New HPC Documentation Website!

New documentation is coming that will replace our current Confluence website (the one you're viewing right now). We will be sending an announcement on when the site will go live. Interested in taking a peek? Check out this page for the beta version. Note: the URL is likely to change.

New GPUs on Ocelote!

We have recently added 22 new P100 GPUs to Ocelote. Need to request multiple GPUs on a node and you're finding Puma queue times too slow? You can now request two GPUs per node on Ocelote using --gres=gpu:2.

Overview

On October 16, 2023, we went live with the Research Desktop Attached Storage Array (R-DAS). R-DAS provides up to 5 TB of no-cost storage capacity for each PI group. Our requirement was to enable our users to easily share data with other research group members. You can treat the allocation as a drive mounted on your local computer. R-DAS is intended for storing open research data, but not controlled or regulated data.

Technical Requirements

R-DAS is a storage service backed by a Qumulo branded storage array. It supports the mounting of SMB shares for SMB 3.1. The supported operating systems are MacOS (Monterey or higher), Linux (kernel 3.7 or higher), and Windows (Windows 10 or 11).

R-DAS storage is not mounted on HPC compute or login nodes.

Performance

The storage array is located in the Research Data Center to benefit from the network infrastructure in the Computer Center. The performance you experience will depend on your network connectivity. The best case is likely wired ethernet in a newer building. Off campus usage requires connection to the VPN, and so performance can be variable. Our testing off campus regularly reached 3 MB/s.

Group Sharing: You can share your allocation with team members if they belong to your group. When they reach step 6 in the "Accessing Your R-DAS Allocation" section below, they will choose the allocation with your net ID.

Contents

Requesting an Allocation

You can request an allocation on R-DAS from https://portal.hpc.arizona.edu/portal:

Go to the Storage tab.
Select Create Shared Desktop Storage under Research Desktop Storage.
Select Create from the window that opens.
A window opens with the MOU. Review it and, if it is acceptable to you, select Agree.
You can now View Shared Desktop Storage

Accessing Your R-DAS Allocation

UA IP Address Required: To access your R-DAS allocation you need to be connected to either the UA campus network, or the UA SSL VPN. For information about connecting to a VPN, see VPN - Virtual Private Network. If you are accessing your R-DAS allocation from an HPC cluster, then you are already on the UA campus network and do not need to connect to the UA SSL VPN.

R-DAS can be accessed from Linux, MacOS, or Windows. The screenshots are intended to be visual aids, but they include information from the consulting team. When you proceed, please enter your own information.

Linux / HPC

Installing Necessary Packages

Please do not run any sudo commands on the HPC clusters. These are meant only for your personal Linux machines. All required packages are already installed on the HPC clusters.

To access your R-DAS allocation from a Linux distribution, you need the samba package. If you are using a GTK based desktop environment, such as MATE and GNOME, then you will also need the Samba backend for GVfs. If you want to access your R-DAS allocation from the command line, you will need the smbclient package. Select your Linux distribution from the list below to view installation instructions:

Debian / Ubuntu

sudo apt install samba gvfs-backends smbclient

Fedora / CentOS

sudo yum install samba gvfs-samba samba-client

Other Linux distributions

Please check the documentation of your distribution.

The smbclient package is not available on the HPC. Please use the GUI method to access your R-DAS allocation from the HPC clusters.

For other Linux distributions, please check their respective documentation to learn how you can install these packages.

GUI

On a desktop environment, such as MATE, GNOME, KDE, you can mount your R-DAS allocation as a local drive with the corresponding file manager (Caja on MATE, GNOME Files, Dolphin on KDE).

Desktop environment on HPC

Follow the steps in the Virtual Desktop guide to launch an Interactive Desktop. This will start a Linux environment with the MATE desktop environment in your browser. You can use and access the HPC resources from this desktop interface.

On a desktop environment you can mount the R-DAS allocation with the following (the screenshots are from Caja on MATE, but the experience is similar across the other deskop environments):

Open the file manager (Caja, GNOME Files, Dolphin).
File manager on HPC
On the HPC Interactive Desktop's MATE desktop environment, you can launch Caja by clicking the file drawer like icon in the top bar, or by selecting Applications > System Tools > Caja.
Press Ctrl + l. This makes the location bar editable.
Enter smb://rdas.hpc.arizona.edu in the location bar, and press Enter.
A few moments later a window opens, prompting for your Username (BLUECAT\ followed by your UA NetID) and Password (UA NetID password). After entering the details, select Connect (on other file managers this maybe OK). Some file managers, such as Caja and GNOME Files, also have a Domain field, whereas others, like Dolphin, do not. Either way, you do not need to modify its default value.
Select the allocation named after your group from the list of allocations displayed.
On some file managers, such as Dolphin, you can right away access your allocation by double clicking on it. On others, such as Caja and GNOME Files, double clicking on it will open another window prompting for your Username (BLUECAT\ followed by your UA NetID) and Password (UA NetID password). Select Connect as user, enter the details, and select Connect. Your allocation will be mounted as a local drive.

CLI

You can interactively browse your R-DAS allocation with smbclient:

smbclient \\\\rdas.hpc.arizona.edu\\<share> -U BLUECAT\\<username>

The <share> is the PI group that you belong to, and <username> is your UA NetID. The command will prompt for a password, enter your UA NetID password. This will start an smb shell. For example:

~ $ smbclient \\\\rdas.hpc.arizona.edu\\sohampal -U BLUECAT\\sohampal
Password for [BLUECAT\sohampal]:
Try "help" to get a list of possible commands.
smb: \>

Type help to get a list of possible commands:

smb: \> help
?              allinfo        altname        archive        backup         
blocksize      cancel         case_sensitive cd             chmod          
chown          close          del            deltree        dir            
du             echo           exit           get            getfacl        
geteas         hardlink       help           history        iosize         
lcd            link           lock           lowercase      ls             
l              mask           md             mget           mkdir          
more           mput           newer          notify         open           
posix          posix_encrypt  posix_open     posix_mkdir    posix_rmdir    
posix_unlink   posix_whoami   print          prompt         put            
pwd            q              queue          quit           readlink       
rd             recurse        reget          rename         reput          
rm             rmdir          showacls       setea          setmode        
scopy          stat           symlink        tar            tarmode        
timeout        translate      unlock         volume         vuid           
wdel           logon          listconnect    showconnect    tcon           
tdis           tid            utimes         logoff         ..             
!

Use the -L flag to get the list of shares on the Array. For example:

smbclient -L \\\\rdas.hpc.arizona.edu -U BLUECAT\\sohampal
Password for [BLUECAT\sohampal]:

	Sharename       Type      Comment
	---------       ----      -------
	Q$              Disk      Default root share for SRVSVC.
	ipc$            IPC       Named Pipes
	upgrade         Disk      for qumulo upgrades
	tmerritt        Disk      Desktop share for tmerritt created on 09/12/2023 12:24 PM
	sarawillis      Disk      Desktop share for sarawillis created on 09/29/2023 10:14 AM
	sohampal        Disk      Desktop share for sohampal created on 10/04/2023 10:12 AM
	chrisreidy      Disk      Desktop share for chrisreidy created on 10/04/2023 11:08 AM
	frios           Disk      Desktop share for frios created on 10/06/2023 11:17 AM
	gondyleroy      Disk      Desktop share for gondyleroy created on 10/06/2023 12:04 PM
	baylyd          Disk      Desktop share for baylyd created on 10/16/2023 10:57 AM
	chopinsong      Disk      Desktop share for chopinsong created on 10/16/2023 04:57 PM
	chader          Disk      Desktop share for chader created on 10/16/2023 04:58 PM
	skibob          Disk      Desktop share for skibob created on 10/16/2023 05:01 PM
	ejahn           Disk      Desktop share for ejahn created on 10/16/2023 05:08 PM
	rychlik         Disk      Desktop share for rychlik created on 10/16/2023 05:10 PM
	lofverstrom     Disk      Desktop share for lofverstrom created on 10/16/2023 05:21 PM
	nirav           Disk      Desktop share for nirav created on 10/16/2023 05:25 PM
	dkp             Disk      Desktop share for dkp created on 10/16/2023 06:17 PM
	xiaosun         Disk      Desktop share for xiaosun created on 10/16/2023 07:33 PM
	chanc           Disk      Desktop share for chanc created on 10/16/2023 08:19 PM
	serena00        Disk      Desktop share for serena00 created on 10/16/2023 10:26 PM
SMB1 disabled -- no workgroup available

Any command that you can run interactively from the smb shell, you can also run non-interactively with the -c flag. For example to list the files and directories in your share, run:

smbclient \\\\rdas.hpc.arizona.edu\\<share> -U BLUECAT\\<username> -c 'ls'

You can also combine multiple commands with ";. For example to list the contents in a directory in your share, run:

smbclient \\\\rdas.hpc.arizona.edu\\<share> -U BLUECAT\\<username> -c 'cd <directory>;ls'

To copy a file from your local system to your R-DAS share use put, and from your R-DAS share to your local system use get:

smbclient \\\\rdas.hpc.arizona.edu\\<share> -U BLUECAT\\<username> -c 'put <file>'

To learn more about smbclient, run man smbclient.

Mac OS

If you are on a Mac, then you can mount your R-DAS allocation as a local drive with the following steps:

Go to Finder.
Select Go from the top menu bar.
From the drop-down menu, select Connect to Server.
In the window that opens, enter smb://rdas.hpc.arizona.edu in the address bar, and select Connect.
After a few moments a window opens prompting for your Name (UA NetID) and Password (UA NetID password). After entering the details, select Connect.
A window opens with the list of allocations on the array. Select allocation named after your group, and then select OK.

Windows

If you are on Windows, you can mount your R-DAS allocation as a local drive with the following steps:

Open Windows Explorer.
Enter \\rdas.hpc.arizona.edu in the location bar, and press Enter.
A few moments later a window opens, prompting for your Username (BLUECAT\ followed by your UA NetID) and Password (UA NetID password). After entering the details, select OK.
Select the allocation named after your group from the list of allocations displayed. You can directly open the allocation by double-clicking on it, or mount it by right clicking on it and selecting Map network drive.

FAQ

For R-DAS questions follow this link.