1. EUROPEAN UNION Polish Infrastructure for Supporting Computational Science in the European Research Space Ab initio grid chemical software ports – transferring knowledge from EGEE to Polish NGI M. Sterzel, P. Lasoń, Ł. Flis, K. Noga, Ł. Kitowski ACC CYFRONET AGH EGEE User Forum 5 Uppsala, 13 March 2010

2. 2 Outline  Aim of this talk Share 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

3. PL-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 3

4. EGEE – software installation models  A VO designated for software application  Gaussian  Turbomole  …  Storage of binaries in LFC catalogue  Direct installation of binaries in $VO_{VO-name}_SW_DIR  Direct compilation & execution  a package source file(s) sent to WN  compiled & executed on WN 4

5. Problems  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 5

6. Solution  Single VO – vo.plgrid.pl  Software installed on each site in admin’s favourite location  ACL for better permission control  Access 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 6

7. Modules... 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) 7

8. modulefile proc 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." } 8

9. module 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 commands  More information at: http://modules.sourceforge.net/ 9

10. An example 10

11. Parallel 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 } 11

12. Monitoring  Software packages are tested on each site supporting vo.plgrid.pl  Why 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 Support  At any time user can check current status of the tests  Currently SAM tests are implemented  A migration from SAM to PL-Grid Nagios is planned for near future 12

13. Monitoring 13

14. Monitoring  Typical test 14

15. Monitoring  Other tests 15

16. Summary  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 16

17. Questions? 17