Protected Environment at CHPC. Sean Igo Center for High Performance Computing September 11, 2014

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1 Protected Environment at CHPC Sean Igo Center for High Performance Computing September 11, 2014

2 Purpose of Presentation Overview of CHPC environment / access Actually this is most of the show Overview of protected (HIPAA-compliant) environment Just like regular CHPC environment, except: Smaller Much more secure Physically Electronically Slide 2

3 Overview of CHPC Resources CHPC's mission: Support Research! Faculty, staff, or thesis/dissertation Can also be class research CHPC's main focus is High Performance Computing: Massively parallel-processing Good for computationally intensive / large data needs Also: access to a single high-powered computer Useful for large amounts of data Or if you need an application you don't have Slide 3

4 Overview of CHPC Resources Other services available: VM Farm: web application hosting, grid, etc. Database consultation and hosting Windows/Macs hosted in datacenter, remote login Limited coding/scripting consultation Data storage and backup Desktop support, like Mr. Turnbull does (I don't know lots about this) Slide 4

5 Overview of CHPC Resources My area of expertise is the HPC (cluster) side Suitable for many researchers' needs even sometimes when other solutions appear better... Ordinary software as well as supercomputing We prefer people use this approach You get access to it immediately with your account Slide 5

6 Overview of CHPC Resources Do we support hadoop? Working on it Currently have a small experimental setup Plans afoot for a larger one Getting some grant support for this would help Slide 6

7 Dedicated Machines Ordinary (but powerful) computers Kept in CHPC datacenter May be owned by research group Purchased with grant money Some are publicly accessible May run any OS Windows: connect with Remote Desktop Linux: connect with command line / X-11 clients Mac: this is uncommon but we have done it...? Slide 7

8 Dedicated Machines When do you need one? high-powered processing single computer licensed software Slide 8

9 Virtual Machines Actually software pretending to be a computer Hosted on a farm in CHPC datacenter From user's perspective, just like dedicated not as powerful often free upon approval of project by CHPC May run any OS, like dedicated Slide 9

10 Virtual Machines When do you need one? web-facing applications special OS version or configuration unusual software setup software distributed as a VM image Be sure you do need one! we'd rather you used the clusters and app tree Slide 10

11 HPC Terms Node - a single computer (high-powered linux PC) Core - one hardware processor nodes at CHPC have 8-16 cores Cluster - a set of nodes with high speed network connections and software to run in parallel Job - a batch processed command run on a cluster Queue - mechanism for ordering jobs Interactive Node - node you log on to to prepare jobs and submit them to the queue Slide 11

12 CHPC Clusters General Clusters (all partly owned by research groups) Ember (12 cores/node) Kingspeak (16 cores/node [some 20]) Some nodes with GPUs are available Lonepeak (12 or 20 cores/node) Protected Environment - high-security for protected health info. apexarch / homer 10 nodes, 104 cores General-access interactive node (apex1) Slide 12

13 Batch System All use of compute nodes go through a batch system Set up program and data Create a batch script for your job, specifying resources Submit script to queue Job waits for resources, then runs You receive notification when it's done Interactive nodes only for preparing input files, analyzing results, compilations, etc. no direct running of jobs 15 min max per process Except on protected cluster's group-owned nodes Slide 13

14 Cluster Environment Recommended approach: Outside World Outside World Remote Login / VPN Account (slow) Account (slow) Interactive Interactive Node Node Queue Queue QSUB Scratch (fast) Scratch (fast) Compute Node Compute Node Compute Node Compute Node Compute Node Compute Node Edit/compile on interactive Create script for batch Submit script to scheduler Script does this: Copy data to scratch Process data Write output to scratch Copy output to account Clean up scratch Slide 14

15 Software available on Clusters Emphasis on scientific computing / software dev. Languages: C/C++, Java, Python, R, Perl, IDEs: e.g. Eclipse, NetBeans moving away from centralized installation ask me if you want to use these Math: Matlab, stats software some; there are licensing issues NLP/AI/ML: my expertise! Weka, SVM software, UIMA, Plus many more and much else available on request Slide 15

16 Access to (linux) Interactive Nodes Need ssh client (recommend PuTTY) cygwin ssh also works fine As should Mac terminal ssh For Xwindowing not recommended off campus Windows XMing Cygwin X server works too (recent distributions use Xming) Macs/linux can do it natively Slide 16

17 Access to dedicated / VM For linux: same as cluster interactive ssh client or Mac / linux native or FastX / X-11 forwarding For Windows: Remote Desktop Windows has it standard Linux can run it too Slide 17

18 Getting Started at CHPC Can be a little confusing! First, get an account Access to general-purpose (non-protected) clusters (linux) Request access to HIPAA/Protected environment Requires a second application form IRB number and project name Then you have access to protected cluster (linux environment) For VM, Windows remote desktop, web hosting, etc: request and arrange through consultation with tech staff in both protected and general-purpose environments Slide 18

19 Getting Started at CHPC Account application online: You need to be doing research for a PI with a CHPC account If your PI isn't signed up, let me know If the online application is unsuitable, paper one is available Slide 19

20 Getting Started at CHPC Getting started guide Problem reporting system Easiest: to OR go to website OR find me Slide 20

21 Security Policies (1) No clear text passwords - use ssh and scp Do not share your account under any circumstances Don t leave your terminal unattended while logged into your account Do not introduce classified or sensitive work onto CHPC systems Except in the protected environment Use a good password and protect it see gate.acs.utah.edu for tips on good passwords Slide 21

22 Security Policies (2) Do not try to break passwords, tamper with files, look into anyone else s directory, etc. your privileges do not extend beyond your own directory Do not distribute or copy privileged data or software Report suspicions to CHPC (security@chpc.utah.edu) Please see Protected environment data subject to additional policies e.g. HIPAA training Slide 22

23 General Information Available on CHPC web pages Can get to from Ramping up a wiki at Available for most packages Not NLP/ML packages, at the moment A bit dated; moving to CHPC wiki (wiki.chpc.utah.edu) Has information on licensing restrictions, example batch scripts, where to get more information on a specific package Also has useful information on running of jobs Slide 23

24 The Protected Environment Protected environment Like general CHPC environment, but smaller Different home directory Same applications available (linux) Cluster, VM farm, dedicated machines, etc. Higher security: HIPAA compliant, soon other standards Requires VPN connection from off campus Physically secure backups Slide 24

25 Why do we have it? PHI security breaches are serious PHI data can be stolen from insecure places laptops / phones and tablets / removable drives this has happened a lot Protected environment conceived to be secure physically: kept in locked cabinet, locked building electronically: heavily firewalled Environment has both storage and computation Slide 25

26 Protected Environment Application Protected environment access Application not yet fully automated Mention in application notes that you need HIPAA/Protected Access based on IRB number We verify users' right to access the specified data Usually receive user accounts and project space for large data Handled case by case Arrange for secure transfer of data Apexarch shares application tree with main clusters Dedicated / VM need their own software, just as on regular side Slide 26

27 VMs / Dedicated Machines Protected VM farm VMs only for use by PI-approved projects Web-based applications using PHI Remote Desktop access Dedicated machines Usually purchased by PI from grant funds Can run any OS Maintained and backed up by CHPC staff Slide 27

28 Finally... Let us know if you need some other package Factors: cost, hardware/os requirements, licensing Report problems by ing Any questions contact me! CHPC Cubicle: 405 INSCC, ask at front desk BMI Office: 2025, near Dr. Chapman's Slide 28

29 Questions? Slide 29

30 Parallelizing Your Task Most packages I've shown are single-processor! Dedicated parallel software would be nice... Can write your own, not always practical Different ways to run existing sw on parallel clusters Many tasks are embarrassingly parallel i.e., capable of being decomposed into sub-problems that do not depend on one another e.g., parsing several text files; can just send 1/n of the files to parsers running on n processors Slide 30

31 Parallelizing Your Task Embarrassingly Parallel is nothing to be ashamed of! However, dividing tasks naively may not give each processor the same amount of work That is, 1/n of the documents/sentences/etc. may not be 1/n of the work Initial tests with MetaMap show that dividing over documents is a terrible way to use it Slide 31

32 Parallelizing Your Task Slightly better: deal tasks to processors as they become available with fine granularity should be very efficient Other things to consider: Per-invocation overhead Integrating results I'm creating scripts to wrap / distribute software calls (command lines) Talk to me if you need something like this Slide 32

33 Default Login Scripts CHPC maintains default login scripts that set up environment, now updated to work in protected environment Copy to your home directory as.tcshrc or.bashrc This is being done on new accounts Can comment out setups for packages not used Currently NLP/ML packages not included Can customize by creating.aliases file that is sourced at end of the CHPC script Slide 33

34 Location of Software Currently we place most installations at: /uufs/chpc.utah.edu/sys/pkg Accessible on clusters and some desktops all NLP / ML software is here Protected environment also uses the chpc.utah.edu tree That is for linux only; Windows / Mac interactive nodes have software installed natively Slide 34

HIPAA Environment, AI and NLP Services at CHPC. Sean Igo Center for High Performance Computing September 23, 2010

HIPAA Environment, AI and NLP Services at CHPC Sean Igo Center for High Performance Computing Sean.Igo@utah.edu September 23, 2010 Purpose of Presentation Brief overview of CHPC environment / access Overview