EUROPEAN UNION

Polish InfrastructurePolish Infrastructurefor Supporting Computational Sciencefor Supporting Computational Science

in the European Research Spacein the European Research Space

Ab initioAb initio grid chemical software ports – grid chemical software ports – transferring knowledge from EGEEtransferring knowledge from EGEE

to Polish NGIto Polish NGI

M. SterzelM. Sterzel, P. Lasoń, Ł. Flis, K. Noga, Ł. Kitowski, P. Lasoń, Ł. Flis, K. Noga, Ł. KitowskiACC CYFRONET AGHACC CYFRONET AGH

EGEE User Forum 5

Uppsala, 13 March 2010

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OutlineOutline

Aim of this talkShare our experience concerning porting and installing scientific applications on Polish Grid Infrastructure

Parts of the talk topics PL-Grid EGEE – models of software installation Our implementation Modules package SAM software tests Final remarks

PL-GridPL-Grid

Consortium: Academic Computer Center Cyfronet AGH – Coordinator Poznań Supercomputing and Networking Center Wrocław Centre for Networking and Supercomputing Interdisciplinary Center for Math. and Computat. Modelling Academic Computer Center in Gdańsk

PL-Grid Project (2009-2012) Got funded March 2, 2009 (via European Structural Funds) Aims to provide the Polish scientific community with an IT

platform based on Grid computer clusters, enabling e-science research in various fields.

Web page: www.plgrid.pl

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EGEE – software installation modelsEGEE – software installation models

A VO designated for software application Gaussian Turbomole …

Storage of binaries in LFC catalogueDirect installation of binaries

in $VO_{VO-name}_SW_DIRDirect compilation & execution

a package source file(s) sent to WN compiled & executed on WN

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ProblemsProblems

A VO designated for software application Only one software package accessible Makes every admin headache when new application added User has to belong to many VOs

Storage of binaries in LFC catalogue More convenient but without care no protection for binaries

Direct installation of binaries

in $VO_{VO-name}_SW_DIR Convenient, but without care we can end up with several

instances of the same software in many places

Direct compilation & execution Useful for small program files only requires working compiler on WN

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SolutionSolution

Single VO – vo.plgrid.plSoftware installed on each site in admin’s favourite

locationACL for better permission controlAccess to each scientific application via Modules

package – software environment management$VO_VO_PLGRID_PL_SW_DIR/scripts contains

a series of shell related Modules configuration files: modules.{bash,tcsh,csh,zsh}

Site which installs software package for the first time provides a module file and SAM test for it

Extensive use of VOMS roles in special cases

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ModulesModules

... Modules – Software Environment Management

Package allows dynamic modification of a user's environment via modulefiles

Each modulefile contains the information needed to configure the shell for a given application

Once the Modules package is initialized, the environment can be modified on a per-module basis using the module command which interprets modulefiles

Modules can be loaded and unloaded dynamically All popular shells are supported System is useful in managing different versions of application(s)

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modulefilemodulefileproc ModulesHelp { } {

puts stderr "\tName: Turbomole”

puts stderr "\tURL http://www.turbomole.com"

puts stderr "\tProvides: dscf,grad,ridft,rdgrad,mpgrad,...”

puts stderr "\tLocal docs: file:\$TURBODIR/DOK”

}

module-whatis "Turbomole computational chemistry package, v6.1”

set TURBODIR /software/local/Turbomole/6.1/TURBOMOLE

setenv TURBODIR $TURBODIR

set TURBOARCH em64t-unknown-linux-gnu

setenv TURBOARCH $TURBOARCH

prepend-path PATH $TURBODIR/bin/$TURBOARCH:$TURBODIR/scripts

prepend-path LD_LIBRARY_PATH $TURBODIR/lib/$TURBOARCH

set curMod [module-info name]

if { [ module-info mode load ] } {

puts stderr " '$curMod' load complete."

}

if { [ module-info mode remove ] } {

puts stderr " '$curMod' unload complete."

}

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modulemodule command command

Load/unload program module: module add adf/adf2009 module rm adf

List all loaded modules: module list

List all available modules: module avail

Remove all loaded modules module purge

and other usefull commandsMore information at:

http://modules.sourceforge.net/

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An exampleAn example

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Parallel executionParallel execution

Modules enables easy support for parallel execution:

#

# check for PBS environment, load appropriate arguments ...

#

if { [info exists ::env(PBS_ENVIRONMENT)] } {

set PBSFILE $env(PBS_NODEFILE)

set NPROC [exec wc -l < $PBSFILE]

setenv NSCM $NPROC

} else {

set NPROC 1

setenv NSCM $NPROC

}

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MonitoringMonitoring

Software packages are tested on each site supporting

vo.plgrid.plWhy automated tests?

to avoid common mistakes (network drive not mounted, expired license, wrong permissions, etc.)

save time

Each test contains a short, application program specific, input file

Tests are checked frequently by First Line SupportAt any time user can check current status of the testsCurrently SAM tests are implementedA migration from SAM to PL-Grid Nagios is planned for

near future

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MonitoringMonitoring

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MonitoringMonitoring

Typical test

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MonitoringMonitoring

Other tests

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SummarySummary

We have provided a unified solution for porting and installing software applications in grid environment

The solution does not enforce any major changes in site’s politics' concerning software installation

Solution is convenient for users as they can access their software using just one command

Automated software tests help site administrators keep track of software packages operation

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Questions?

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