1 Workstations Thin Clients Overview Why use a

1 Workstations & Thin Clients

Overview § Why use a Bio. HPC computer? § Comparison between workstation and thin client § Network requirements § Basics of the Linux Graphical User Interface § Running Code Locally § Submitting Jobs to the Cluster § Run Graphical Jobs on the Cluster § Use Windows on a Bio. HPC system 2

Why use a Bio. HPC Workstation or Thin Client? § They run the same environment as the cluster –Red Hat Enterprise 6 (RHEL 6) –Features such as bash, sbatch, and modules are preconfigured § It’s easier to work with large data sets –Drag-and-Drop files in the Graphic user interface (GUI) –You don’t have to use an FTP client, Samba shares, or web 3

Workstations Dell Optiplex T 5810 Series 6 Core Processor 16 GB RAM 1 TB HDD Nvidia GPU $2400 4

Thin Clients Intel NUC Quad Core Processor 16 GB RAM 250 GB SSD $700 5

Comparison of Technical Specs 6 § 10 GB Network Card § 1 GB Network Connection § Discreet Nvidia GPU Card § Integrated graphics § Includes a keyboard and mouse § Requires a keyboard and mouse

Comparison of Functions § 10 GB Network Card – 1 GB file transfers in ~ 2 seconds § Test CUDA on the Nvidia GPU – Image processing, machine learning § 384 GB of space for Windows Virtual Machines 7 § 1 GB Network Connection – 1 GB file transfers in ~ 15 seconds § 50 GB of space for Windows Virtual Machines

1 GB File Transfer Speed Comparison Time in Seconds 10 GB (Workstation) 1 GB (Thin Client) Wi. Fi (SAMBA) 0 10 20 30 40 Time in Seconds 8 50 60 70 80

Monitors 9 Standard 24” Monitor Premium 27” IPS Display Dell P 2417 H ASUS PB 278 Q $250 $400+

Network Requirements All Bio. HPC systems require a 10 GB network connection. Price varies for port installation or activation. Telecom requests can be placed in People. Soft. Allow 1 to 2 weeks. Ask your Administrative Assistants for assistance. IP reservation requests can be placed here: https: //irrequests. swmed. org/Site. Pages/IP/IPRequests. aspx Make sure you put in the notes that you need a 10 GB IP address! 10

GUI Interface § GUI desktop similar to Windows. Red Hat OSX § Your roaming profile maintains your files and settings on all Bio. HPC workstations. 11 Windows 10

Basic Settings § You must set the proxy configuration in your profile to access the Internet outside of the UTSW firewall. System>Preferences>Proxy Setting § Prevent folders from opening in separate windows Edit > Preferences > Click on the “Behavior” tab and check “Always open in browser windows” 12

Basic Settings § Create Directory Shortcuts Create bookmarks to quickly access commonly used directories - /home 2, /project, /work 13

Keyboard Shortcuts Print screen – Prt Sc Launch terminal – Disabled by default but you can change to Ctrl+T Paste within terminal – Ctrl+Shift+V You can change shortcuts under System > Preferences > Keyboard Shortcuts 14

System Utilities § Disk Usage Analyzer Applications > System Tools > Disk Usage Analyzer Shows the status of your storage quotas. Remember to empty the trash if you need space. § System Monitor Applications > System Tools > System Monitor The Resources tab shows the load on the CPU and memory. This is useful for monitoring system resources when testing code on a workstation. 15

Storage on the Bio. HPC Cluster Storage Limits /home 2 – 50 GB /project and /work – 5 TB Hard vs Soft Limit Soft – Users are notified that they are nearing the limit Hard – Write requests are denied Directory Backups /home 2 – Backed up twice a week (mirror) /work – Backed up once a week (mirror) /project – Incremental backups 16

Storage Quotas View storage usage on the command line Home Directory $ quota –s Project Directory $ lfs quota –h /project 17

Storage Quotas View storage when connected to the cluster via SSH $ biohpc_quota Need More Space? Ask your department chair to place a request with Bio. HPC and include the PI’s name, directory paths and amount of space needed. 18

Modules are used to deploy multiple versions of different software tools. See what modules are available $ module avail Load a module $ module load <name> Loaded modules need to be added each session. View loaded modules $ module list Remove a module $ module rm <name> 19

Matlab Example See the different versions of Matlab $ module avail matlab Load the Matlab Module $ module load matlab/2013 a Run Matlab $ matlab 20

Applications § An admin account is required to install RPM packages. – Email biohpc-help@utsouthwestern. edu to request an installation § You can install binaries in your home 2 directory. – For example: . /configure –prefix=/home 2/username/folder 21

Scripting Web Job Submission on the portal website can help you create scrips: https: //portal. biohpc. swmed. edu/sbatch/#/script § This provides a GUI interface for writing scripts. § The same script can be run locally and on the cluster. bash vs Sbatch 22 bash Sbatch • Runs Locally • Good for testing • You don’t have to wait in the SLURM queue • Runs on the Cluster • More powerful resources • Multiple Nodes

Run a Job Locally Workstations and thin clients come with Bash preconfigured to test scripts before submitting them to the cluster. § Run a script on a workstation with bash § Check the Output Folder 23 Output File

Submit a Job to the Cluster § Run sbatch § Check the queue with the squeue command § Check the output folder 24

Remote GUI You can run a remote Graphical User Interface (GUI) session on a single Bio. HPC node. This is useful if you want to run a graphical program like Matlab and you need more than the 16 GB of RAM on your workstation. § Create a remote. GUI job. $ remote. GUI § Connect to the GUI session with the Tiger. VNC client. $ cat remote. GUI. txt 25

Remote GPU A remote GPU session is just like a GUI session, but it utilizes a node with a high-end Nvidia GPU card. § Create a GPU job. Requires SSH. $ remote. GPU § Connect to the GPU session with the Tiger. VNC client. $ cat remote. GPU. txt 26

Virtual Machines The Bio. HPC Virtual. Box Image Manager let’s you copy VMs to your local machine. Workstations have a 384 GB limit and Thin Clients have a 50 GB limit. 27

Windows 2013 Mount Bio. HPC Storage 28

Access Bio. HPC Storage in Windows Project 29 Home

Virtual Box Settings Adjust the amount of RAM and number of cores the VM can utilize. 4 GB of RAM and 2 cores works well for most applications. 30

Increase Virtual Drive Increase the Size of the Drive $ VBox. Manage modifyhd <absolute path to file> --resize <size in MB> Example I have a 40 GB drive that I want to be 45 GB the command would be. $ VBox. Manage modifyhd <absolute path including the name and extension> -resize 46080 You can not shrink a guest drive with Virtual. Box due to the inherent danger of loosing data or making the guest non-bootable. 31

Limitations Downtime for system upgrades will be announced two weeks in advance. Major downtimes of a day or more are scheduled biannually You will not be able to login to workstations or thin clients. Incompatible Applications Open. MPI, RDMA, GPU Direct will only work on the cluster Connect to Nucleus with SSH to submit these jobs. Power Leave Bio. HPC systems powered on at all times, unless instructed otherwise. 32

For More Information § https: //portal. biohpc. swmed. edu § Email the ticket system: biohpc-help@utsouthwestern. edu 33