bwgrid Treff MA/HD Sabine Richling, Heinz Kredel Universitätsrechenzentrum Heidelberg Rechenzentrum Universität Mannheim 19.

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1 bwgrid Treff MA/HD Sabine Richling, Heinz Kredel Universitätsrechenzentrum Heidelberg Rechenzentrum Universität Mannheim 19. January 2011 Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

2 Course Organization What is bwgrid Treff? Participants Current users of the bwgrid Clusters HD/MA Students and scientists interested in Grid Computing Members of the Universities Heidelberg and Mannheim Scope bwgrid Status and Plans Lectures and/or Workshops User contributions To meet you in person Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

3 bwgrid Treff History Course Organization Date Site Main Focus HD bwgrid Status and Interconnection HD/MA HD Batch-System and Parallel execution of serial jobs HD Parallel Programming with Java (Part I) HD Parallel Programming with Java (Part II) MA Matlab & Matlab Clones MA Statistics Software R HD Chemistry Software with Schrödinger Presentation HD Globus Toolkit Workshop Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

4 Course Organization bwgrid Treff 19. January 2011 Agenda for today: Status of the bwgrid Cluster MA/HD GLOBUS TOOLKIT WORKSHOP Installation of Globus Toolkit on your own computer Working at other bwgrid clusters Using the central bwgrid storage in Karlsruhe Discussion of topics for the next meetings Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

5 bwgrid News bwgrid Introduction Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

6 What is bwgrid? bwgrid News bwgrid Virtual Organization (VO) D-Grid Community project of the Universities in Baden-Württemberg VO bwgrid is open for all members of the participating Universities bwgrid Resources Compute clusters at 8 locations Central storage unit in Karlsruhe bwgrid Objectives Verifying the functionality and the benefit of Grid concepts for the HPC community in Baden-Württemberg Managing organisational, security, and license issues Development of new cluster and Grid applications Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

7 bwgrid News bwgrid Resources Compute cluster: Mannheim/Heidelberg: 280 nodes Direct Interconnection Frankfurt Karlsruhe: 140 nodes Stuttgart: 420 nodes Tübingen: 140 nodes Mannheim (interconnected to a single cluster) Heidelberg Ulm (Konstanz): 280 nodes Hardware in Ulm Karlsruhe Stuttgart Freiburg: 140 nodes Esslingen Esslingen: 180 nodes more recent Hardware Central storage: Freiburg Tübingen Ulm (joint cluster with Konstanz) München Karlsruhe: 128 TB (with Backup) 256 TB (without Backup) Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

8 bwgrid News bwgrid Cluster Mannheim/Heidelberg Configuration Belwue VORM Benutzer Benutzer PBS Benutzer Benutzer VORM LDAP Admin AD Cluster Mannheim InfiniBand Obsidian + ADVA passwd InfiniBand Cluster Heidelberg Lustre bwfs MA Lustre bwfs HD Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

9 bwgrid News Status of the bwgrid Cluster MA/HD Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

10 bwgrid News bwgrid Cluster Mannheim/Heidelberg Current Status bwgrid storage in Heidelberg Current temporary home directories No Backup! limited to 100 GB per user Workspaces for temporary data bwgrid storage in Mannheim Damaged old home directories Plan: Access open until 1. March 2011 Project descriptions for Many project description are missing Important: Publications!, coworkers, text, pictures, links Account still needed, if project is completed? Need more time? Please, inform us. Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

11 Globus Toolkit Workshop Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

12 Introduction Prerequisites for bwgrid Access DFN Grid certificate Membership in the VO bwgrid Grid Middleware client (Globus Toolkit) Information leaflet available at: HD: Zugangsmöglichkeiten MA: cluster Zugangsberechtigung Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

13 Introduction Access to bwgrid resources: How does it work? VOMRS 1. Registration with grid certificate 3. List with DNs (grid-mapfile) 2. Approves DN (= distinguished name) User VO 5. Access with Middleware Client Tools gsissh/gsiscp - GridFTP - Web Services 4. Preparations: Setup Middleware client Prepare certificate files Grid-Proxy for Single Sign-on 4. Preparations: Setup Middleware server Provide accounts for DNs Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

14 Introduction Middlewares at bwgrid resources Globus Toolkit Version recommended 4.0 release available at all bwgrid sites client should have the same version Planned: UNICORE 5.0/6.0, Globus Toolkit 5 In development: bwgrid Portal Web Access to bwgrid via different Middlewares Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

15 Introduction Globus Toolkit Workshop Agenda Installation of Globus Toolkit on your own computer Working at other bwgrid clusters Using the central bwgrid storage in Karlsruhe Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

16 Installation & Preparation Installation & Preparation Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

17 Installation & Preparation Installation of Globus Toolkit How to get Globus Toolkit? Login to your computer where you want to install Open Globus Toolkit web site: Menu: Globus Toolkit Download Stable Releases: Globus Toolkit Downloads Source Downloads: Full Toolkit Source Download Download page for gt4.0.8-all-source-installer.tar.bz2 Enter Survey Data Download and save file Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

18 Installation & Preparation Installation of Globus Toolkit How to build Globus Toolkit? Determine and make installation directory, e.g.: TARGET DIR="/home/user/opt/gt/4.0.8" mkdir -vp "$TARGET DIR" Unpack source and change to source directory: tar -jxvf gt4.0.8-all-source-installer.tar.bz2 cd gt4.0.8-all-source-installer Configure (Java is only needed for web services, ignore warnings):./configure --prefix "$TARGET DIR" Build and install: make gsi-openssh (sufficient for gsissh and gsiscp) make gridftp (necessary for globus-url-copy) make install Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

19 Installation & Preparation Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

20 Useful Globus Toolkit Commands Installation & Preparation Security Authentication & Authorization grid-proxy-init Generate a new proxy certificate grid-proxy-destroy Destroy the current proxy certificate grid-proxy-info Display proxy certificate information GSI-OpenSSH gsissh Secure remote login gsiscp Secure remote file copy gsisftp Secure file transfer Data Management GridFTP globus-url-copy Multi-protocol data movement Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

21 Installation & Preparation Preparations Part I Export your PKCS12 certificate from your browser. In Firefox: Edit Preferences Advanced Encryption View Certificates Your Certificates Backup... You will get a file named cert yourname.p12 for instance. Convert the private key of your certificate to the pem-format: openssl pkcs12 -in cert yourname.p12 \ -out userkey.pem -nocerts Convert the public key of your certificate to the pem-format: openssl pkcs12 -in cert yourname.p12 \ -out usercert.pem -clcerts -nokeys Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

22 Installation & Preparation Preparations Part II Copy the keys to a.globus directory in your home directory: mkdir -p $HOME/.globus mv userkey.pem usercert.pem $HOME/.globus/ Protect your certificate files: chmod -c 700 $HOME/.globus chmod -c 600 $HOME/.globus/user* Obtain and include CA certificates: mkdir -p $HOME/.globus/certificates cd $HOME/.globus/certificates wget " \ igtf/current/accredited/ \ igtf-preinstalled-bundle-classic.tar.gz" tar xvzf igtf-preinstalled-bundle-classic.tar.gz Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

23 Installation & Preparation Set Environment (for each session) Set environment variables (can be included in ḃashrc): export GLOBUS LOCATION=$TARGET DIR source $GLOBUS LOCATION/etc/globus-user-env.sh Create a grid-proxy-certificate: grid-proxy-init -debug The grid-proxy-certificate expires after 12 hours. To inquire an existing grid-proxy-certificate: grid-proxy-info Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

24 Working at other bwgrid clusters Working at other bwgrid clusters Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

25 Working at other bwgrid clusters bwgrid compute clusters Addresses ( Benutzerinformationen Zugang): Mannheim/Heidelberg: gtbw.grid.uni-mannheim.de Ulm/Konstanz: koios.rz.uni-ulm.de Stuttgart: gridway.dgrid.hlrs.de Freiburg: globus.bfg.uni-freiburg.de Tübingen: gt4.uni-tuebingen.de Karlsruhe: bwgrid-cluster.scc.kit.edu Esslingen: grid01.hs-esslingen.de Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

26 Working at other bwgrid clusters Connection to bwgrid sites To connect to a globus toolkit server: gsissh -p 2222 gt servername Option -X for X forwarding Options -v or -vv for more information in case of errors Example: Connect and gain site information gsissh -p 2222 bwgrid-cluster.scc.kit.edu Note login messages: Dokus, Support, News Conditions for using bwgrid: man bw-grid Available software modules: module avail Batch class limits: qstat -q Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

27 Working at other bwgrid clusters File Transfer to and from bwgrid sites To transfer files to a globus server: gsiscp -P 2222 local file gt servername: To fetch files from a globus server: gsiscp -P 2222 gt servername:remote file. Takes normal scp options Between globus servers option -P 2222 not necessary Example: Connect, copy files and run example job gsissh -p 2222 bwgrid-cluster.scc.kit.edu gsiscp -r gtbw.grid.uni-mannheim.de:\ /opt/bwgrid/mpi/openmpi/1.4.2-gnu-4.1/examples. cd examples module load mpi/openmpi/1.4.2-gnu-4.1 mpicc hello.c -o hello qsub bwgrid-mpi.pbs qstat Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

28 Central bwgrid Storage in Karlsruhe Central bwgrid Storage in Karlsruhe Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

29 Central bwgrid Storage in Karlsruhe bwgrid Storage Configuration 2 File Systems: Backup (/bwfs/backup), 128 TByte (with Backup) Restore request via ticket at Work (/bwfs/work), 256 TByte (without Backup) User documentation: Common address bwgrid-se.scc.kit.edu for 6 access nodes bwgrid-se[1-6].scc.kit.edu (10GE) gsissh and gridftp (faster) Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

30 Central bwgrid Storage in Karlsruhe bwgrid Storage Configuration Schema des zentralen Storage BelWü Dateisystem Kapazität Schreibdurchsatz backup 128 TB 1500 MB/s work 256 TB 3700 MB/s Lesedurchsatz 1900 MB/s 4200 MB/s Gateway Gateway Gateway Gateway Gateway Gateway InfiniBand DDR Interconnect MGS MDS OSS OSS MGS MDS OSS OSS OSS OSS OSS OSS Zentrales Storage Element für bwgrid (R. Laifer, O. Schneider, A. Trunov) Steinbuch Centre for Computing Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

31 Central bwgrid Storage in Karlsruhe bwgrid Storage Example Login: gsissh -p 2222 bwgrid-se.scc.kit.edu Home directory is in Backup file system: pwd Link to Work file system is available: ll work Copy job result to work file system of the bwgrid storage: From cluster to storage with gsiscp: gsiscp bwgrid-mpi.oxxx bwgrid-se.scc.kit.edu:work/ From cluster to storage with gridftp: globus-url-copy file:$home/examples/bwgrid-mpi.oxxx \ gsiftp://bwgrid-se.scc.kit.de:2811/~/work/ Whole directory from cluster to storage with gridftp: globus-url-copy -r -cd file:$home/examples/ \ gsiftp://bwgrid-se.scc.kit.de:2811/~/work/examples/ Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

32 Further Meetings Further Meetings Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

33 Further Meetings bwgrid Treff Further Meetings Date Site Main Focus HD bwgrid Status and Interconnection HD/MA HD Batch-System and Parallel execution of serial jobs HD Parallel Programming with Java (Part I) HD Parallel Programming with Java (Part II) MA Matlab & Matlab Clones MA Statistics Software R HD Chemistry Software with Schrödinger Presentation HD Globus Toolkit Workshop Feb 2011 HD??? Mar 2011 MA??? Apr 2011 MA??? Richling/Kredel (URZ/RUM) bwgrid Treff WS 2010/ / 33

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