by using command '''rserver'''.
<pre>
[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 ~]$
</pre>

===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:

<pre>
SSH port forwarding from laptop
ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu
</pre>
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 above example would be '''ssh -L 8700:c0082:8700 ravi89@cheaha.rc.uab.edu''' . If you are on a Windows system, you can set up port forwarding on your system, using the methods defined [https://docs.uabgrid.uab.edu/wiki/Setting_Up_VNC_Session#Port-forwarding_from_Windows_Systems here].

<pre>
Connection string for local browser
http://localhost:8700
</pre>
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'

<pre>
Authorization info for Rstudio
Username: ravi89
Password: ................
</pre>
Each RStudio server session is secured with a random temporary password, which you can find under '''Authorization info for Rstudio''' . Use this info to login to Rstudio server, on your web browser.

===Default parameters===
If you use '''rserver''' without any additional parameters, it would start with the following default parameters
<pre>
Partition: Express
Time: 02:00:00
mem-per-cpu: 1024
ntasks: 1
</pre>

===Setting parameters===
You can set your own parameters with '''rserver''' like time, partition etc.

'''Example:'''
<pre>
rserver --time=05:00:00 --partition=short --mem-per-cpu=4096
</pre>

List of parameters that you can set up with rserver:
<pre>
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

</pre>