Christos Papachristos FORTH-ICS, Distributed Computing Systems Lab Crete, 19 th Jun 06 - 1 Procedures on how to enter the GRID Christos Papachristos ([email protected])

Christos PapachristosFORTH-ICS, Distributed Computing Systems Lab Crete, 19th Jun 06 - 1

Procedures on howto enter the GRID

Christos Papachristos([email protected])

Site Manager of theHG-05-FORTH and GR-04-FORTH-ICS nodes

Distributed Computing Systems Lab


Answers provided to…

• Who can apply for registration?• What is the registration procedure?

• Who should be contacted?• What are the Virtual Organizations?• What tools do I need and where can I find them?

• How do I submit jobs to the Grid?• What is the procedure of submitting jobs?• Tutorials on job submission.• Failed jobs. Who should be contacted?

• Where can I see the status of the Grid?• What does the infrastructure look like?• Is there any user support?• ..and some other Grid related issues.


Who can apply for registration?

The whole Greek research community• Universities• Technical Education Centers• Research Centers

The Eligible (global) Grid User Community is defined to be people from: • the academic research and education community;

• public funded bodies, institutes and research laboratories working in areas related to research and education;

• other bodies and organisations, such as commercial companies, who are collaborating on academic research and education with the above institutes.

EGEE Access Users Policy (AUP)


Registration procedure

1. Register yourself as a HellasGRID user

2. Get an account to a User Interface node (UI)

3. Acquire a digital certificate from your accredited National Certification Authority (CA)

4. Join an existing Virtual Organization (VO)


HellasGRID registration. Step 1

•The first step in order to enroll is to fill the User Registration form at the HellasGrid website

http://www.hellasgrid.gr/user-request

•This will send a notification to the User Support Team which will get in touch with you in order to clarify your needs and help you with your first steps in joining the EGEE Grid infrastructure.


Get a UI account. Step 2

In order to become a user of the EGEE Grid Infrastructure you should: • Gain access to a User Interface (UI) machine which hosts the required

client software for developing and running applications in the EGEE Grid

• A UI is a Linux box having the appropriate client software that will help you send and execute your applications in the Grid

The choices on how to obtain a UI account are:• Set up your own UI node

• Obtain access to a local UI, already installed in your organization hellasgrid-ui.ics.forth.gr. Send an email at

{cpapachr, hargikas}@ics.forth.gr

• Request for a UI account in the GRNET node


Get a UI account. Step 2.1

• In practice everyone can install and setup a UI with the required EGEE tools following the instructions in the LCG-2 Installation Guide.

• Also the Italian SA1 EGEE Activity has made available a package called UIPnP which can be installed in any Linux machine and turn it into a User Interface (you can even install it as a regular non-root user). Note though that it is pre-configured for accessing the Italian EGEE sites and some manual configuration steps are required at the moment in order to be useful for EGEE-SEE users (for instructions see How to customize UIPnP for SEE-VO).


Acquire a Digital Certificate. Step 3

In order to access the Grid you need a Digital Certificate.

First of all a fax has to be sent to the National Certification Authority (fax: 2310 99 43 09) with names and IDs.

Then:1. Login to your UI account and execute the following2. $grid-cert-request

1. The command will produce a .globus directory with 3 files: .globus/usercert.pem size=0.globus/usercert_request.pem size<>0.globus/userkey.pem size<>0

3. The user-cert-request.pem file has to be emailed to the HellasGrid-CA ([email protected]).


Acquire a Digital Certificate. Step 3.1

4. After you receive your signed certificate1. Overwrite the usercert.pem file with the signed certificate (e.g

#cp [email protected] /home/cpapachr/.globus/usercert.pem

5. Import your certificate to your email and web browsers1. Transform the certificate to pkcs12 format by executing the following

command in the UI: #openssl pkcs12 -in usercert.pem -inkey userkey.pem -export -out certkey.p12

2. Follow the instructions to import the certificate to the browser http://lcg.web.cern.ch/LCG/users/registration/load-cert.html

6. Return a signed email to the HellasGRID CA accepting the certificate.


Join an existing VO. Step 4

VO=Virtual Organization. A group of scientists with common research interests.

Most popular VOs can be found here,

https://lcg-registrar.cern.ch/virtual_organization.html

Most VOs are those of CERN dealing with experiments based on data that will be produced from the LHC (Large Hadron Collider) which will be fully operational in 2007.

In our region we have the SEE VO which is supported by 27 sites.

http://mon.egee-see.org


Our SEE VO

• In order to make life easier for the regional users, speed up and simplify the process of new application induction, SEE has established its own VO called SEE-VO.

• This VO will be the most adequate for SEE users that do not fit in any of the existing VOs.

• In order to request acceptance to the SEE-VO as a user you have to fill the following request form: https://www.grid.auth.gr/services/voms/SEE/request.php

• Please note that this page has to be visited using the browser on which you have already loaded your digital certificate otherwise the process cannot be completed.


Brief summary of the procedure…

grid-cert-request

UI CA

usercert-request.pem

Public key is signed andthe Certificate is issued

login

Usercert.pemFax your IDAcceptance email

Generate pkcs12 fileImport pkcs12 file into mailer/browser

%HOME/.globus/usercert-request.pem%HOME/.globus/userkey.pem%HOME/.globus/usercert.pem

Start using the GRID


Ready to use the infrastructure!


A simplified overview of a job workflow

UIJDL

ResourceResourceBrokerBroker

StorageStorageElementElement

ComputeComputeElementElement

Author.&Authen.

Input “sandbox”

Input “sandbox” + Broker Info

Output “sandbox”

Output “sandbox”

grid

-pro

xy-in

it








How do I submit jobs to the Grid?

• Create a proxy certificate

• Write your own .jdl file (JDL:Job Description Language file)

• Submit your job

• Retrieve the status of the job

• Get the output of the job


Step 1- Creating a proxy certificate

[cpapachr@hellasgrid-ui cpapachr]$ grid-proxy-init -debug -verify

User Cert File: /home/cpapachr/.globus/usercert.pem

User Key File: /home/cpapachr/.globus/userkey.pem

Trusted CA Cert Dir: /etc/grid-security/certificates

Output File: /tmp/x509up_u0

Your identity: /C=GR/O=HellasGrid/OU=ics.forth.gr/CN=Christos Papachristos

Enter GRID pass phrase for this identity:

Creating proxy ..++++++++++++

......++++++++++++

Done

Proxy Verify OK

Your proxy is valid until: Wed Jun 14 02:49:17 2006

[cpapachr@hellasgrid-ui cpapachr]$


Step 2 – Creating the JDL file

• test.jdl

• test.sh

Executable = "test.sh";StdOutput = "test.out";StdError = "test.err";InputSandbox = {"./test.sh"};OutputSandbox = {"test.out","test.err"};Requirements = other.GlueCEUniqueID=="grid001.ics.forth.gr:2119/jobmanager-lcgpbs-dteam";RetryCount = 0;

#!/bin/bashecho Hostname: `hostnameècho Working Directory: `pwdècho Running As: ìdècho Executed in: `dateècho Enviroment Variables: ènv`


Step 3 – Submitting the job

[cpapachr@hellasgrid-ui cpapachr]$ edg-job-submit --vo dteam test.jdl

Selected Virtual Organisation name (from --vo option): dteamConnecting to host rb.isabella.grnet.gr, port 7772Logging to host rb.isabella.grnet.gr, port 9002

********************************************************************************************* JOB SUBMIT OUTCOME The job has been successfully submitted to the Network Server. Use edg-job-status command to check job current status. Your job identifier (edg_jobId) is:

- https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQKeep this URL for further reference to the job already submitted

*********************************************************************************************

[cpapachr@hellasgrid-ui cpapachr]$


Step 4 – Querying the job status

[cpapachr@hellasgrid-ui cpapachr]$ edg-job-status https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQ

*************************************************************BOOKKEEPING INFORMATION:Status info for the Job : https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQCurrent Status: ScheduledStatus Reason: Job successfully submitted to GlobusDestination: grid001.ics.forth.gr:2119/jobmanager-lcgpbs-dteamreached on: Tue Jun 13 15:54:26 2006

Finally after a couple of minutes…

[cpapachr@hellasgrid-ui cpapachr]$ edg-job-status https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQ

*************************************************************BOOKKEEPING INFORMATION:Status info for the Job : https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQCurrent Status: Done (Success)Exit code: 0Status Reason: Job terminated successfullyDestination: grid001.ics.forth.gr:2119/jobmanager-lcgpbs-dteamreached on: Tue Jun 13 16:00:07 2006


Step 5 – Retrieving the results

[cpapachr@hellasgrid-ui cpapachr]$ edg-job-get-output https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQ

Retrieving files from host: rb.isabella.grnet.gr ( for https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQ )

********************************************************************************* JOB GET OUTPUT OUTCOME

Output sandbox files for the job: - https://rb.isabella.grnet.gr:9000/GgfNDFsgB0L3btK_2CRfKQ have been successfully retrieved and stored in the directory: /tmp/jobOutput/cpapachr_GgfNDFsgB0L3btK_2CRfKQ

*********************************************************************************


Tutorials on job submission

• The LCG-2 User Guide describing almost everything

https://edms.cern.ch/file/454439//LCG-2-UserGuide.html

• A small tutorial with information on JDL files and job submission

https://edms.cern.ch/file/498081//UserScenario2.pdf

• There is also MPI support (MPICH v1.2.5). A test example can be found here

http://quattor.web.lal.in2p3.fr/packages/mpi/


Failed job submissions

Who do I contact if my jobs fail?• GGUS system is the main user support framework.

https://gus.fzk.de/pages/home.php

• Contact via email as well:

<MyVO>[email protected] (<MyVO>=atlas, biomed, ...)

[email protected]


Monitoring the Grid

• Where can I see the status of the Grid?• The Grid Operations Centre (GOC) maintains a map with the overall state

of the grid and links to various monitoring pages.

• http://goc.grid-support.ac.uk/gridsite/monitoring/

• http://goc02.grid-support.ac.uk/googlemaps/lcg.html

• Our ROC also keeps track of the regional Grid resources of the SEE• http://goc.grid.sinica.edu.tw/gstat/SouthEasternEurope.html

• http://mon.egee-see.org/gridice/site/site.php


Monitoring services to check

• GridICE monitoring server

http://mon.egee-see.org

• General status of the Grid

http://goc.grid.sinica.edu.tw/gstat/

• Network latency monitoring

http://mon.egee-see.org/cgi-bin/smokeping.cgi


A closer look at the infrastructure

The HG-05-FORTH site


HG-05-FORTH

• Hardware• 60 nodes with dual Intel xeon

processors• 3.4GHz each• SATA disk 80GB

• 4 nodes with dual Intel xeon processors

• 3.4GHz each• 2 SCSI disks RAID (80GB

each)• 4.2TB of storage

(300GBx12disks)• 6 CISCO 3750 switches

• Software• 1 CE• 1 SE (SE_dpm_mysql)• 1 MON BOX• 1 Quattor• 60 WNs• GPFS on SE and quattor (storage)

All running:• LCG middleware v. 2_7_0• Operating System: SL3.05


User Support Team

Operated by NCSR “Demokritos” - Institute of Nuclear Physics (http://grid.inp.demokritos.gr/)

Responsibilities – To guide new users in their first steps in the Grid and provide continuous support in their activities.

Email ([email protected])

Wiki (http://wiki.egee-see.org/index.php/Users)

Mailing list ([email protected]) – Includes all registered grid users

Newsletter – Published every ~2 months in Greek. Provides local and EGEE-wide news update (http://grid.inp.demokritos.gr/indexegeenewsletter.htm)


For urgent matters

The site managers can be contacted.

{cpapachr, hargikas}@ics,forth.gr

Documents

Christos Papachristos FORTH-ICS, Distributed Computing Systems Lab Crete, 19 th Jun 06 - 1 Procedures on how to enter the GRID Christos Papachristos ([email protected])