Globus-style Proxy Certificate + MyProxy credentials Windows

righteousgaggleData Management

Jan 31, 2013 (4 years and 6 months ago)

203 views


Web: www.omii.ac.uk Email: info@omii.ac.uk

Running applications on interoperable Grid
infrastructures, focusing on OMII
-
UK
supported software
-

HPC
-
BP Interoperability Tutorial

OGF28, Munich

s.crouch@omii.ac.uk


Steve Crouch
, David
Wallom
,
Matteo

Turilli
, Morris Riedel,
Shahbaz

Memon
,
Balazs

Konya, Gabor
Roczei
, Peter Stefan, Andrew
Grimshaw
,
Mark Morgan ,
Katzushige

Saga, Justin Bradley, Richard Boardman


Web: www.omii.ac.uk Email: info@omii.ac.uk

Objectives


To give participants practical experience of:

o
Using individual middleware clients to submit jobs to HPC
-
BP compliant services

o
Using the HPC
-
BP
interop

demo framework, used for
previous HPC
-
BP demos, to submit jobs to HPC
-
BP
compliant services


To give participants opportunity (and starting point)
to learn about:

o
Basic techniques and approaches for interoperability


what
do I need, and how can I do this?

o
Some of the limitations of standards support across
middlewares



what can’t I do?


Web: www.omii.ac.uk Email: info@omii.ac.uk

Tutorial Approach


‘Presentation
-
lite




Learn at your own pace via online web tutorial…


…or follow my lead



Pragmatic



Generous in terms of time



Tutorial remains available after OGF28



Ask for help!


Web: www.omii.ac.uk Email: info@omii.ac.uk

Schedule


Session 1: Using individual clients to invoke HPC
-
BP
services

o
Overview of the demo + demo, Introduction to
GridSAM

o
Download, Install and Configure
GridSAM


o
Submit a Trivial Compute
-
only JSDL Job to HPC
-
BP Compliant
Services

o
Download, Build and Configure the BES++ Client

o
Running the BES++ Client Against HPC
-
BP Compliant Services


Session 2: Using HPC
-
BP demo framework to invoke
multiple HPC
-
BP services simultaneously

o
Download, Install and Configure the Demo Framework

o
Running the Demo Against Multiple HPC
-
BP Compliant Services

o
The Demo in Detail: Adding Another Endpoint to the Demo


Web: www.omii.ac.uk Email: info@omii.ac.uk




The Interoperability Demonstrator


Web: www.omii.ac.uk Email: info@omii.ac.uk

Background


Motivation:

o
Researchers are often reaching the limits of locally available
resources to conduct research

o
They are beginning to realise the potential of using much larger
-
scale resources

o
Compute resources are becoming more numerous and available
across Europe


However, using different Grid middleware deployments
is traditionally difficult

o
Middleware clients for different deployments not compatible

o
Require different security policies/configuration for each


Web: www.omii.ac.uk Email: info@omii.ac.uk

Background


Possible solutions:

o
Maintain infrastructure that enables use of different clients for each
middleware


interoperation


Not scalable
-

user learning curve, operation and maintenance

o
Each middleware supports a common service interface, enabled through
adoption of accepted open standards


interoperability


Need only learn, use and maintain single client infrastructure


Still leaves security!



What can be practically achieved, in terms of interoperability, with
middlewares

that adopt OGF compute
-
related standards?

o
What is possible?

o
Limitations?


Demonstrate through proof
-
of
-
concept, client
-
side, application
-
focused demo



Web: www.omii.ac.uk Email: info@omii.ac.uk

History


Initiated by UK National
Grid Service, OMII
-
UK
and FZJ


Initially shown at OGF27,
Banff, Canada, Oct 09


SuperComputing
, Nov 09


ETSI
Plugtests
, FZJ, UK
AHM, Dec 09


GIN
-
CG, OGF28, Mar 10


Demonstrators: David
Wallom
, Peter Stefan,
Morris/
Shahbaz

Memon
,
Steve Crouch

Video available at
http://www.omii.ac.uk/wiki/Videos


Web: www.omii.ac.uk Email: info@omii.ac.uk

Compute Related Standards
-

OGF

Job Management

OGSA
-
BES

(GFD 108)

HPC Domain Specific Profile

HPC Basic Profile

(GFD 114)

Architecture

OGSA EMS Scenarios

(GFD 106)

Use Cases

Grid Scheduling Use Cases


(GFD 64)

Education

ISV Primer

(GFD 141)

Agreement

WS
-
Agreement

(GFD 107)

Programming Interface

DRMAA

(GFD 22/133)

Programming Interface

SAGA

(GFD 90)

Accounting

Usage Record

(GFD 98)

Information

GLUE Schema 2.0

(GFD. 147)

Job Definition

File Transfer

HPC File Staging

(GFD 135)

Job Description

JSDL

(GFD 56/136)

Application Description

HPC Application

(GFD 111)


Application Description

SPMD Application

(GFD 115)


Job Parameterization

Parameter Sweep

(GFD. 149)


Extend

Uses

Produces

Describes

Supports

Profiles


Web: www.omii.ac.uk Email: info@omii.ac.uk

Standards/Data Protocols/Security Supported


Standards:

o
HPC Basic Profile v1.0


OGSA BES (Basic Execution Service) v1.0


JSDL (Job Submission Description Language) v1.0


HPC Profile Application Extension v1.0

o
HPC File Staging Profile


UNICORE, GridSAM


Data protocols:

o
UNICORE, ARC, BES++


ftp

o
GridSAM


GridFTP


Security:

o
Direct middleware
-
> certificate CA trust (just import CAs)





Web: www.omii.ac.uk Email: info@omii.ac.uk

Participation


Currently:

o
DEISA/FZJ


UNICORE,
SuSE
, AMD 64
-
bit, 1 core

o
NorduGrid
/NIIF


ARC NOX Release,
Debian

Linux, i686, 16 core

o
UK NGS/OMII
-
UK


GridSAM
, Scientific Linux 4.7, AMD 64
-
bit, 256
core

o
NAREGI
-
NII/Platform Computing


BES++, 2 nodes


Coming soon:

o
University of Virginia Campus Grid


GENESIS2,
Ubuntu

Linux, i686, 8
core

o
POZNAN Supercomputing Centre


SMOA Computing



Platform Computing BES++ Client used as
interop

client


Web: www.omii.ac.uk Email: info@omii.ac.uk

Example Application: Plasma Charge Minimization


Provided by David
Wallom
, NGS


Undergraduate project


Total system energy minimization
of point charges around the
surface of a sphere


Three different applications

o
Pre processing


generate input files

o
Main processing


parallel distributed
processing

o
Post
-
processing


choose optimal
solution


Web: www.omii.ac.uk Email: info@omii.ac.uk

System Requirements


System requirements:

o
Linux
-

see the Linux client pre
-
requisites in
OMII
-
UK
Development Kit supported platforms

o
Sun Java JDK 1.6 or above

o
C compiler
-

gcc and related development libraries

o
Lexical analyser
-

flex

o
Parser generator
-

bison


Soon to appear on OGF Forge


hopefully by
end of week


Web: www.omii.ac.uk Email: info@omii.ac.uk

JSDL Template

<?xml version="1.0" ?>

<JobDefinition xmlns="http://schemas.ggf.org/jsdl/2005/11/jsdl">


<JobDescription>


<Application>


<HPCProfileApplication
xmlns="http://schemas.ggf.org/jsdl/2006/07/jsdl
-
hpcpa">


<Executable
>@MINEM_INSTALL_LOCATION@
/update_file</
Executable>


<Argument>input.txt</Argument>


<Argument>output.txt</Argument>


<Output>stdout.txt</Output>


<Error>stderr.txt</Error>


@OPTIONAL_WORKING_DIR_ELEMENT@


</HPCProfileApplication>


@OPTIONAL_JOBRESOURCE_CREDENTIAL@


</Application>



<DataStaging>


<FileName>input.txt</FileName>


<CreationFlag>overwrite</CreationFlag>


<Source>


<URI>
@INPUT_FILE_URI@
</URI>


</Source>


@OPTIONAL_HPCFSP_CREDENTIAL@


</DataStaging>


<DataStaging>


<FileName>output.txt</FileName>


<CreationFlag>overwrite</CreationFlag>


<Target>


<URI>
@OUTPUT_FILE_URI@
</URI>


</Target>


@OPTIONAL_HPCFSP_CREDENTIAL@


</DataStaging>

<DataStaging>


<FileName>stdout.txt</FileName>


<CreationFlag>overwrite</CreationFlag>


<Target>


<URI>
@STDOUT_FILE_URI@
</URI>


</Target>


@OPTIONAL_HPCFSP_CREDENTIAL@


</DataStaging>


<DataStaging>


<FileName>stderr.txt</FileName>


<CreationFlag>overwrite</CreationFlag>


<Target>


<URI>
@STDERR_FILE_URI@
</URI>


</Target>


@OPTIONAL_HPCFSP_CREDENTIAL@


</DataStaging>


</JobDescription>


</JobDefinition>


Web: www.omii.ac.uk Email: info@omii.ac.uk

Endpoint Configuration

# UNICORE interop config file

endpoint_file=unicore.xml

application_type=HPCProfileApplicatio
n

application_type_namespace=http://sc
hemas.ggf.org/jsdl/2006/07/jsdl
-
hpcpa

working_dir=

data_mode=ftp

data_input_base=ftp://zam1161v01.za
m.kfa
-
juelich.de:8004/ogf27/unicore

data_output_base=ftp://zam1161v01.za
m.kfa
-
juelich.de:8004/ogf27/unicore

minem_install=/tmp/minem

myproxy=no

hpcfsp=yes

hpcfsp_username=interopdata

hpcfsp_password=89zukunft()


auth_utoken=yes

auth_x509=yes

auth_x509_credential=auth/client.pem

auth_x509_keypass=not_used

auth_x509_cert_dir=auth/certificates

auth_utoken_username=ogf

auth_utoken_password=ogf



Web: www.omii.ac.uk Email: info@omii.ac.uk

How it Fits Together…


BES++

Client

UNICORE

GridSAM

ARC

FTP

GridFTP

FTP

Client

Job Service

Data Service

Minem

Application

minem
-
interop.pl

MyProxy

Minem

Minem

Minem

Security
Service

1. Create Minem input
files

1

2. Generate JSDLs from
template

2

7. Select best result

7

8. Generate/upload
image to web server

8

5. Monitor jobs until
completion

5

BES++

FTP

4. Submit JSDLs across
middlewares

4

6. Download output files

6

3. Upload input files

3

Minem


Web: www.omii.ac.uk Email: info@omii.ac.uk

The Demo…



Web: www.omii.ac.uk Email: info@omii.ac.uk

Future Work


Standards integration:

o
Integrate GENESIS II and SMOA Computing

o
Replacement of BES++ Client with SAGA


SAGA BES adapter currently in development!


Schedule across BES/non
-
BES endpoints (e.g.
Globus
)

o
GLUE2 (e.g. using OMII
-
UK
Grimoires

software)


Service discovery (static)


Dynamic allocation (dynamic)

o
Integrate CREAM
-
BES?


Security: ‘Static’ trust set up of security, proper VO set up?


Middleware client ‘audit’ of interoperability?

o
Leads to ability to configure and use different middleware HPC
-
BP clients…


Use of HARC for advance reservation


Clean up the code, upload to OGF Forge within GIN
-
CG


Participation very much an open process


if you wish to donate an
HPC
-
BP compliant endpoint, please let me know!


Web: www.omii.ac.uk Email: info@omii.ac.uk

Future Direction


Interface:

o
Workflow engine
integration


To replace/provide
alternative to the Perl
script


Taverna2 good candidate

o
Application abstraction


Use of endpoints:

o
Utilise production
-
level
deployments

o
Utilise production
-
level
security

Abstraction level

Utilise production
-
level
deployments

Now

Future


Web: www.omii.ac.uk Email: info@omii.ac.uk

Dissemination


Thanks to the OMII
-
UK publicity machine:

o
HPCWire
:
http://www.hpcwire.com/offthewire/European
-
Grid
-
Interoperability
-
Goes
-
Global
-
79343767.html


o
SuperComputing

Online:
http://www.supercomputingonline.com/latest/european
-
interoperability
-
goes
-
global


o
EGEE:
http://www.eu
-
egee.com/index.php?id=193&tx_ttnews[tt_news]=125&tx_ttnews[backP
id]=65&cHash=90bb3f97cc

o
http://www.d4science.eu/aggregator/sources/2?page=1


o
http://www.it
-
tude.com/grid_interoperability_eu.html


o
http://www.beliefproject.org/zero
-
in/zero
-
in
-
fourth
-
issue
-
emagazine/news


o
+ numerous OMII
-
UK website articles & UK NGS articles


Just type ‘European Interoperability Goes Global’ into
Google…


Web: www.omii.ac.uk Email: info@omii.ac.uk

GridSAM

OMII
-
UK

London e
-
Science Centre, Imperial
College, London

Institute of Computing Technology,
Chinese Academy of Sciences (Beijing)


Web: www.omii.ac.uk Email: info@omii.ac.uk

GridSAM Overview


What is
GridSAM

to the resource owners?

o
A web service to uniformly expose a computational resource


Condor (via local or SSH submission)


Portable Batch Scheduler (PBS) (via local or SSH submission)


Globus


Sun
GridEngine


Platform Load Sharing Facility (LSF)


Single machine through Fork or SSH

o
Acts as a client to these resources


What is
GridSAM

to end
-
users?

o
A means to access computational resources in an open standards
-
based
uniform way

o
A set of end
-
user command
-
line tools and client
-
side APIs to interact
with
GridSAM

Web Services


Submit and monitor compute jobs


Cross
-
protocol file transfer (
gsiftp
, ftp,
sftp
,
WebDav
, http, https, soon SRB,
iRODS
) via Commons
-
VFS (
http://sourceforge.net/projects/commonsvfsgrid
)



Web: www.omii.ac.uk Email: info@omii.ac.uk

Supported OGF Standards


OGSA Basic Execution Service (BES) v1.0


JSDL v1.0


HPC Basic Profile v1.0


HPC Profile Application Extension v1.0


HPC File Staging Profile v1.0


HPC Common Case Profile: Activity Credential
v0.1


JSDL SPMD Application Extension v1.0


Web: www.omii.ac.uk Email: info@omii.ac.uk

GridSAM


Publications & Enabled Activities

+ in 2009/2010


ICHEC Bioinformatics Portal, eSysBio,
NAREGI/RENKEI


Web: www.omii.ac.uk Email: info@omii.ac.uk

For Resource Owners…


Computational

Resource

Manager

DRM



One of:

PBS (Torque/OpenPBS/PBSPro)

LSF, Condor, Sun GridEngine,
Globus, Fork

GridSAM

Service

X509

certificate

Linux Many flavours:

RHEL 3,4,5, Fedora 7,8,
Scientific Linux 4

Java: JDK 1.5.0+

Linux +
Java

Tomcat/

Axis

Tomcat: 5.0.23, 5.0.28, 5.5.23

Axis: v1.2.1

Persistence provided by one of:

Hypersonic, PostgreSQL, or
existing MySQL


Web: www.omii.ac.uk Email: info@omii.ac.uk

For End
-
Users…


GridSAM

Service

JSDL

HTTPS/HTTP

WS
-
Security:

X509

User/Password

Service
Interface

Any/all of:

GridSAM native interface, OGSA
-
BES v1.0, HPC Basic Profile v1.0



MyProxy

(for
Globus
/

GridFTP
)

+ MyProxy

credentials

Windows/

Linux +
Java

GridSAM

Client

Many flavours:

RHEL 3,4,5, Fedora 7,8,
Debian, Ubuntu, Scientific
Linux 4, Windows XP,
Windows Vista

Java: JDK 1.5.0+

Axis

X509

certificate

Generic
BES/HPC
Basic Profile

Client

OSGA
-
BES

HPC Basic
Profile


Web: www.omii.ac.uk Email: info@omii.ac.uk

Open Community Development


GridSAM is Open Source,
Open Community
Development


GridSAM SourceForge project:

o
99.03% activity, 1 release/month

o
SVN source code repository

o
Developer & discuss mailing lists


http://sourceforge.net
/projects/gridsam/


Web: www.omii.ac.uk Email: info@omii.ac.uk

GridSAM e.g. with Condor


A staged event
-
driven architecture

o
Submission pipeline is constructed as a
network of stages

connected by
event queues

o
Each stage performs a specific action upon incoming events

Example Pipeline: Condor


Web: www.omii.ac.uk Email: info@omii.ac.uk

Planned Future Developments


For end
-
users:

o
Full support for JSDL Resource selection across PBS,
Globus
, Condor & Fork
DRMs

o
JSDL Parameter Sweep Extension

o
Support for SRB and
iRODS


For resource owners:

o
LCAS/LCMAPS support

o
Packaging option as a standalone, manually configurable
web archive (WAR) file


Direct PBS deployment throughout NGS sites


Web: www.omii.ac.uk Email: info@omii.ac.uk



The tutorial begins… all you need is to go to:


http://www.omii.ac.uk/wiki/HPCBPTutorial