Workstations & Thin Clients · §They run the same environment as the cluster –RHEL6 –Bash, sbatch, and modules are preconfigured §It’s easier to work with large data sets

Workstations & Thin Clients

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§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

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§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?

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Dell Optiplex T5810 Series

6 Core Processor

16GB RAM

Nvidia GPU

$2400

Workstations

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Intel NUC

Quad Core Processor

16GB RAM

$700

Thin Clients

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§ 10GB Network Card

§ Hardware Rendering

§ Test CUDA on the Nvidia GPU

§ Includes a keyboard and mouse

Comparison

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§ 1GB Network Connection

§ Software Rendering

§ Requires a keyboard and mouse

Standard 24” MonitorDell P2414H

$300

Monitors

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Premium 27” IPS DisplayASUS PB278Q

$430+

Network Requirements

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AllBioHPC systemsrequirea10GBnetworkconnection.

Pricevariesforportinstallationoractivation.

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

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RedHat

OSX Windows10

§ 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

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§ Create Directory Shortcuts

Create bookmarks to quickly access the project and work folders.

Basic Settings

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Keyboard Shortcuts

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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

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Storage Quotas

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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.

Storage Continued

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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

Modules

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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>

Create Your Own Module

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Working with David.

§ You can not install RPM packages, but you can email [email protected] to request an installation

§ You can install binaries in your home2 directory.

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

Applications

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Script creator on the portal website: 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

Scripting

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Bash Sbatch• RunsLocally• Goodfor testing• Youdon’thavetowaitin

theSLURMqueue

• RunsontheCluster• More powerfulresources• MultipleNodes

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

Run a Job Locally

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Submit a Job to the Cluster

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§ 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

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Virtual Machines

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TheBioHPC VirtualBox ImageManagerlet’syoucopyVMstoyourlocalmachine.Workstationshavea384GB limitandThinClientshavea50GB limit.

Windows

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2013

MountBioHPC Storage

Access BioHPC Storage in Windows

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Project Home

Virtual Box Settings

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AdjusttheamountofRAMandnumberofcorestheVMcanutilize.

4GBorRAMand2coresworkswellformostapplications.

Increase Virtual Drive

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

ExampleIhavea40GBdrivethatIwanttobe45GBthecommandwouldbe.

$VBoxManage modifyhd <absolutepathincludingthenameandextension>--resize46080

YoucannotshrinkaguestdrivewithVirtualBox duetotheinherentdangerofloosingdataormakingtheguestnon-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

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§ https://portal.biohpc.swmed.edu

§ Email the ticket system: [email protected]

For More Information

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