Workstations & Thin Clients

Transcription

1 1 Workstations & Thin Clients

2 Overview Why use a BioHPC computer? System Specs Network requirements OS Tour Running Code Locally Submitting Jobs to the Cluster Run Graphical Jobs on the Cluster Use Windows on a BioHPC system 2

3 Why use a BioHPC system? They run the same environment as the cluster RHEL6 Bash, sbatch, and modules are preconfigured It s easier to work with large data sets Drag-and-Drop files in the GUI You don t have to use an FTP client or the web interface 3

4 Workstations Dell Optiplex T5810 Series 6 Core Processor 16GB RAM Nvidia GPU $2400 4

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

6 Comparison 10GB Network Card Hardware Rendering Test CUDA on the Nvidia GPU 1GB Network Connection Software Rendering Requires a keyboard and mouse Includes a keyboard and mouse 6

7 Monitors Standard 24 Monitor Dell P2414H $300 Premium 27 IPS Display ASUS PB278Q $430+ 7

8 Network Requirements All BioHPC systems require a 10GB network connection. Price varies for port installation or activation. Telecom requests can be placed in PeopleSoft. Ask your Administrative Assistants for assistance. IP reservation requests can be placed here: Make sure you put in the notes that you need a 10GB IP address! 8

9 GUI Interface GUI desktop similar to Windows. Red Hat OSX Windows 10 Your roaming profile maintains your files and settings on all BioHPC workstations. 9

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 10

11 Basic Settings Create Directory Shortcuts Create bookmarks to quickly access the project and work folders. 11

12 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 12

13 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. 13

14 Storage Quotas View storage usage on the command line $ biohpc_quota Need More Space? Ask your department chair to place a request with BioHPC and include the PI s name, directory paths and amount of space needed. 14

15 Storage Continued Storage Limits /home2 50GB /project and /work varies depending on department Hard vs Soft Limit Soft Users are notified that they are nearing the limit Hard Write requests are denied Directory Backups /home2 Backed up twice (mirror) /work Backed up twice (mirror) /project Incremental backups 15

16 Modules Modules are used to deploy multiple versions of different software tools. See what modules are available $ module avail View loaded modules $ module list Load a module $ module load <name> Remove a module $ module rm <name> 16

17 Create Your Own Module Working with David. 17

18 Applications You can not install RPM packages, but you can to request an installation You can install binaries in your home2 directory. For example:./configure prefix=/home2/username/folder 18

19 Scripting Script creator on the portal website: This provides a GUI interface for writing scripts. The same script can be run locally and on the cluster. Bash vs Sbatch Bash Runs Locally Good for testing You don t have to wait in the SLURM queue Sbatch Runs on the Cluster More powerful resources Multiple Nodes 19

20 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 20

21 Submit a Job to the Cluster Run sbatch Check the queue with the squeue command Check the output folder 21

22 Remote GUI and GPU Run a Graphical User Interface on a single HPC cluster node. $ remotegui Connect to the GUI session with the VNC client. $ cat remotegui.txt Run a GUI session that utilizes one of the Nvidia GPUs. Requires SSH. $ remotegpu 22

23 Virtual Machines The BioHPC VirtualBox Image Manager let s you copy VMs to your local machine. Workstations have a 384GB limit and Thin Clients have a 50GB limit. 23

24 Windows 2013 Mount BioHPC Storage 24

25 Access BioHPC Storage in Windows Project Home 25

26 Virtual Box Settings Adjust the amount of RAM and number of cores the VM can utilize. 4GB or RAM and 2 cores works well for most applications. 26

27 Increase Virtual Drive Increase the Size of the Drive $ VBoxManage modifyhd <absolute path to file> --resize <size in MB> Example I have a 40GB drive that I want to be 45GB the command would be. $ VBoxManage modifyhd <absolute path including the name and extension> -- resize You can not shrink a guest drive with VirtualBox due to the inherent danger of loosing data or making the guest non-bootable. 27

28 Limitations Downtime Downtime for system upgrades will be announced two weeks in advance. You will not be able to login to workstations or thin clients. Incompatible Applications Power OpenMPI, RDMA, GPU Direct will only work on the cluster Connect to Nucleus with SSH to submit these jobs. Leave BioHPC systems powered on at all times, unless instructed otherwise. 28

29 For More Information the ticket system: 29