CryoSPARC-Sapelo2 - Revision history

Shtsai at 00:24, 5 April 2026

2026-04-05T00:24:32Z

← Older revision		Revision as of 20:24, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]		[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]

	=== Category ===		== Category ==

	Engineering		Engineering

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	4.3.1		4.3.1

	=== Author / Distributor ===		== Author / Distributor ==

	See https://guide.cryosparc.com/		See https://guide.cryosparc.com/

	=== Description ===		== Description ==

	"CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data." For more information, please see https://guide.cryosparc.com/.		"CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data." For more information, please see https://guide.cryosparc.com/.
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	'''NOTE''': Users are required to be added into GACRC '''cryosparc''' group before they can run this software from Sapelo2. Please fill out the [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25844 GACRC General Support form] to request. We will reach out to you after we received your request.		'''NOTE''': Users are required to be added into GACRC '''cryosparc''' group before they can run this software from Sapelo2. Please fill out the [https://uga.teamdynamix.com/TDClient/2060/Portal/Requests/ServiceDet?ID=25844 GACRC General Support form] to request. We will reach out to you after we received your request.

	=== Configurations ===		== Configurations ==
	'''Master node VM:'''		'''Master node VM:'''

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	#		#

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

	===== User login =====		=== User login ===

	User needs to establish a SSH tunnel to expose the port 39000 from the master node to a local computer.		User needs to establish a SSH tunnel to expose the port 39000 from the master node to a local computer.
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	Once you established the ssh tunnel by running the above command, you can open a browser (Chrome) on the local machine and navigate to<code><nowiki>http://localhost:39000</nowiki></code>. The cryoSPARC User Interface should be presented with the cryoSPARC login page.		Once you established the ssh tunnel by running the above command, you can open a browser (Chrome) on the local machine and navigate to<code><nowiki>http://localhost:39000</nowiki></code>. The cryoSPARC User Interface should be presented with the cryoSPARC login page.

	===== 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.
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	* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on the worker node is '''4'''.		* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on the worker node is '''4'''.

	===Documentation (v4.0+)===		==Documentation (v4.0+)==

	About cryoSPARC: https://guide.cryosparc.com/		About cryoSPARC: https://guide.cryosparc.com/
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	Tutorial videos: https://guide.cryosparc.com/processing-data/tutorial-videos		Tutorial videos: https://guide.cryosparc.com/processing-data/tutorial-videos

	===Installation===		==Installation==

	*Version 4.3.1 master is installed on the master node (cryosparc.gacrc.uga.edu).		*Version 4.3.1 master is installed on the master node (cryosparc.gacrc.uga.edu).
	*Version 4.3.1 workers are installed on one worker GPU node (NVIDIA Tesla A100 GPU node).		*Version 4.3.1 workers are installed on one worker GPU node (NVIDIA Tesla A100 GPU node).

	===System===		==System==
	64-bit Linux		64-bit Linux

Moses: /* User login */

2023-10-12T18:00:22Z

User login

← Older revision		Revision as of 14:00, 12 October 2023
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	User needs to establish a SSH tunnel to expose the port 39000 from the master node to a local computer.		User needs to establish a SSH tunnel to expose the port 39000 from the master node to a local computer.

	If you are using a Linux or Apple desktop or laptop, you can use the following command in Terminal to establish the ssh tunnel: <blockquote>'''~~ssh -N -L~~ ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu'''</blockquote>If you are using a Windows desktop or laptop, please download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' to use in place of the ssh client:<blockquote>'''plink -ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu'''</blockquote>		If you are using a Linux or Apple desktop or laptop, you can use the following command in Terminal to establish the ssh tunnel: <blockquote>'''ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu'''</blockquote>If you are using a Windows desktop or laptop, please download the '''[https://the.earth.li/~sgtatham/putty/latest/x86/plink.exe plink program]''' to use in place of the ssh client:<blockquote>'''plink -ssh -N -L 39000:10.2.0.60:39000 username@cryosparc.gacrc.uga.edu'''</blockquote>
	'''Note:''' Please put the plink.exe in the current directory where you have a command window open.		'''Note:''' Please put the plink.exe in the current directory where you have a command window open.

Moses: /* An important note related to job restarting */

2023-10-04T17:21:56Z

An important note related to job restarting

← Older revision		Revision as of 13:21, 4 October 2023
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	* 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.
	* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on the worker node is '''4'''.		* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on the worker node is '''4'''.

	~~======An important note related to job restarting======~~
	After you killed and cleared a job, if you want to restart it in cryoSPARC, please '''do NOT''' click and use "'''Queue Job on default'''" listed in "'''ACTIONS'''" to restart the job. We found that "'''Queue Job on default'''" will always put the job to rb6-3 worker node by default and we cannot change this default behavior of cryoSPARC.

	After you killed and cleared a job, if you want to restart it in cryoSPARC, please go back to your current Workplace in cryoSPARC GUI and click "'''Building'''" in the job card, then click "'''Queue'''" in the right-bottom corner of cryoSPARC GUI to re-queue the job, as shown in Figure 1 (1 is for "Building"; 2 is for "Queue"). Then follow instructions in '''Run job using "Lane Sapelo2 Default (cluster)"''' to rerun your job.
	~~[[File:Restart job.png\|thumb\|Figure 1. How to restart a job in cryoSPARC GUI, after the job is killed and cleared.\|alt=]]~~

	===Documentation (v4.0+)===		===Documentation (v4.0+)===

Moses: /* Note: This page is under construction by the GACRC team (as of 2023-10-03, deadline: 10-05) */

2023-10-04T17:20:49Z

Note: This page is under construction by the GACRC team (as of 2023-10-03, deadline: 10-05)

← Older revision		Revision as of 13:20, 4 October 2023
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	[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]		[[Category:Sapelo2]][[Category:Software]][[Category:Engineering]]

	~~=='''Note: This page is under construction by the GACRC team (as of 2023-10-03, deadline: 10-05)'''==~~

	=== Category ===		=== Category ===

Moses: /* Documentation */

2023-10-03T20:04:03Z

Documentation

← Older revision		Revision as of 16:04, 3 October 2023
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	[[File:Restart job.png\|thumb\|Figure 1. How to restart a job in cryoSPARC GUI, after the job is killed and cleared.\|alt=]]		[[File:Restart job.png\|thumb\|Figure 1. How to restart a job in cryoSPARC GUI, after the job is killed and cleared.\|alt=]]

	===Documentation===		===Documentation (v4.0+)===

	About cryoSPARC: https://guide.cryosparc.com/		About cryoSPARC: https://guide.cryosparc.com/

	~~User Interface and Usage Guide~~: https://guide.cryosparc.com/processing-data/~~user~~-~~interface~~-~~and~~-~~usage~~-~~guide~~		Get Started with CryoSPARC: Introductory Tutorial: https://guide.cryosparc.com/processing-data/get-started-with-cryosparc-introductory-tutorial

	~~Accessing~~ the ~~cryoSPARC User~~ Interface https://guide.cryosparc.com/~~setup~~-~~configuration~~-~~and-management~~/~~how~~-to-~~download~~-~~install~~-~~and-configure/accessing~~-~~cryosparc~~		A Tour of the CryoSPARC Interface: https://guide.cryosparc.com/application-guide-v4.0+/a-tour-of-the-cryosparc-interface

	~~All Job Types in cryoSPARC~~: https://guide.cryosparc.com/~~processing~~-~~data~~/~~all~~-~~job~~-~~types~~-~~in-cryosparc~~		Using the CryoSPARC Interface: https://guide.cryosparc.com/application-guide-v4.0+/using-the-cryosparc-interface

	~~Management~~ and ~~Monitoring~~: https://guide.cryosparc.com/~~setup~~-~~configuration-and-management/management-and~~-~~monitoring~~		Creating and Running Jobs: https://guide.cryosparc.com/application-guide-v4.0+/creating-and-running-jobs

	~~Cluster (Slurm) integration: https://guide.cryosparc~~.~~com/setup-configuration-and-management~~/~~how-to-download-install~~-and-~~configure/downloading-and-installing-cryosparc#connect-a-cluster-to-cryosparc~~

	~~Introductory Tutorial: https://guide.cryosparc.com/processing-data/cryo-em-data-processing-in-cryosparc-introductory~~-~~tutorial~~

	Tutorial videos: https://guide.cryosparc.com/processing-data/tutorial-videos		Tutorial videos: https://guide.cryosparc.com/processing-data/tutorial-videos

Moses: /* Documentation */

2023-10-03T19:55:53Z

Documentation

← Older revision		Revision as of 15:55, 3 October 2023
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	Management and Monitoring: https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring		Management and Monitoring: https://guide.cryosparc.com/setup-configuration-and-management/management-and-monitoring

	Cluster (Slurm) integration: ~~<nowiki>~~https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/downloading-and-installing-cryosparc#connect-a-cluster-to-cryosparc~~</nowiki>~~		Cluster (Slurm) integration: https://guide.cryosparc.com/setup-configuration-and-management/how-to-download-install-and-configure/downloading-and-installing-cryosparc#connect-a-cluster-to-cryosparc

	Introductory Tutorial: https://guide.cryosparc.com/processing-data/cryo-em-data-processing-in-cryosparc-introductory-tutorial		Introductory Tutorial: https://guide.cryosparc.com/processing-data/cryo-em-data-processing-in-cryosparc-introductory-tutorial

	~~Tutorials and Usage Guides~~: https://guide.cryosparc.com/processing-data/~~tutorials~~-~~and-case-studies~~		Tutorial videos: https://guide.cryosparc.com/processing-data/tutorial-videos

	===Installation===		===Installation===

Moses at 19:52, 3 October 2023

2023-10-03T19:52:28Z

← Older revision		Revision as of 15:52, 3 October 2023
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	* 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.
	* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on worker node is '''4'''.		* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on the worker node is '''4'''.

	======An important note related to job restarting======		======An important note related to job restarting======

Moses: /* Run job using "Lane Sapelo2 Default (cluster)" */

2023-10-03T19:52:04Z

Run job using "Lane Sapelo2 Default (cluster)"

← Older revision		Revision as of 15:52, 3 October 2023
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	* 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.
	* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1 ~~or 4~~. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on worker node is '''4'''.		* If the job needs to run on GPU devices, cryoSPARC will queue the job with a default number of GPU devices , for example 1. You can change this number by yourself in cryoSPARC GUI when you create the job. Please note that the maximum number of GPU devices installed on worker node is '''4'''.

	======An important note related to job restarting======		======An important note related to job restarting======

Moses at 19:50, 3 October 2023

2023-10-03T19:50:08Z

← Older revision		Revision as of 15:50, 3 October 2023
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	* gacrc-cryo is the '''service account''' that will run cryoSPARC workflow jobs for all cryoSPARC users.		* gacrc-cryo is the '''service account''' that will run cryoSPARC workflow jobs for all cryoSPARC users.
	* Some tasks can only be handled by gacrc-cryo, like ~~start or stop cryosparcm from the master~~ node, user management, connect or update worker ~~nodes~~ to master, etc..		* Some tasks can only be handled by gacrc-cryo, like make a new lane of worker node(s), user management, and connect or update worker node(s) to master, etc..
	* Regular CryoSPARC users can run cryosparcm ~~from~~ the master node to check cryoSPARC status, using cryosparcm status ~~and~~ cryosparcm checkdb.		* Regular CryoSPARC users can run cryosparcm on the master node to check cryoSPARC status, using cryosparcm status or cryosparcm checkdb.

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

Moses at 19:47, 3 October 2023

2023-10-03T19:47:57Z

← Older revision		Revision as of 15:47, 3 October 2023
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	* mongodb is installed and run on the master node		* mongodb is installed and run on the master node
	'''Worker nodes:'''		'''Worker nodes:'''
	* One NVIDIA Tesla A100 node: Intel Xeon processors (64 ~~CPU~~ cores), 1TB RAM memory ~~on host~~, ~~and~~ 4 NVIDIA Tesla A100 GPU cards ~~with 80GB~~ device memory per card.		* One NVIDIA Tesla A100 node: Intel Xeon processors (64 cores), 1TB host RAM memory, 4 NVIDIA Tesla A100 GPU cards (80GiB device memory per card), and NVMe SSD 3570GB local drive.
	* cryoSPARC recommends using SSD for caching particle data. /lscratch/gacrc-cryo is set up on the worker node for this purpose.		* cryoSPARC recommends using SSD for caching particle data. /lscratch/gacrc-cryo is set up on the worker node for this purpose.
	* The amount of space that cryoSPARC can use in /lscratch/gacrc-cryo is capped at 100GB.		* The amount of space that cryoSPARC can use in /lscratch/gacrc-cryo is capped at 100GB.