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PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011
Cindy ZhengFor
PRAGMA Grid/Cloud TeamAnd the PRAGMA communities
Pacific Rim Application and Grid Middleware Assemblyhttp://www.pragma-grid.nethttp://goc.pragma-grid.net
PRIME 2011 Tutorial
PRAGMA Grid/Cloud Access
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Grid and Cloud
• What are they?– Collection of resources for sharing
• Differences– Grid
• Resources glued by agreed and verifiable trust– Certification– GLOBUS
• Provide system/software environment for some applications and users
– Cloud• Users setup applications on systems• Cloud provide mechanisms to allow users run
their systems as virtual machine (VM) in shared resources
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Grid Trust• Organizations and policies
– International Grid Trust Federation (IGTF)• APGridPMA• EUGridPMA• TAGPMA
– Accreditation• Software
– Certificate Authorities (CA)• Set up CA services, policies• Issue/manage certificates (user, server, services, …)
– GLOBUS• Identify users and resources in a cohesive fashion• Map user certificate to a local account• Interface local job managers
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
PRAGMA CAs
• PRAGMA-UCSD CA (https://goc.pragma-grid.net/ca)– Accredited by APGrid PMA– Included in IGTF distribution– Only issue a certificate when needed
• PRAGMA Experimental CA(http://rocks-56.sdsc.edu/exp-ca)– Only accepted by PRAGMA grid site
• PRIME 2011 students will use PRAGMA experimental CA unless your project involved with other grids
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Grids/Clouds and PRAGMA Grid/Cloud
• Grids/Clouds– Most are centrally funded
• PRAGMA grid/Cloud is unique– Grass-root
• Voluntary contribution• Open (PRAGMA member or not, pacific rim or not)• Long-term collaborative working experiment
– Heterogeneous• Funding• No uniform infrastructure management• Open to all sciences and applications• All varieties of site policies, system and network environments
– Friendly, helpful, close relationships– More challenging and rewarding
• Good for development, collaborations, integrations and testing
PRAGMA Grid/CloudPRAGMA Grid/Cloud
26 institutions in 16 countries/regions, 22 compute sites, 9VM sites (+ 6 site in preparation)
UZHSwitzerland
NECTECKUThailand
UoHydIndia
MIMOSUSMMalaysia
HKUHongKong
ASGCNCHCTaiwan
HCMUTHUTIOIT-HanoiIOIT-HCMVietnam
AISTOsakaUUTsukubaJapan
IHPC/NGONTUSingapore MU
Australia
KISTIKMUKorea
JLUChina
SDSCUSA
CICESEUNAMMexico
UChileChile
CeNAT-ITCRCosta Rica
BESTGridNew Zealand
CNICChina
LZUChina
UZHSwitzerland
LZUChina
UValleColumbia
ASTIPhilippines
IndianaUUSA
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
PRAGMA Grid Software Layershttp://goc.pragma-grid.net/pragma-doc/userguide/join.html
Local job scheduler (require one)
Globus (required)
Application Middleware
Applications
Infrastructure Middleware
SGE PBS LSF SQMS …
Ninf-G Nimrod/G Mpich-GX … Gfarm SCMSWeb MOGASCSF
Phylogenetic …FMO CSTFTSavannah MM5 AMBERSiesta
…
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011
PRAGMA Grid/Cloud Compute Resourceshttp://goc.pragma-grid.net/pragma-doc/computegrid.html
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
PRAGMA Grid/Cloud Members and Teamhttp://goc.pragma-grid.net/wiki/index.php/Site_status_and_tasks
• Team members– >240 and growing– one management contact / site– 1~3 technical support contact / site– 1~4 application drivers / application– 1~5 members / Middleware development team
• Experts– Application (various scientific domains)– Middleware (various grid middleware)– Security (grid security)– …
• Communications– Email– Mailing list – [email protected]– Coordinator – [email protected]
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
PRAGMA Cloud Access
• Cloud computing is new– Access procedure has not been formalized
• Contact Cindy for detail info and arrangements
• The rest of the slides shows how to access PRAGMA grid
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Obtain PRAGMA Grid Access• Find guide document at
http://goc.pragma-grid.net/wiki/images/5/51/PRIME-accounts.doc
• Be aware– When cut/paste a command line
• Microsoft word may change – A hyphen to a line character– Double-hyphen to a long line character
• Learn UNIX concepts and commands You need for your project
Know howUnderstanding (Know why)
Account application as an example Learn more online, googlehttp://mally.stanford.edu/~sr/computing/basic-unix.html Try them, hands-on
But be careful with “rm” (remove) command!
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Same Basic UNIX Commands• List files
$ ls$ ls -l (show file permission, ownership, etc.)$ ls -a (show all files, including hidden files)
• Change directory$ cd (go to my home directory)$ cd ~/.ssh (go to .ssh subdirectory under my home directory)
• Copy files locally$ cp <local-source-file> <local-destination-path>
• Copy files between local and remote systems use SSH key$ scp <local-source-file> <remote-host-name>:<remote-path>$ scp <remote-host-name>:<remote-path> <local-destination-
path>• Remember the command, but forgot how to use it
$ <command> --help$ man <command>
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Need an UNIX System on Laptop (Step 1.1)
• UNIX on laptop– MAC OS 10
HDApplicationsUtilitiesTerminal
– WindowsInstall CygwinClick
– LINUXLogin
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Create SSH Key(Step 1.2)
• Secure remote login• Generate key files
$ ssh-keygen -t rsa Use default path for ssh key files Good passphrase (hard to guess, no dictionary words) Remember the passphrase
• View SSH key files (private vs. public) From Cygwin
$ ls ~/.ssh-r--------@ 1 cindyzheng staff 951 Mar 19 01:10 id_rsa-rw-r--r--@ 1 cindyzheng staff 234 Mar 19 01:10 id_rsa.pub-rw-r--r--@ 1 cindyzheng staff 8414 Mar 19 01:10 known_hosts
From Windowsc:\Program files\Cygwin\Home\<Your-user-name-on-laptop>\.ssh
• Backup SSH key files• USB drive, take with you• Can be used thereafter• Only on secure systems• Possibly compromised key
• Immediately inform all public key holders (system administrators)
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Account Application(Step 2)
• Email to Cindy– Your full name – Institution name: UCSD– Address of the institution: UCSD– Country of the institution: USA– Your phone number– Your fax number <optional>– Your email address– The purpose of using PRAGMA grid: PRIME– Your/your institution's contribution to PRAGMA (can be work,
resources): work– Prefered login names (1st, 2nd, 3rd, but may or may not be granted)– Prefered UNIX shell (may or may not be granted) <optional>– Hostname(s) and IP address(es) of the system(s) which you launch your
applications (This is required for PRAGMA grid site systems to open their firewalls in order to allow you access.) <ask your foreign advisor for it>
– Your ssh PUBLIC key (NEVER and NEVER give anyone your private key file!! Nor your ssh password!!)
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Cindy
• Create user info pack
• Create an UNIX user account on rocks-200.sdsc.edu
• Email user– Account name on rocks-200.sdsc.edu– Certificate request license id
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Test SSH key(Step 3)
• Login to rocks-200.sdsc.edu$ ssh <username>@rocks-200.sdsc.eduEnter passphrase
Last login: Tue Apr 5 11:37:56 2011 from dyn137-110-115-232.ucsd.edu
Rocks 5.3 (Rolled Tacos)Profile built 04:25 15-Apr-2010
Kickstarted 22:21 14-Apr-2010
• In case ssh fails$ ssh –v <username>@rocks-200.sdsc.eduEmail output to Cindy
First time login on rocks system, ssh-keygen ran automaticallyAccept default ssh file pathEmpty password
• Only used internally• not recommended elsewhere
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Make a User Certificate Request(Step 3)
$ cd$ /opt/pragma-ca/bin/grid-certreq -sv ra.pragma-grid.net:pragma-exp_ra -new <license_id> -g
"SMIME user" -sou ---------(Sample output)------------- creating a certificate signing request ------------------------------------------- generate private key (size 1024 bit) ...................................................oo ....................oo ------- input user subject information -------- email can be omitted by putting a char of '.’ input ou : PRIME type exactly as this input user name : Cindy Zheng input your full name input user email : [email protected] input your email address, must! ------- please confirm your inputs ------------ GROUP : SMIME user SUBJECT : CN=Cindy Zheng, [email protected] do you continue operation? (yes/no/retry)[y]: press return trying to connect RA server : ra.pragma-grid.net (11412) ... ok. request for issuing a new certificate ... ok. your request is accepted. (AcceptID=0000003) <- remember it CA operator will send an email to tell a result. save a CA certificate file : /home/cindy/.globus/cacert.pem <- note cert request files location save a private key file : /home/cindy/.globus/userkey.pem <- note cert request files location Input PASS Phrase: type a good password Verifying - Input PASS Phrase: retype the password (remember it!) • Email Cindy the acceptID
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Cindy
• Issue user certificate– Off-line CA server
• Inform user via email
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Retrieve User Certificate(Step 4)
• Login to rocks-200.sdsc.edu$ ssh <username>@rocks-200.sdsc.edu When prompt, enter your SSH password
• Retrieve user certificate$ /opt/pragma-ca/bin/grid-certreq -sv ra.pragma-
grid.net:pragma-exp_ra -em <your-email> -recv <your-acceptID>
trying to connect RA server : ra.pragma-grid.net (11412) request for exporting a certificate ... ok save a CA certificate file : /home/cindy/.globus/cacert.pem save a certificate file : /home/cindy/.globus/usercert.pem
• View and understand certificate files$ ls -l .globus-rw-r--r-- 1 cindyzheng staff 2878 Mar 23 18:26 cacert.pem-rw-r--r-- 1 cindyzheng staff 4998 Mar 23 18:26 usercert.pem-r-------- 1 cindyzheng staff 1743 Mar 23 18:26 userkey.pem
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Backup Certificate Files(Step 4)
• Copy .globus directory from rocks-200.sdsc.edu to your laptopStart Cygwin/terminal on your laptop
(Should land in your home directory)$ scp -r
<username>@rocks-200.sdsc.edu:/export/home/<username>/.globus .
• Copy c:\Program files\Cygwin\Home\<Your-user-name-on-laptop>\.globus to your USB backup disk• Take with you anywhere• Can be used usually 1 year• Only on secure systems• Possibly compromised certificate
• Immediately inform certificate issuer (Cindy)
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Test Globus Authentication(Step 5)
On rocks-200.sdsc.edu:• Create a proxy
$ grid-proxy-init Your identity: /O=grid/O=pragma/OU=PRIME/CN=Cindy Zheng
Enter GRID pass phrase for this identity: <- input passphrase Creating proxy .......................................................... Done Your proxy is valid until: Thu Apr 7 02:18:11 2011• Test globus authentication
$ globusrun -a -r rocks-200.sdsc.edu GRAM Authentication test successful• Email Cindy if successful, otherwise email output to Cindy• To create longer proxy, specify hours
$ grid-proxy-init –hours 100
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Test Job Submission(Step 5)
$ globus-job-run rocks-200.sdsc.edu/jobmanager-sge /bin/date/opt/gridengine/default/spool/rocks-65/active_jobs/330008.1/pe_hostfilecompute-0-12Tue Apr 21 13:06:18 PDT 2009rm: cannot remove `/tmp/330008.1.all.q/rsh': No such file or directory ignore this for now
Note: depending on how busy the system is, you may need to wait a bit.To find out the status of SGE queue, open/login to another shell and run$ qstat –f
queuename qtype used/tot. load_avg arch states----------------------------------------------------------------------------…----------------------------------------------------------------------------all.q@compute-0-6.local BIP 1/2 0.06 lx26-x86 328085 0.56000 data jas dr 04/15/2009 23:29:01 1 ----------------------------------------------------------------------------… ##################################################################### - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - ##################################################################### 330010 0.00000 data zhengc qw 04/21/2009 13:18:39 1
Email Cindy if successful, otherwise email output to Cindy
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Cindy
• Add your email to pragma-grid-team list
• Email [email protected] ask site adminitrators to create account on their systems
• Site administrator will email your username to you and me after your account is created
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Test Access To Your Host Site(Step 6)
• Host system name/ip (where you will be launching your applications from)
• Do the same tests as you have done with rocks-200.sdsc.edu– Test SSH (Slide 20)– Test Globus authentication (Slide 29)– Test job submission (Slide 30)
• More testing tipso http://goc.pragma-grid.net/wiki/index.php/
User_Testingo Google
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Test Access to Each Site(Step 6)
• Test SSH– Find the target system name athttp://goc.pragma-grid.net/wiki/index.php/Site_status_and_tasks– Test SSH from your host system to the target host (should work)– Test SSH from your laptop to the remote host (May work)– Issues about firewall and site policies
• Test Globus authentication– From the system at your host site– To the target system
• Test job submission– From the system at your host site– To the target system
• Problem with any test– Save output– Check tips at
• http://goc.pragma-grid.net/wiki/index.php/User_Testing • Google
– Email site contact and cc [email protected]
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Process At A Glance
Laptop
platform
windows
MAC
Step 1.1
Install
Cygwin
Step 1.2
Create a
SSH key
Step 2
Email application Create
account on
rocks-200
PRIME Student Cindystart
Step 3 Test SSH,
Request certificateIssue
certificateStep 4
Retrieve certificate
Step 5
Test Globus authentication and job submission
confirmation
Step 6
Test SSH, Globus and job submission to each site
sites reply
Request
to all sites
PRIME Tutorial, 4/22/2009Prime Tutorial 4/22/2011Prime Tutorial 4/22/2011
Use PRAGMA Grid
• Information onlinegoc.pragma-grid.net member sites (hostname, contacts, user guide, …) computational grid (resource table, jobmanager, cpu
architecture, …) Applications (as examples) SCMSWeb (realtime system status, software catalog, etc.)wiki.pragma-grid.net For Users
• Ask questions (email, skype) Email, skype Site contact – always cc Cindy Looking for experts – ask Cindy If Cindy is not around, [email protected]