BioHPC Cloud Storage

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[web] portal.biohpc.swmed.edu

[email] biohpc-help@utsouthwestern.edu

Updated for 2015-06-10

Overview

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What is the cloud service/storage?

Services we provide to BioHPC user?

– BioHPC cluster

– BioHPC Lamella Storage System

– BioHPC File Exchange

How can I use BioHPC cloud storage?

– Basic File Management

– File Synchronization

– File Transfer

– File Sharing

– BioHPC manager account

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Cloud Service ( Cloud Computing and Cloud Storage )

Image retrieved from http://giannisgiataganas.blogspot.com/2010/06/lets-talk-about-cloud.html, http://www.nec.com/en/global/solutions/cloud/portfolio/storage.html

Cloud storage (one of the fundamental components of cloud computing) is a service model in which data is maintained, managed and backed up remotely and made available to users over a network (typically the Internet).

Cloud computing refers to the delivery of computing resources over the network.

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Image retrieved from http://www.bcni.ca/cloud-services/

• Security

• Reliability

• Speed

• Ease-of-use

• Storage space

How to Evaluate a Cloud Storage Service

7 Best Cloud Storage Service 2015

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Ranking retrieved from http://www.pcadvisor.co.uk/features/internet/3506734/best-cloud-storage-dropbox-google-drive-onedrive-icloud/– by Martyn Casserly, 09 February 15

Security

Storage space

Other Limitations of Web-based Storage System

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Why We Need BioHPC Cloud Service

UTSouthwestern General Cloud Policy: UTSW information must never be stored in unapproved online file storage systems.

Dropbox: 2~18 GB (5 TB @ $75/month)Google Drive: 15 GB (30 TB @ $299.99/month)BioHPC Cloud: 150GB + access to BioHPC storage system (~ 1 PBs)

• Max upload/download speed ~ 10 MB/s• Web browser do not support folder uploading• Upload/download limit for single file (size)

BioHPC Cloud Storage

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As a BioHPC user, you will have access to:

• BioHPC Cluster/home2/username 50 GB quota per user/work/department/group/username 5 TB quota per group/project/department/group/username 5 TB quota per group

• BioHPC File Exchange (web-interface)https://cloud.biohpc.swmed.edu 50 GB quota per user

• BioHPC Lamella Cloud Storage (web-interface), on campus only, private cloudhttps://lamella.biohpc.swmed.edu 100 GB quota per userGateway to BioHPC Cluster (via FTP, SAMBA or WebDAV)

Initial Setup on Lamella

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* Mount External Storage

— Setting up Lamella to access BioHPC cluster (home, project, and work space)

lysosome username password homeproject

For home leave blank

For private project space:department/lab/user

For lab shared project space:department/lab/shared

BioHPC Endosome/Lysosome

What can we do with BioHPC cloud storage system

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• Basic File Managementview, move, rename, download, upload, delete your files and etc.

• File Synchronizationowncloud client

• File TransferClusterSambaFTPWebDAV (not recommended)

• File SharingShared FolderBioHPC File Exchange (https://cloud.biohpc.swmed.edu)BioHPC Lamella Cloud Storage (https://lamella.biohpc.swmed.edu)

• BioHPC manager accountA lab manager can share data to non-BioHPC users

Navigation bar:

– Allows navigation between different parts

New/Upload button:

– Allows you to create new files or upload existing ones from your device

– you can also drop files from Explorer or Finder onto the file view.

– With New button, you can create a text file, folder or download a file from the provided URL.

Search/Settings:

– Search allows you to look for files and directories

New/Upload button:

– Clicking on small thumbnails or icons of the files/directory

– Select multiple files can e deleted or downloaded as ZIP

Viewing Files

– Can display text files, PDFs, and image files

– If displaying of a file is not possible, a download process will start

Moving files

– Dragging and dropping files/directory

Basic File Management

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File Synchronization

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BioHPC Cluster(work or project folder)

Lamella Cloud Storage

< 100 GB

> 100 GB

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* File Synchronization

File Synchronization

Before setting up file synchronization:

1) Estimate the total size of your dataif the total size of your data is always < 100GB, you may direct

synchronize your data to lamella, otherwise use your BioHPC project directory.

2) Estimate the total free space on your local diskif the total size of your data is always < free space on your local disk,

you may synchronize everything from lamella, otherwise chose what to sync.

Rule of thumb : Your data size should always smaller than your container

File Synchronization

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download and install owncloud client from https://portal.biohpc.swmed.edu/content/software/

connect to lamella.biohpc.swmed.edu -> username/password

* File Synchronization

File Synchronization

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Chose What to Sync

total data size < local disk space

total data size > local disk space

Total data size = actual file stored in lamella locally (up to 100 GB) + mounted folders (up to 10 TB)

Anything your deleted from your PC will be removed from BioHPC cloud storage server as well.

* File Synchronization

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File Transfer

Lysosome

Lamella Cloud Storage

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If your are using a BioHPC thin client or workstation you have direct access to your BioHPC storage.

File Transfer

Separate training session – July 14th.

Accessing BioHPC Storage Directly from thin client, workstation

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File Transfer

Accessing BioHPC Storage Directly via SSH

Host Name: nucleus.biohpc.swmed.eduPort: 22

Download and install PuTTY from https://portal.biohpc.swmed.edu/content/software/

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Computer -> Map Network Drive

Folder is: \\lamella.biohpc.swmed.edu\username home\\lamella.biohpc.swmed.edu\project\department\group project\\lamella.biohpc.swmed.edu\work\department\group work

Check ‘Connect using different credentials’Enter your BioHPC username and password when prompted.

File Transfer

Accessing BioHPC Storage Directly from Windows via Samba

Accessing BioHPC Storage Directly from Mac OSX via Samba

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Finder -> Go -> Connect to Server

Folder is: smb://lamella.biohpc.swmed.edu/username homesmb://lamella.biohpc.swmed.edu/project/department/group projectsmb://lamella.biohpc.swmed.edu/work/department/group work

Enter your BioHPC username and password when prompted.

File Transfer

File Transfer

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Host: lamella.biohpc.swmed.eduUsername: Your BioHPC usernamePassword: Your BioHPC passwordPort: Empty

Transfer data to/from BioHPC cloud storage via FTP

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Accessing your Files from Windows via WebDAV

1) Increase the maximum size of WebDav downloads to 4GB

regedit -> HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\WebClient\Parameters\FileSizelimitinBytes

By default Windows limits the maximum size of WebDav downloads to ~50 MB

File Transfer

Not recommended but still useful when you need direct access to the local

storage of BioHPC Lamella or File Exchange system from your PC

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2) Mount your lamella storage to PC

Start -> Computer -> Map Network Drive

* You could mount BioHPC File Exchange storage to your PC in a similar way .

(https//cloud.biohpc.swmed.edu/remote.php/webdav)

File Transfer

Accessing your Files from Windows via WebDAV

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File Transfer

Cyberduck – A Client support FTP, WebDAV for both Mac and Windows

• Download and install Cyberduck from https://portal.biohpc.swmed.edu/content/software/

• Once installed into your 'Applications' folder, start Cyberduck, choose 'Open Connection' and configure as in the image below:

Accessing your Files from Mac OSX via WebDAV

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Uploading / Downloading Speed

Max Uploading andDownloading Speed*

Lamella Cloud Storage(Samba)

400MB/s

BioHPC File-Exchange(webDav)

10 MB /s

Lamella Cloud Storage(webDav)

100 MB /s

Lamella Cloud Storage(FTP )

300 MB ~ 1.4 GB/s

• Upload and download speed depends on your actual network connection• We don’t set up a limitation on max concurrent sessions

File Transfer

File Sharing

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• Sharing data with all BioHPC user/work/shared /project/shared

• Sharing data inside your department/work/department_name/shared /project/department_name/shared

• Sharing data inside your group/work/department_name/group_name/shared /project/department_name/group_name/shared

If you have a workstation connected to our BioHPC cloud or you know how to use

command line to connect to BioHPC cloud, you can share your data on cluster directly.

Shared folders had already been set up at different levels

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Sharing data with UTSW collaborators

File Sharing

BioHPC Lamella Cloud Storage

https://lamella.biohpc.swmed.edu

Share with linkShare with BioHPC user or group(Email notification)

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Sharing data with non UTSW collaborators

File Sharing

BioHPC File Exchange

https://cloud.biohpc.swmed.edu

Share with link(Email notification, setup password & expiration date)

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A lab manager ( BioHPC manager account ) sharing data to non-BioHPC users

Lysosome

Lab Manager Lab manger account : only provide storage space under

/project/department/group/manager_name

,and this is the home directory of manager account

Lab Facilities, e.g.: scanning EM

images

non-BioHPC user A

non-BioHPC user B

non-BioHPC user C

directly saved to manager’s home directory

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A lab manager ( BioHPC user ) sharing data to non-BioHPC users

Lysosome

Lamella Cloud Storage

Lab Manager

non-BioHPC user A

non-BioHPC user B

non-BioHPC user C

Share data for user to download

A lab manager sharing data to non-BioHPC users

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Step 1: mount manager’s home directory to your lab facility to save data

Support PC, Mac and Linux/Unix

A lab manager sharing data to non-BioHPC users

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Step 2: Sharing data with non BioHPC users with a linkpassword protection (recommended) set up an expiration date (recommended) email notification

A lab manager sharing data to non-BioHPC users

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Step 3: non BioHPC users download data by providing correct password

For More Information

• Read related articles from https://portal.biohpc.swmed.eduLamella - Internal Cloud StorageBioHPC File Exchange - External Cloud Storage

• Email the ticket system: biohpc-help@utsouthwestern.edu