CryoSPARC-Sapelo2 - Revision history

Shtsai at 17:35, 5 August 2026

2026-08-05T17:35:31Z

← Older revision		Revision as of 13:35, 5 August 2026
Line 44:		Line 44:

	== User Login ==		== User Login ==
	There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly.		The method to access the CryoSPARC web interface is to connect through the UGA VPN and access the CryoSPARC web server directly.
	~~<!--~~ SSH tunneling remains available as an alternative if needed. -->		<!-- There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly.
			SSH tunneling remains available as an alternative if needed. -->

	=== VPN + Direct Web Access ===		=== VPN + Direct Web Access ===

Moses at 16:25, 5 August 2026

2026-08-05T16:25:51Z

← Older revision		Revision as of 12:25, 5 August 2026
Line 83:		Line 83:
	<!-- -->		<!-- -->
	<!-- The CryoSPARC login page should appear. -->		<!-- The CryoSPARC login page should appear. -->

	=== Troubleshooting ===		=== Troubleshooting ===
	If you are unable to access the CryoSPARC web interface:		If you are unable to access the CryoSPARC web interface:

Moses at 16:25, 5 August 2026

2026-08-05T16:25:10Z

← Older revision		Revision as of 12:25, 5 August 2026
Line 44:		Line 44:

	== User Login ==		== User Login ==
	There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.		There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly.
			<!-- SSH tunneling remains available as an alternative if needed. -->

	=== VPN + Direct Web Access ===		=== VPN + Direct Web Access ===

Moses at 16:24, 5 August 2026

2026-08-05T16:24:12Z

← Older revision		Revision as of 12:24, 5 August 2026
Line 46:		Line 46:
	There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.		There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.

	=== ~~Method 1 (Recommended):~~ VPN + Direct Web Access ===		=== VPN + Direct Web Access ===
	# Connect to the UGA VPN using the Cisco Secure Client (Cisco AnyConnect) and select '''remote.uga.edu'''.		# Connect to the UGA VPN using the Cisco Secure Client (Cisco AnyConnect) and select '''remote.uga.edu'''.
	#: '''Note:''' Even if you are working on campus, you must still connect to the UGA VPN before accessing the CryoSPARC web server.		#: '''Note:''' Even if you are working on campus, you must still connect to the UGA VPN before accessing the CryoSPARC web server.

Moses at 16:23, 5 August 2026

2026-08-05T16:23:43Z

← Older revision		Revision as of 12:23, 5 August 2026
Line 56:		Line 56:
	#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.		#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.

	!=== Method 2: SSH Tunnel ===		<!-- === Method 2: SSH Tunnel === -->
	!Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer.		<!-- Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer. -->
	!		<!-- -->
	!If you are using Linux or macOS, run the following command in a terminal:		<!-- If you are using Linux or macOS, run the following command in a terminal: -->
	!		<!-- -->
	!<pre>		<!-- <pre> -->
	!ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu		<!-- ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu -->
	!</pre>		<!-- </pre> -->
	!		<!-- -->
	!If you are using Windows, download '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' and run:		<!-- If you are using Windows, download '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' and run: -->
	!		<!-- -->
	!<pre>		<!-- <pre> -->
	!plink -ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu		<!-- plink -ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu -->
	!</pre>		<!-- </pre> -->
			<!-- -->
	!Place <code>plink.exe</code> in your current working directory, or specify its full path when running the command.		<!-- Place <code>plink.exe</code> in your current working directory, or specify its full path when running the command. -->
			<!-- -->
	!Unless you have configured SSH public key authentication, you will be prompted for your UGA MyID password and Duo authentication. After authentication succeeds, the SSH session will remain open. This is expected !and indicates that the tunnel has been established successfully.		<!-- Unless you have configured SSH public key authentication, you will be prompted for your UGA MyID password and Duo authentication. After authentication succeeds, the SSH session will remain open. This is expected !and indicates that the tunnel has been established successfully. -->
			<!-- -->
	!With the SSH tunnel active, open your web browser and navigate to:		<!-- With the SSH tunnel active, open your web browser and navigate to: -->
			<!-- -->
	!<pre>		<!-- <pre> -->
	!http://localhost:39000		<!-- http://localhost:39000 -->
	!</pre>		<!-- </pre> -->
			<!-- -->
	!The CryoSPARC login page should appear.		<!-- The CryoSPARC login page should appear. -->

	=== Troubleshooting ===		=== Troubleshooting ===

Moses at 16:19, 5 August 2026

2026-08-05T16:19:00Z

← Older revision		Revision as of 12:19, 5 August 2026
Line 56:		Line 56:
	#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.		#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.

	=== Method 2: SSH Tunnel ===		!=== Method 2: SSH Tunnel ===
	Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer.		!Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer.
			!
			!If you are using Linux or macOS, run the following command in a terminal:
			!
			!<pre>
			!ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu
			!</pre>
			!
			!If you are using Windows, download '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' and run:
			!
			!<pre>
			!plink -ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu
			!</pre>

	~~If you are using Linux~~ or ~~macOS, run~~ the ~~following~~ command ~~in a terminal:~~		!Place <code>plink.exe</code> in your current working directory, or specify its full path when running the command.

	~~<pre>~~		!Unless you have configured SSH public key authentication, you will be prompted for your UGA MyID password and Duo authentication. After authentication succeeds, the SSH session will remain open. This is expected !and indicates that the tunnel has been established successfully.
	~~ssh -N -L 39000:10~~.2.0.~~60:39000 username@cryosparc.gacrc.uga.edu~~
	~~</pre>~~

	~~If you are using Windows~~, ~~download '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]'''~~ and ~~run~~:		!With the SSH tunnel active, open your web browser and navigate to:

	<pre>		!<pre>
	~~plink -ssh -N -L 39000~~:~~10.2.0.60~~:39000 ~~username@cryosparc.gacrc.uga.edu~~		!http://localhost:39000
	</pre>		!</pre>

	~~Place <code>plink.exe</code> in your current working directory, or specify its full path when running the command.~~		!The CryoSPARC login page should appear.

	Unless you have configured SSH public key authentication, you will be prompted for your UGA MyID password and Duo authentication. After authentication succeeds, the SSH session will remain open. This is expected and indicates that the tunnel has been established successfully.

	~~With the SSH tunnel active, open your web browser and navigate to:~~

	~~<pre>~~
	~~http://localhost:39000~~
	~~</pre>~~

	The CryoSPARC login page should appear.

	=== Troubleshooting ===		=== Troubleshooting ===

Moses: /* How to run cryoSPARC from Sapelo2 */

2026-07-10T15:29:16Z

How to run cryoSPARC from Sapelo2

Moses: /* User Login */

2026-07-10T15:27:29Z

User Login

← Older revision		Revision as of 11:27, 10 July 2026
Line 85:		Line 85:
	The CryoSPARC login page should appear.		The CryoSPARC login page should appear.

	===== Troubleshooting =====		==== Troubleshooting ====
	If you are unable to access the CryoSPARC web interface:		If you are unable to access the CryoSPARC web interface:

Moses: /* User Login */

2026-07-10T15:26:45Z

User Login

← Older revision		Revision as of 11:26, 10 July 2026
Line 48:		Line 48:
	There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.		There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.

	=== Method 1 (Recommended): VPN + Direct Web Access ===		==== Method 1 (Recommended): VPN + Direct Web Access ====

	# Connect to the UGA VPN using the Cisco Secure Client (Cisco AnyConnect) and select '''remote.uga.edu'''.		# Connect to the UGA VPN using the Cisco Secure Client (Cisco AnyConnect) and select '''remote.uga.edu'''.
	#: '''Note:''' Even if you are working on campus, you must still connect to the UGA VPN before accessing the CryoSPARC web server.		#: '''Note:''' Even if you are working on campus, you must still connect to the UGA VPN before accessing the CryoSPARC web server.
Line 59:		Line 58:
	#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.		#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.

	=== Method 2: SSH Tunnel ===		==== Method 2: SSH Tunnel ====

	Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer.		Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer.

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	The CryoSPARC login page should appear.		The CryoSPARC login page should appear.

	=== Troubleshooting ===		===== Troubleshooting =====

	If you are unable to access the CryoSPARC web interface:		If you are unable to access the CryoSPARC web interface:

Moses: /* How to run cryoSPARC from Sapelo2 */

2026-07-10T15:26:07Z

How to run cryoSPARC from Sapelo2

← Older revision		Revision as of 11:26, 10 July 2026
Line 42:		Line 42:

	'''cryoSPARC project space:''' '''/scratch/gacrc-cryo'''		'''cryoSPARC project space:''' '''/scratch/gacrc-cryo'''
	#

	== How to run cryoSPARC from Sapelo2 ==		== How to run cryoSPARC from Sapelo2 ==

	=== User ~~login ===~~		=== User Login ===

	=~~= User Login~~ ==

	There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.		There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.

← Older revision		Revision as of 11:29, 10 July 2026
Line 42:		Line 42:

	'''cryoSPARC project space:''' '''/scratch/gacrc-cryo'''		'''cryoSPARC project space:''' '''/scratch/gacrc-cryo'''
	~~== How to run cryoSPARC from Sapelo2 ==~~

	~~=== User Login ===~~

			== User Login ==
	There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.		There are two ways to access the CryoSPARC web interface. The recommended method is to connect through the UGA VPN and access the CryoSPARC web server directly. SSH tunneling remains available as an alternative if needed.

	==== Method 1 (Recommended): VPN + Direct Web Access ====		=== Method 1 (Recommended): VPN + Direct Web Access ===
	# Connect to the UGA VPN using the Cisco Secure Client (Cisco AnyConnect) and select '''remote.uga.edu'''.		# Connect to the UGA VPN using the Cisco Secure Client (Cisco AnyConnect) and select '''remote.uga.edu'''.
	#: '''Note:''' Even if you are working on campus, you must still connect to the UGA VPN before accessing the CryoSPARC web server.		#: '''Note:''' Even if you are working on campus, you must still connect to the UGA VPN before accessing the CryoSPARC web server.
Line 58:		Line 56:
	#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.		#: '''Note:''' Your registered UGA email address may be an email alias rather than your official '''MyID@uga.edu''' address. Please use the email address that was registered with your CryoSPARC account.

	==== Method 2: SSH Tunnel ====		=== Method 2: SSH Tunnel ===
	Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer.		Users may also access CryoSPARC by establishing an SSH tunnel to expose port 39000 from the CryoSPARC master node to their local computer.

Line 85:		Line 83:
	The CryoSPARC login page should appear.		The CryoSPARC login page should appear.

	==== Troubleshooting ====		=== Troubleshooting ===
	If you are unable to access the CryoSPARC web interface:		If you are unable to access the CryoSPARC web interface:

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	** A screenshot of the error message or the login/password reset screen, if applicable.		** A screenshot of the error message or the login/password reset screen, if applicable.

	=== Run cryoSPARC workflow jobs ===		== Run cryoSPARC workflow jobs ==

	==== Project space selection ====		=== Project space selection ===
	A project in cryoSPARC is a high level container corresponding with a project directory on the file system, which stores all associated Jobs of a project. Each project in cryoSPARC is entirely contained within a file system directory. All the jobs and their respective intermediate and output data created within a project will be stored within the project directory.		A project in cryoSPARC is a high level container corresponding with a project directory on the file system, which stores all associated Jobs of a project. Each project in cryoSPARC is entirely contained within a file system directory. All the jobs and their respective intermediate and output data created within a project will be stored within the project directory.

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	* This folder is owned by gacrc-cryo. Regular cryoSPARC users have access and read permissions which allow them to browse files in this folder and copy files from this folder to their own storage spaces on Sapelo2.		* This folder is owned by gacrc-cryo. Regular cryoSPARC users have access and read permissions which allow them to browse files in this folder and copy files from this folder to their own storage spaces on Sapelo2.

	==== Run job on the master node ====		=== Run job on the master node ===
	cryoSPARC will use the master node to run some types of workflow jobs, for example, "Import Movies", "Inspect Picks", and the interactive job "Select 2D Classes". When a job is created, if cryoSPARC will use the master node to run the job, you will be notified about this in cryoSPARC GUI.		cryoSPARC will use the master node to run some types of workflow jobs, for example, "Import Movies", "Inspect Picks", and the interactive job "Select 2D Classes". When a job is created, if cryoSPARC will use the master node to run the job, you will be notified about this in cryoSPARC GUI.

	==== Run job using "Lane Sapelo2 Default (cluster)" ====		=== Run job using "Lane Sapelo2 Default (cluster)" ===

	* In cryoSPARC, queue a job to "'''Lane Sapelo2 Default (cluster)'''"; The job will be dispatched to the worker node via Slurm. Please note, gacrc-cryo, instead of your own Sapelo2 user account, is the user account owning and running the job. We highly recommend you to use this method to run cryoSPARC workflow jobs on Sapelo2.		* In cryoSPARC, queue a job to "'''Lane Sapelo2 Default (cluster)'''"; The job will be dispatched to the worker node via Slurm. Please note, gacrc-cryo, instead of your own Sapelo2 user account, is the user account owning and running the job. We highly recommend you to use this method to run cryoSPARC workflow jobs on Sapelo2.
	* cryoSPARC will decide on how many CPU cores and how much memory it will use to run a workflow job, depend on the type of the job and your data size. Currently, we configured that from each worker node cryoSPARC can use up to '''20GB''' memory and '''4''' CPU cores.		* cryoSPARC will decide on how many CPU cores and how much memory it will use to run a workflow job, depend on the type of the job and your data size. Currently, we configured that from each worker node cryoSPARC can use up to '''20GB''' memory and '''4''' CPU cores.