Workstations & Thin Clients · 2019. 6. 27. · resources when testing code on a workstation. System Utilities 12. Modules 13 Modules are used to deploy multiple versions of different

Workstations & Thin Clients

1

§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

Overview

2

§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

Why use a BioHPC system?

3

Dell Optiplex T5810 Series

6 Core Processor

16GB RAM

Nvidia GPU

$2400

Workstations

4

Intel NUC

Quad Core Processor

16GB RAM

$700

Thin Clients

5

§ 10GB Network Card

§ 1TB HDD

§ Hardware Rendering

§ Test CUDA on the Nvidia GPU

Comparison

6

§ 1GB Network Connection

§ 256GB SSD

§ Software Rendering

Network Requirements

7

AllBioHPC systemsrequirea10GBnetworkconnection.

Pricevariesforport installationoractivation.

TelecomrequestscanbeplacedinPeopleSoft.AskyourAdministrativeAssistantsforassistance.

IPreservationrequestscanbeplacedhere:https://irrequests.swmed.org/SitePages/IP/IPRequests.aspx

Makesureyouputinthenotesthatyouneeda10GB IPaddress!

§ GUI desktop similar to Windows.

§ Your roaming profile maintains your files and settings on all BioHPC workstations.

GUI Interface

8

§ 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”

Basic Settings

9

§ Create Directory Shortcuts

Create bookmarks to quickly access the project and work folders.

Basic Settings

10

Keyboard Shortcuts

11

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

§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.

System Utilities

12

Modules

13

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>

§You can install binaries in your home2 directory.

– For example: ./configure –prefix=/home2/username/folder

§You can not install RPM packages, but you can email biohpc-help@utsouthwestern.edu to request an installation.

Applications

14

Workstations and thin clients come with Bash and SBGrid preconfigured to test scripts before submitting them to the cluster.

§Run a script on a workstation with bash

§Check the Output Folder

Run a Job Locally

15

Submit a Job to the Cluster

16

§Run sbatch

§Check the queue with the squeue command

§Check the output folder

§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

Remote GUI and GPU

17

Virtual Machines

18

TheBioHPC VirtualBox ImageManagerlet’syoucopyVMstoyourlocalmachine.Workstationshavea384GB limitandThinClientshavea50GB limit.

Windows

19

2013

MountBioHPC Storage

Increase Virtual Drive

20

IncreasetheSizeoftheDrive$VBoxManage modifyhd <absolutepathtofile>--resize<sizeinMB>

ExampleIhavea40GBdrivethatIwanttobe45GBthecommandwouldbe.

$VBoxManage modifyhd <absolutepathincluding thenameandextension> --resize46080

Youcannotshrink aguestdrivewithVirtualBox duetotheinherentdangerofloosing dataormaking theguestnon-bootable.

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

OpenMPI, RDMA, GPU Direct will only work on the cluster

Connect to Nucleus with SSH to submit these jobs.

Power

Leave BioHPC systems powered on at all times, unless instructed otherwise.

Limitations

21

§https://portal.biohpc.swmed.edu

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

For More Information

22