Helix/bwVisu/CryoSPARC - Revision history

H Schumacher: Added fix for error "zlib inflate failed"

2025-07-29T11:36:12Z

Added fix for error "zlib inflate failed"

← Older revision		Revision as of 13:36, 29 July 2025
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	== Known Issues ==		== Known Issues ==
	* For the default lane 'localhost', the total installed memory of a compute node is displayed. Note that you can only use the memory that you requested for the CryoSPARC application.		* For the default lane 'localhost', the total installed memory of a compute node is displayed. Note that you can only use the memory that you requested for the CryoSPARC application.
			* The error "zlib inflate failed" can be avoided by using a compression level higher than 0.

S Richling at 12:58, 23 June 2025

2025-06-23T12:58:09Z

← Older revision		Revision as of 14:58, 23 June 2025
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	== CryoSPARC Documentation ==		== CryoSPARC Documentation ==
	You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].		You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].

			== Known Issues ==
			* For the default lane 'localhost', the total installed memory of a compute node is displayed. Note that you can only use the memory that you requested for the CryoSPARC application.

S Richling: /* CryoSPARC Documenation */

2025-06-05T21:58:17Z

CryoSPARC Documenation

← Older revision		Revision as of 23:58, 5 June 2025
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	CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code>		CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code>

	== CryoSPARC ~~Documenation~~ ==		== CryoSPARC Documentation ==
	You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].		You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].

S Richling: /* The database */

2025-06-05T21:57:16Z

The database

← Older revision		Revision as of 23:57, 5 June 2025
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	=== The database ===		=== The database ===
	~~Note that the~~ CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.		The CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.

	=== Downloads ===		=== Downloads ===

S Richling: /* Documentation for CryoSPARC */

2025-06-05T21:56:28Z

Documentation for CryoSPARC

← Older revision		Revision as of 23:56, 5 June 2025
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	CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code>		CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code>

	== ~~Documentation~~ ~~for CryoSPARC~~ ==		== CryoSPARC Documenation ==
	You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].		You can find usage information and tutorials for CryoSPARC at [https://cryosparc.com/docs CryoSPARC Docs].

S Richling at 21:56, 5 June 2025

2025-06-05T21:56:05Z

← Older revision		Revision as of 23:56, 5 June 2025
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	== CryoSPARC in bwVisu ==		== CryoSPARC in bwVisu ==
			=== The application ===
	The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.		The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.

			=== The database ===
	Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.		Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.

		⚫	=== Downloads ===
		⚫	When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.

	== CryoSPARC and Topaz ==		== CryoSPARC and Topaz ==
	CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code>		CryoSPARC can use an existing installation of the Topaz software. When asked for the path to the Topaz executable, specify: <code>/opt/bwhpc/common/bio/topaz/0.25/bin/topaz</code>

⚫	== Downloads ~~from CryoSPARC~~ ==
⚫	When you download results from the CryoSPARC application, they are initially saved in your home directory on bwForCluster Helix. From there, you can download the results to your own system via the file browser in bwVisu.

	== Documentation for CryoSPARC ==		== Documentation for CryoSPARC ==

S Richling: /* CryoSPARC in bwVisu */

2025-06-05T21:52:28Z

CryoSPARC in bwVisu

← Older revision		Revision as of 23:52, 5 June 2025
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	== CryoSPARC in bwVisu ==		== CryoSPARC in bwVisu ==
	The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute ~~node~~. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.		The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute resources. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.

	Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.		Note that the CryoSPARC application creates a database in the <code>.cryosparc</code> directory in your home directory on bwForCluster Helix the first time it is used. You can only start one CryoSPARC application at a time. Do not attempt to start more than one CryoSPARC application. This could damage your database.

S Richling: /* CryoSPARC License */

2025-06-05T21:51:33Z

CryoSPARC License

← Older revision		Revision as of 23:51, 5 June 2025
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	== CryoSPARC License ==		== CryoSPARC License ==
	For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The ~~licnese~~ ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.		For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The license ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.

	== CryoSPARC in bwVisu ==		== CryoSPARC in bwVisu ==

S Richling: /* CryoSPARC License */

2025-06-05T21:46:38Z

CryoSPARC License

← Older revision		Revision as of 23:46, 5 June 2025
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	== CryoSPARC License ==		== CryoSPARC License ==
	For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one ~~licence~~ ID, which you can use every time you start CryoSPARC in bwVisu.		For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one license ID, which you can use every time you start CryoSPARC in bwVisu.

	== CryoSPARC in bwVisu ==		== CryoSPARC in bwVisu ==

S Richling: /* CryoSPARC@bwVisu */

2025-06-05T21:40:30Z

CryoSPARC@bwVisu

← Older revision		Revision as of 23:40, 5 June 2025
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	For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.		For starting CryoSPARC in bwVisu you need your personal CryoSPARC license ID. To obtain a license ID, go to [https://cryosparc.com/download CryoSPARC] and fill out the form. The licnese ID will be send by e-mail. You only need one licence ID, which you can use every time you start CryoSPARC in bwVisu.

	== CryoSPARC@bwVisu ==		== CryoSPARC in bwVisu ==
	The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.		The CryoSPARC application at bwVisu starts a CryoSPARC master process and a worker process on the allocated compute node. You must request enough time and resources for the work you intend to do within a CryoSPARC session. If the application stops due to the time limit, you can restart the application and continue your pipeline from completed CryoSPARC jobs.