February 23, 2015

XSEDE New User/Allocation Mini-Tutorial

Vincent C. Betro, Ph.D.

University of Tennessee NICS/ORNL

XSEDE Training Manager

Outline

•  What’s  XSEDE?  •  How  do  I  get  an  alloca7on?  •  What  is  the  User  Portal?  

– We’ll  create  an  account  today  

•  What  is  available  there?  – Globus  File  Transfer  – Common  job  running  interface  – Gateways  – Training  

Don’t sweat taking notes!

•  This  presenta7on  is  located  at:  – h"p://hpcuniversity.org/trainingMaterials/192  

•  Extreme  Science  and  Engineering  Discovery  Environment  

•  Follow  on  NSF  project  to  TeraGrid  in  2012  

•  Centers  operate  machines,  and  XSEDE  provides  seamless  infrastructure  for  allocaKons,  access,  and  training  

•  Researchers  propose  resource  use  through  XRAS  

•  Supports  thousands  of  scienKsts  in  fields  such  as:  –  Chemistry  –  BioinformaKcs  –  Materials  Science  –  Data  Sciences  

XSEDE Allocations

•  Want  to  use  XSEDE  resources  to  teach  a  class?  – hIps://portal.xsede.org/alloca7ons-­‐overview#types-­‐educa7on  

•  Just  looking  to  try  out  a  larger  resource  or  a  special  resource  your  campus  doesn’t  have?  – hIps://portal.xsede.org/alloca7ons-­‐overview#types-­‐startup  

 

XSEDE Allocations

•  See  a  Campus  Champion  (Morgan  State  needs  someone…you?)  

•  Ready  to  scale  up  your  research?  – hIps://portal.xsede.org/alloca7ons-­‐overview#types-­‐research  

XSEDE Allocations •  WriKng  and  SubmiRng  a  Successful  XSEDE  AllocaKon  Proposal  Recorded:  April  9,  2014  Topics  covered  in  detail  include:  

•  research  objecKves    •  computaKonal  methodologies  •  jusKficaKon  for  SUs  needed    •  applicaKon  efficiencies  

•  View:  Example  requests  from  several  domains  •  Read  AddiKonal:  AllocaKon  Request  Guidelines  and  Tips  

XSEDE Allocations

When  wriKng  your  research  requests  consider  the  following  objecKves  and  guidelines:  •  Research  must  be  clear  and  concise.    •  Outline  all  the  proposed  computa7onal  algorithms  and  simula7ons  

•  Include  any  input  parameters  to  be  inves7gated  and  explain  the  choice  of  simula7on  parameters.  

•  Describe  any  previous  results  and  progress.    •  Jus7fy  the  choice  of  resources.  •  Jus7fy  the  amount  of  7me  requested.    

Now  what?  

Yeah!  I  got  an  XSEDE  

allocaKon!  

XSEDE User Portal (XUP)

•  URL:  portal.xsede.org  •  Single  point-­‐of-­‐entry  to  informaKon  about  XSEDE  services  and  uKliKes  for  using  them  

•  Anyone  can  create  an  XUP  user  account  and  access  non-­‐project  features  

•  Only  XSEDE  allocaKon  project  members  can  access  project  features  

Using the XUP

•  Create  and  login  to  your  XUP  Account  •  Use  XSEDE  resources  responsibly  •  Get  added  to  your  XSEDE  project  •  Navigate  your  personal  My  XSEDE  webpage  •  Navigate  the  informaKon  in  the  XUP  

Create and login to your XUP account

1.  From  the  XUP  homepage,  click  CREATE  ACCOUNT  

2.  Complete  the  User  Account  Form  

3.  Verify  your  account  request  

4.  Select  your  username  and  password  

5.  Login  to  the  XUP  

portal.xsede.org

Click the CREATE ACCOUNT link to access the XUP User Account Form

XSEDE Acceptable Use Policy

•  Must  accept  the  User  ResponsibiliKes  Form  acer  creaKng  your  XUP  account  and  again  at  the  beginning  of  each  allocaKon  you  receive.  

•  Choose  a  strong  password  and  protect  it.  •  Close  SSH  terminals  and  log  out  of  the  User  Portal  when  you  

are  finished  with  your  session.  •  Report  Suspicious  AcKvity  :  email  help@xsede.org  or  call  

1-­‐866-­‐907-­‐2383  immediately,  regardless  of  the  Kme  of  day.  

XSEDE  Cybersecurity  Tutorial  h"p://www.citutor.org  

Get Added to Your XSEDE project

•  PIs  automaKcally  have  full  access  to  their  project’s  account.    

•  The  PI  is  responsible  for  managing  users  on  their  account.  

•  Ask  the  PI,  or  their  allocaKon  manager,  to  add  your  XUP  username  to  the  project.  

Your My XSEDE webpage (1) WELCOME TO XUP •  Quick access to

commonly used features.

(2) LATEST UPDATES •  Latest information

specific to your user account.

(3) MY ACTIVE ALLOCATIONS •  Summary of the active

projects for which you are either a PI or member.

Update your XUP User Profile

MY XSEDEàProfile  View and or change your user information (organization, address).  Make sure your email address is correct. XSEDE staff will use it to

communicate with you regarding your allocation.

Navigating the XUP

•  My  XSEDE  •  Resources  •  DocumentaKon  •  AllocaKons  

•  Training  •  User  Forums  •  Help  •  About  

View the XSEDE Systems Monitor •  Resources  -­‐>  Systems  Monitor   Provides  technical  and  status  informaKon  for  all  of  XSEDE's  resources.   The  STATUS  column  indicates  whether  the  system  is  up  or  down.  If  down,  can  click  on  status  to  find  when  the  machine  is  expected  to  come  back  up.    

Accessing XSEDE Resources Authentication Methods 1.  Password

•  XUP credentials •  Site-password •  One-time password

2.  Key-based

Single Sign-On •  Enables logging in once to

access all of your allocated resources

Connection Methods 1.  GSI-OpenSSH 2.  OpenSSH

XSEDE SSO Login Hub An  SSO  enabled    connec7on  point  to  XSEDE  resources  

Ø SSH  to  login.xsede.org  using  your  XUP  credenKals  

Ø Move  among  resources  using  gsissh  command  

Moving Files - Globus Online •  A  fast,  reliable,  and  secure  file  transfer  service  geared  to  the  big  data  needs  of  the  research  community.  

•  Moves  terabytes  of  data  in  thousands  of  files  •  AutomaKc  fault  recovery  •  Easy  to  use  •  No  client  socware  installaKon  •  Consolidated  support  and  troubleshooKng  •  Supports  file  transfer  to  any  machine  •  Accounts  are  free  -­‐  www.globusonline.org  

Globus Online Dashboard

Sign in with XSEDE login

Logging in with your XSEDE credentials

Connecting globus account

Creating a login on globus.org

Globus Online File Transfer

Choosing a file to move…

Running  Jobs  Overview  

Compute Nodes

Home Scratch

File System

Job Data

Data

Researcher

Login

Login Nodes

Command Line

Use for tasks such as file editing, code compilation,

data backup, and job submission.

Read/write data from compute nodes to Scratch directory.

Store project files Such as source code, scripts, and input data sets to Home directory.

Run jobs by submitting your batch script to the compute nodes using the "qsub" command.

When you connect to a resource, you are on a login node shared by many users.

Your job is submitted to a queue and will wait in line until nodes are available. Queues are managed by a job scheduler that allows jobs to run efficiently.

Batch Script

Commands for code execution, copy input files to scratch,… Specify number/type of nodes, length of run, output directory, …

Login Nodes

•  When  you  login  to  an  XSEDE  resource,  you  connect  to  a  login  node.    

•  Use  login  nodes  for  basic  tasks  such  as  file  ediKng,  code  compilaKon,  data  backup,  and  job  submission.  

•  Do  not  run  compute  jobs  on  the  login  nodes.    

Where do I run compute jobs?

Running Compute Jobs

•  Jobs  are  run  on  the  compute  nodes  by  submiRng  a  batch  script  on  a  login  node  

•  All  jobs  are  placed  in  a  batch  queue  acer  they  are  submi"ed.  

•  All  XSEDE  compute  resources  use  a  batch  scheduler  for  running  jobs.  

•  Resource  User  Guides  on  the  XUP  have  details  on  your  system’s  scheduler.  

 

•  portal.xsede.org  à  Help      Submit  Kcket  

•  portal.xsede.org  à  My  XSEDE  à  Tickets  – Submit  Kcket  – View  past  Kckets  (both  open  and  closed)  

•  Can  also  email  help@xsede.org  or  call                            1-­‐866-­‐907-­‐2383,  at  any  hour  (24/7)  

   

Need help? Reporting and Tracking Issues

Discussing your problems… User Portal: User Forums •  The  User  Forums  are  a  great  place  to  ask  quesKons,  get  help,  or  discuss  ideas  about  XSEDE.  

More “helpful” resources xsede.orgàUser  Services  •  Resources  available  at  each  Service  Provider  

•  User  Guides  describing  memory,  number  of  CPUs,  file  systems,  etc.  

•  Storage  faciliKes  •  Socware  (Comprehensive  Search)  

•  Training:  portal.xsede.org  à  Training  •  Course  Calendar  •  On-­‐line  training  •  CerKficaKons  

•  Get  face-­‐to-­‐face  help    from  XSEDE  experts  at  your  insKtuKon;  contact  your  local  Campus  Champions.    

•  Extended  CollaboraKve  Support  (formerly  known  as  Advanced  User  Support  (AUSS))      

XSEDE Moodle Site If  you  are  interested  in  receiving  a  Mozilla  badge  for  taking  the  full  

version  of  this  New  User  Training,  please  visit:    h"ps://www.hpc-­‐training.org/xsede/moodle/login/index.php      starKng  May  1  to  take  a  quiz  about  XSEDE  and  earn  a  badge!    Also,  be  

on  the  lookout  for  other  courses  and  badge  opportuniKes!  

ACM SIGHPC Education Chapter

       Check  out  the  following  link  to  get  more  involved  with  contribuKng  to  HPC  training  efforts  across  the  country  and  world!  

 h"p://sighpceducaKon.acm.org/  

Contact Info Dr.  Vincent  Charles  Betro  Training  Manager,  XSEDE  University  of  Tennessee    NaKonal  InsKtute  for  ComputaKonal  Sciences  Oak  Ridge  NaKonal  Laboratory  Phone:  865-­‐576-­‐8905  email:  vbetro@tennessee.edu  

February 23, 2015

Thanks for listening and welcome to XSEDE!