RCSWiki - Recent changes [en]

Book online training sessions

Dmitri — Tue, 08 Sep 2026 16:16:06 GMT

Upcoming Sessions

@@ Line 51: / Line 51: @@
 Please reach out to us at [mailto:support@hpc.ucalgary.ca support@hpc.ucalgary.ca] for more help.
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 * Thursday, 2026-09-03, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Pedro Martinez
 : https://ucalgary.zoom.us/meeting/register/P5o5h152RAKtu5PJeWdSiQ
 == Past sessions ==

Open OnDemand

Dschulz — Tue, 01 Sep 2026 23:48:57 GMT

Custom RStudio Container Images

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 After requesting for a RStudio Server session through Open OnDemand, you will see a session information box similar to the one below. Each session will use a randomised password.
 [[File:RStudio Server launch on OOD.png|alt=RStudio Server launch on Open OnDemand|none|thumb|RStudio Server launch on Open OnDemand]]
-Because RStudio Server runs within an Apptainer environment, some features may not be working as expected. We are still testing this app -- If you notice any issues, please reach out to RCS.
+Because RStudio Server runs within an Apptainer environment, some features may not work as expected.
 === VS Code Server ===

List of courses on TALC

Pemartin — Tue, 01 Sep 2026 21:54:42 GMT

Fall 2026

← Older revision		Revision as of 21:54, 1 September 2026
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	* ENSF 620 L01 – Advanced Data Analytics, by Dr Ethan MacDonald (Sep 1 - Dec 24).		* ENSF 620 L01 – Advanced Data Analytics, by Dr Ethan MacDonald (Sep 1 - Dec 24).

			* PHYS 605 – Advanced Data Analysis, by Dr Claudia Gomes da Rocha (Sep 2 - Dec 24).

	=== Summer 2026 ===		=== Summer 2026 ===

List of courses on TALC

Dmitri — Tue, 01 Sep 2026 20:30:34 GMT

Fall 2026

← Older revision		Revision as of 20:30, 1 September 2026
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	* MDSC 523, AI Applications for Health, by Dr Constance Li (Sep 21 - Dec 10).		* MDSC 523, AI Applications for Health, by Dr Constance Li (Sep 21 - Dec 10).

	* ENSF 519.53, ~~...~~, by Dr Yani Ioannou (...).		* ENSF 519.53, Applied Deep Learning, by Dr Yani Ioannou and Dr Yufan Feng (Sep 2 - Dec 4).

			* ENSF 620 L01 – Advanced Data Analytics, by Dr Ethan MacDonald (Sep 1 - Dec 24).

	=== Summer 2026 ===		=== Summer 2026 ===

Book online training sessions

Dmitri — Tue, 01 Sep 2026 18:50:15 GMT

Book your training session here

← Older revision		Revision as of 18:50, 1 September 2026
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	* Tuesday, 2026-08~~-18~~, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov		* Tuesday, 2026-09-08, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov
	: https://ucalgary.zoom.us/meeting/register/~~bEyyKYlGTUKiVNF-HdQqHQ~~		: https://ucalgary.zoom.us/meeting/register/UQHXeXb4SBOxvifWaFwNuA

	* Thursday, 2026-08-20, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Dmitri Rozmanov		* Thursday, 2026-09-10, '''11:30 am''' - 01:00 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Dmitri Rozmanov
	: https://ucalgary.zoom.us/meeting/register/~~wjlu8kr4TPOx_K2pXdvMzw~~		: https://ucalgary.zoom.us/meeting/register/dVJL9v7qQWm1DZA0538Jsw


	== Past sessions ==		== Past sessions ==

			* Tuesday, 2026-08-18, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov
			* Thursday, 2026-08-20, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Dmitri Rozmanov

	* Tuesday, 2026-08-11, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Pedro Martinez		* Tuesday, 2026-08-11, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Pedro Martinez

Apptainer

Pemartin — Mon, 24 Aug 2026 17:12:11 GMT

Merge Singularity to Apptainer page content

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 = General =
 == Accessing data outside the container ==
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 To bind the <code>/work</code>, and <code>/bulk</code>, and <code>/scratch</code> file systems,
 you have to add the <code>-B</code> option to your '''apptainer command line'''. Like this:
-  apptainer -B /work,/bulk,/scratch ....
+  # apptainer -B /work,/bulk,/scratch ....
 This change ensures that these file systems will be available for programs running from inside the container.

List of courses on TALC

Dmitri — Wed, 19 Aug 2026 21:32:02 GMT

Current Courses

← Older revision		Revision as of 21:32, 19 August 2026
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	* MDSC 523, AI Applications for Health, by Dr Constance Li (Sep 21 - Dec 10).		* MDSC 523, AI Applications for Health, by Dr Constance Li (Sep 21 - Dec 10).

			* ENSF 519.53, ..., by Dr Yani Ioannou (...).

	=== Summer 2026 ===		=== Summer 2026 ===

Category:How-Tos

Dmitri — Tue, 18 Aug 2026 21:39:58 GMT

ARC

← Older revision		Revision as of 21:39, 18 August 2026
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	* [[How to use local storage on ARC's compute nodes]]		* [[How to use local storage on ARC's compute nodes]]

	* [[How to access ResearchFS ~~stroage~~ from ARC]]		* [[How to access ResearchFS storage from ARC]]

	= SLURM =		= SLURM =

How to access ResearchFS stroage from ARC

Dmitri — Tue, 18 Aug 2026 21:39:27 GMT

Dmitri moved page How to access ResearchFS stroage from ARC to How to access ResearchFS storage from ARC without leaving a redirect

← Older revision		Revision as of 21:39, 18 August 2026
(7 intermediate revisions by the same user not shown)
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			= Background =

			[[Storage_Options#ResearchFS \| ResearchFS]]
			is a University of Calgary-hosted storage solution funded and operated by '''RCS'''.
			It is available by request to faculty and staff for storing '''active research data'''.


			'''ResearchFS''' storage is presented to researchers as mountable Windows '''SMB/CIFS''' network shares.
			Direct mounting of '''ResearchFS shares''' on ARC is not supported.
			Data can instead be transferred between the '''ARC cluster''' and '''ResearchFS''' using '''rclone'''.


	[https://rclone.org/ Rclone] is a command-line program for managing files on remote storage systems.		[https://rclone.org/ Rclone] is a command-line program for managing files on remote storage systems.
	On the ~~ARC cluster~~, ~~it can be used to download data from and upload data to~~ the ~~'''UofC ResearchFS''' storage.~~		It can access ResearchFS directly using the SMB protocol, without mounting the network share on ARC.

	~~ResearchFS storage is presented to researchers as Windows '''SMB/CIFS'''~~ network ~~shares.~~
	~~On Linux, SMB shares can be accessed using software such as Samba or, as described here, directly using '''rclone'''~~.

	= Rclone configuration =		= Rclone configuration =
Line 22:		Line 30:
	Obscuring a password is '''not encryption''' and should not be considered secure storage for your UofC password.		Obscuring a password is '''not encryption''' and should not be considered secure storage for your UofC password.

	~~Kerberos provides a more appropriate way to authenticate to ResearchFS without storing your UofC password in the rclone configuration file.~~

	~~Choose~~ the ~~following options during <code>~~rclone config~~</code>:~~		'''Kerberos''' is a secure network authentication protocol that allows users to authenticate to services in a consistent and secure way. It is a more appropriate way to authenticate to '''ResearchFS''' and avoids storing your UofC password in the '''rclone''' configuration file.


			Run
			$ rclone config

			and choose the following options:
	* New remote		* New remote
	* Name --> ResearchFS		* Name --> ResearchFS
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	To list the shares available on ResearchFS:		To list the shares available on ResearchFS:
			$ rclone lsf ResearchFS:
	$ rclone lsf ResearchFS:

	To list files and directories inside your share:		To list files and directories inside your share:
			$ rclone lsf ResearchFS:my_share/
	$ rclone lsf ResearchFS:my_share/

	= Transferring directories between ResearchFS and ARC =		= Transferring directories between ResearchFS and ARC =

	To copy the '''contents''' of a local directory named <code>arc_data</code> to a directory named <code>arc_data</code> on ResearchFS:		To copy the '''contents''' of a local directory named <code>arc_data</code> to a directory named <code>arc_data</code> on ResearchFS:
			$ rclone copy -P arc_data ResearchFS:my_share/arc_data

	~~$ rclone copy -P arc_data ResearchFS:my_share/arc_data~~		The <code>-P</code> option displays the progress of the transfer,
			including the amount of data transferred, transfer speed, and estimated completion time.
	The <code>-P</code> option displays the progress of the transfer, including the amount of data transferred, transfer speed, and estimated completion time.

	To copy the contents of the ResearchFS directory back to a local <code>arc_data</code> directory on ARC:		To copy the contents of the ResearchFS directory back to a local <code>arc_data</code> directory on ARC:
			$ rclone copy -P ResearchFS:my_share/arc_data arc_data
	$ rclone copy -P ResearchFS:my_share/arc_data arc_data

	Note that <code>rclone copy</code> copies the '''contents''' of the source directory into the specified destination.		Note that <code>rclone copy</code> copies the '''contents''' of the source directory into the specified destination.
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	For example:		For example:
			$ rclone copy -P arc_data ResearchFS:my_share/arc_data
	$ rclone copy -P arc_data ResearchFS:my_share/arc_data

	copies the contents of the local <code>arc_data</code> directory into <code>my_share/arc_data</code> on ResearchFS.		copies the contents of the local <code>arc_data</code> directory into <code>my_share/arc_data</code> on ResearchFS.
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	After transferring important data, you can use <code>rclone check</code> to compare the source and destination:		After transferring important data, you can use <code>rclone check</code> to compare the source and destination:
			$ rclone check arc_data ResearchFS:my_share/arc_data
	$ rclone check arc_data ResearchFS:my_share/arc_data

	To check a transfer in the opposite direction:		To check a transfer in the opposite direction:
			$ rclone check ResearchFS:my_share/arc_data arc_data
	$ rclone check ResearchFS:my_share/arc_data arc_data

	The <code>check</code> operation compares the files at the source and destination without modifying either location.		The <code>check</code> operation compares the files at the source and destination without modifying either location.
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	= Links =		= Links =

	[[How-~~Toos~~]]		[[How-Tos]]

How to access ResearchFS stroage from ARC

Dmitri — Tue, 18 Aug 2026 19:10:23 GMT

Created page with " [https://rclone.org/ Rclone] is a command-line program for managing files on remote storage systems. On the ARC cluster, it can be used to download data from and upload data to the '''UofC ResearchFS''' storage. ResearchFS storage is presented to researchers as Windows '''SMB/CIFS''' network shares. On Linux, SMB shares can be accessed using software such as Samba or, as described here, directly using '''rclone'''. = Rclone configuration = '''rclone''' can access '''..."

New page

[https://rclone.org/ Rclone] is a command-line program for managing files on remote storage systems.
On the ARC cluster, it can be used to download data from and upload data to the '''UofC ResearchFS''' storage.

ResearchFS storage is presented to researchers as Windows '''SMB/CIFS''' network shares.
On Linux, SMB shares can be accessed using software such as Samba or, as described here, directly using '''rclone'''.

= Rclone configuration =

'''rclone''' can access '''SMB/CIFS''' storage using its native
[https://rclone.org/smb/ SMB/CIFS connector]
without mounting the share on the cluster.

'''WARNING''': When configuring a new remote using the interactive

$ rclone config

command, do '''not''' enter your UofC password into the rclone configuration.
Instead, leave the password blank and enable '''Kerberos''' authentication.

If a password is provided, rclone stores an obscured version of it in its configuration file.
Obscuring a password is '''not encryption''' and should not be considered secure storage for your UofC password.

Kerberos provides a more appropriate way to authenticate to ResearchFS without storing your UofC password in the rclone configuration file.

Choose the following options during <code>rclone config</code>:

* New remote
* Name --> ResearchFS
* Storage --> smb
* Host --> researchfs.uc.ucalgary.ca
* Port --> default (445)
* User --> <your_uofc_IT_username>
* Samba password --> leave blank
* Domain --> UC
* SPN --> leave blank
* use_kerberos --> true
* Edit advanced config --> No
* Keep this remote? --> Yes
* Quit

'''Alternatively''', if you already have an rclone configuration file, you can edit it directly.

Add the following section to <code>~/.config/rclone/rclone.conf</code>:

<syntaxhighlight lang="ini">
[ResearchFS]
type = smb
host = researchfs.uc.ucalgary.ca
user = <uofc_username>
domain = UC
use_kerberos = true
</syntaxhighlight>

= Obtaining a Kerberos ticket =

Before accessing ResearchFS, you need a valid Kerberos ticket.

Obtain one with:

<pre>
$ kinit
Password for username@UC.UCALGARY.CA:
</pre>

Enter your UofC password when prompted.
The password is used to obtain a Kerberos ticket and is not stored in the rclone configuration.

You can check your Kerberos tickets with:

<pre>
$ klist

Ticket cache: FILE:/tmp/krb5cc_11111111
Default principal: username@UC.UCALGARY.CA

Valid starting Expires Service principal
08/14/26 15:06:05 08/15/26 01:06:05 krbtgt/UC.UCALGARY.CA@UC.UCALGARY.CA
renew until 08/21/26 15:05:58
</pre>

The Kerberos credential cache (for example, <code>/tmp/krb5cc_11111111</code>) contains the ticket that rclone uses when authenticating to ResearchFS.

Kerberos tickets have a limited lifetime.
The expiration time is shown by <code>klist</code>.
If your ticket has expired, run <code>kinit</code> again to obtain a new one.

= Accessing ResearchFS shares =

To list the shares available on ResearchFS:

$ rclone lsf ResearchFS:

To list files and directories inside your share:

$ rclone lsf ResearchFS:my_share/

= Transferring directories between ResearchFS and ARC =

To copy the '''contents''' of a local directory named <code>arc_data</code> to a directory named <code>arc_data</code> on ResearchFS:

$ rclone copy -P arc_data ResearchFS:my_share/arc_data

The <code>-P</code> option displays the progress of the transfer, including the amount of data transferred, transfer speed, and estimated completion time.

To copy the contents of the ResearchFS directory back to a local <code>arc_data</code> directory on ARC:

$ rclone copy -P ResearchFS:my_share/arc_data arc_data

Note that <code>rclone copy</code> copies the '''contents''' of the source directory into the specified destination.
It does not automatically append the source directory name to the destination path.

For example:

$ rclone copy -P arc_data ResearchFS:my_share/arc_data

copies the contents of the local <code>arc_data</code> directory into <code>my_share/arc_data</code> on ResearchFS.

If a transfer is interrupted, the same <code>rclone copy</code> command can be run again.
Files that have already been successfully transferred and are unchanged do not need to be copied again.

=== Verifying transferred data ===

After transferring important data, you can use <code>rclone check</code> to compare the source and destination:

$ rclone check arc_data ResearchFS:my_share/arc_data

To check a transfer in the opposite direction:

$ rclone check ResearchFS:my_share/arc_data arc_data

The <code>check</code> operation compares the files at the source and destination without modifying either location.
It reports missing or different files, making it useful for verifying that a transfer completed successfully.

= Links =

[[How-Toos]]

Category:How-Tos

Dmitri — Tue, 18 Aug 2026 19:08:52 GMT

ARC

← Older revision		Revision as of 19:08, 18 August 2026
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	* [[How to use ARC scratch space]]		* [[How to use ARC scratch space]]
	* [[How to use local storage on ARC's compute nodes]]		* [[How to use local storage on ARC's compute nodes]]

			* [[How to access ResearchFS stroage from ARC]]

	= SLURM =		= SLURM =

Book online training sessions

Pemartin — Mon, 17 Aug 2026 21:39:36 GMT

← Older revision		Revision as of 21:39, 17 August 2026
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	* Tuesday, 2026-08-11, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Pedro Martinez		* Tuesday, 2026-09-01, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Pedro Martinez
	: https://ucalgary.zoom.us/meeting/register/~~WK2Poma6QuKI8zW5FcoLjQ~~		: https://ucalgary.zoom.us/meeting/register/RGY_MbOaRq24mXCLY0KSOw

	* Thursday, 2026-08-13, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Pedro Martinez		* Thursday, 2026-09-03, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Pedro Martinez
	: https://ucalgary.zoom.us/meeting/register/~~mOTuo8EVTjeK6wXGN9vHmg~~		: https://ucalgary.zoom.us/meeting/register/P5o5h152RAKtu5PJeWdSiQ


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	== Past sessions ==		== Past sessions ==

			* Tuesday, 2026-08-11, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Pedro Martinez
			* Thursday, 2026-08-13, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Pedro Martinez

	* Tuesday, 2026-08-04, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov		* Tuesday, 2026-08-04, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov

List of courses on TALC

Dmitri — Mon, 17 Aug 2026 17:11:57 GMT

Courses

← Older revision		Revision as of 17:11, 17 August 2026
Line 73:		Line 73:
	=== Fall 2026 ===		=== Fall 2026 ===

	* MDSC 523, AI Applications for Health, by Dr Constance Li (~~...~~).		* MDSC 523, AI Applications for Health, by Dr Constance Li (Sep 21 - Dec 10).

	=== Summer 2026 ===		=== Summer 2026 ===

	* RNASeq Analysis Workshop, by Dr Paul Gordon, TA Dr Haley Pedersen (July 22 and 23).		* RNASeq Analysis Workshop, by Dr Paul Gordon, TA Dr Haley Pedersen (July 22 and 23).

			== Past Courses ==

	=== Spring 2026 ===		=== Spring 2026 ===

	* MDGE 755, Computational immunology, by Dr. Nathan Bracey (June 8 - June 30).		* MDGE 755, Computational immunology, by Dr. Nathan Bracey (June 8 - June 30).

	~~== Past Courses ==~~

	=== Winter 2026 ===		=== Winter 2026 ===

Storage Options

Fridman — Mon, 17 Aug 2026 15:20:14 GMT

Secure Compute Data Storage (SCDS)

← Older revision		Revision as of 15:20, 17 August 2026
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	=== Secure Compute Data Storage (SCDS) ===		=== Secure Compute Data Storage (SCDS) ===
	Secure Computing Data Storage (SCDS) is a service provided by Research Computing Services that allows researchers to store restricted and confidential data. Collaboration with Level 4 data stored in SCDS is possible using ~~ShareFile, a secure file sharing and collaboration tool~~ by ~~Citrix~~.		Secure Computing Data Storage (SCDS) is a service provided by Research Computing Services that allows researchers to store restricted and confidential data. Collaboration with Level 4 data stored in SCDS is possible using Onedrive for business by Microsoft.

	{\| class="wikitable"		{\| class="wikitable"

List of courses on TALC

Dmitri — Fri, 14 Aug 2026 21:33:09 GMT

Current Courses

← Older revision		Revision as of 21:33, 14 August 2026
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	== Current Courses ==		== Current Courses ==

			=== Fall 2026 ===

			* MDSC 523, AI Applications for Health, by Dr Constance Li (...).

	=== Summer 2026 ===		=== Summer 2026 ===

Book online training sessions

Dmitri — Tue, 11 Aug 2026 16:38:15 GMT

Book your training session here

← Older revision		Revision as of 16:38, 11 August 2026
Line 61:		Line 61:


	* Tuesday, 2026-08-04, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov		* Tuesday, 2026-08-18, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov
	: https://ucalgary.zoom.us/meeting/register/~~6ee64t6ESA6Iq2TfK1koiA~~		: https://ucalgary.zoom.us/meeting/register/bEyyKYlGTUKiVNF-HdQqHQ

	* Thursday, 2026-08-06, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Dmitri Rozmanov		* Thursday, 2026-08-20, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Dmitri Rozmanov
	: https://ucalgary.zoom.us/meeting/register/~~7sgsCammQLaQhh1qCp0A4Q~~		: https://ucalgary.zoom.us/meeting/register/wjlu8kr4TPOx_K2pXdvMzw


	== Past sessions ==		== Past sessions ==

			* Tuesday, 2026-08-04, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Dmitri Rozmanov
			* Thursday, 2026-08-06, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Dmitri Rozmanov

	* Tuesday, 2026-07-21, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Pedro Martinez		* Tuesday, 2026-07-21, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 1. '''Introduction to HPC.''' Pedro Martinez
	* Thursday, 2026-07-23, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Pedro Martinez		* Thursday, 2026-07-23, '''11:00 am''' - 12:30 pm ('''1.5 hours'''). Training session 2. '''Introduction to job scheduling.''' Pedro Martinez