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Hands-On Session: Computing Element (CE) and site BDII Installation and Configuration

Hands-On Session: Computing Element (CE) and site BDII Installation and Configuration. Regional SEE-GRID-SCI Training for Site Administrators Institute of Physics Belgrade March 5-6, 2009. Dusan Vudragovic Institute of Physics Serbia dusan@scl.rs.

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Hands-On Session: Computing Element (CE) and site BDII Installation and Configuration

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  1. Hands-On Session:Computing Element (CE) and site BDII Installation and Configuration Regional SEE-GRID-SCI Training for Site Administrators Institute of Physics Belgrade March 5-6, 2009 Dusan Vudragovic Institute of Physics Serbia dusan@scl.rs The SEE-GRID-SCI initiative is co-funded by the European Commission under the FP7 Research Infrastructures contract no. 211338

  2. Overview A CE is a grid batch queuewith a “grid gate” front-end: Information system Job request L&B Logging Loc. Info system Gatekeeper A&A Grid gate node Local resource management system:Condor / PBS / LSF master Homogeneous set of worker nodes (WNs)

  3. OS installation & configuration • Newest Scientific Linux series 4 (currently 4.7) should be installed (not SL5) • Only 32-bit distribution is supported by lcg-CE and BDII_site so far • We have chosen to install all base packages from 5 SL4.7 CDs, then remove unnecessary • Packages with great chances not to be used should be removed to speed up future software updates, i.e. openoffice.org • Remove all LAM and OPENMPI packages, we'll be using MPICH • Remove java-1.4.2-sun-compat package! • Virtual environment is a possible solution

  4. Further OS tuning • Adjust services/daemons started at the boot time • it is recommended to change the default runlevel to 3 in /etc/inittab • disable yum auto-update, since this may bring trouble when new gLite updates appear • If you install MPI_CE, it is suggested to disable SELINUX by replacing “SELINUX=enforcing” with line “SELINUX=disabled” in the file /etc/selinux/config • Configure NTP service • Example of configuration file /etc/ntp.conf can be found on http://glite.phy.bg.ac.yu/GLITE-3/ntp.conf • touch /etc/ntp.drift /etc/ntp.drift.TEMP • chown ntp.ntp /etc/ntp.drift /etc/ntp.drift.TEMP • chkconfig ntpd on

  5. Repository adjustment • DAG repo should be enabled by changing "enabled=0" into "enabled=1" in /etc/yum.repos.d/dag.repo • Base SL repos must be PROTECTED, not allowing DAG packages to replace them! Add line “protect=1” to /etc/yum.repos.d/sl.repo and /etc/yum.repos.d/sl-errata.repo • Following new files must be created in /etc/yum.repos.d: • lcg-ca.repo (Certification authorities packs) • glite.repo (all gLite packages) • jpackage5.0.repo (java stuff) • contents of these files follow.....

  6. Repository adjustment • Local repository at SCL has been available since November 2008. Configuration files for the majority of repos can be found at http://rpm.scl.rs/yum.conf/

  7. File system import/export • Application software filesystem • All WNs must have shared application software filesystem where VO SGMs (software grid managers) will install VO-specific software. • If it's supposed to be located on CE itself, following (or similar) line must be appended to /etc/exports/opt/exp_soft 147.91.12.0/255.255.255.0(rw,sync,no_root_squash) • If you want to map application software filesystem from other node (usually SE), append this line to /etc/fstab:se.csk.kg.ac.yu:/opt/exp_soft /opt/exp_soft nfs hard,intr,nodev,nosuid,tcp,timeo=15 0 0Do not forget to create /opt/exp_soft directory! • Shared /home filesystem: • In order to provide appropriate MPI support, entire /home must be shared among WNs. • Procedure is equal to procedure for app. soft. filesystem

  8. gLite software installation • Valid host certificate must be present at /etc/grid-security • gLite software binaries, libraries and other stuff are organized using meta-package paradigm. In order to install necessary packages for lcg-CE/BDII node with MPI support, following packages must be installed: • glite-BDII • lcg-CE • glite-TORQUE_server • glite-TORQUE_utils • glite-MPI_utils • Due to temporary packaging inconsistency in glite-MPI_utils described in link, YUM command line must be: • yum install lcg-CE glite-BDII glite-TORQUE_server glite-TORQUE_utils glite-MPI_utils torque-2.1.9-4cri.slc4 maui-client-3.2.6p19_20.snap.1182974819-4.slc4 maui-server-3.2.6p19_20.snap.1182974819-4.slc4 maui-3.2.6p19_20.snap.1182974819-4.slc4 torque-server-2.1.9-4cri.slc4 torque-client-2.1.9-4cri.slc4

  9. SSH configuration • SSH must allow hostbased authentication between CE and WNs, as well as among WNs each other • This is especially important if grid site supports MPI • Helper script available in gLite can be found at/opt/edg/sbin/edg-pbs-knownhosts • Script configuration can be adjusted in/opt/edg/etc/edg-pbs-knownhosts.conf • Put all relevant FQDNs into /etc/ssh/shosts.equiv • This is standard procedure for hostbased SSH • Identical procedure applies to all WNs

  10. gLite configuration • All grid sevices must be configured properly using YAIM tool. Official info available at https://twiki.cern.ch/twiki/bin/view/LCG/YaimGuide400 • Templates for input YAIM files can be taken fromhttps://viewvc.scl.rs/viewvc/yaim/trunk/?root=seegrid • Since YAIM is mainly a set of bash scripts, bash-like syntax must be used in input files • Required input files are: • site-info.def • users.conf • wn-list.conf • groups.conf • directory vo.d with one file per VO • YAIM config. files must not be readable for users!

  11. gLite configuration • site-info.def • Main configuration input source • Contains proper paths to all other configuation files • users.conf • Defines UNIX pool users for each Virtual Organization • Helpful script at http://glite.phy.bg.ac.yu/GLITE-3/generate-pool-accounts-AEGIS-v4 • Example: ./generate-pool-accounts-AEGIS-v4 seegrid 20000 seegrid 2000 200 10 10 >> users.conf • groups.conf • Defines groups per VO, template can be employed as is. • wn-list.conf • Simple list of FQDNs of available Worker Nodes • vo.d/ • Directory containing a file per each supported VO.

  12. gLite configuration • Following http://wiki.egee-see.org/index.php/SEE-GRID_MPI_Admin_Guide ,/opt/globus/setup/globus/pbs.inshould be replaced withhttp://cyclops.phy.bg.ac.yu/mpi/pbs.in before YAIM invocation in order to force WN to use local scratch instead of shared /home for single CPU jobs • YAIM invocation command for lcg-CE/BDII_site combination with MPI support has to be:/opt/glite/yaim/bin/yaim -c -s /path/to/site-info.def -n MPI_CE -n lcg-CE -n TORQUE_server -n TORQUE_utils -n BDII_site • Note that MPI_CE has to be first in the line • In case that YAIM returns an error anywhere in the procedure, check data in site-info.def and other input files and restart YAIM

  13. MAUI post-configuration steps • Verify that /var/spool/maui/maui.cfg contains the following line:ADMIN3 edginfo rgma edguser tomcat • Reserve a node for SAM test jobs in MAUI:QOSCFG[qossam] MAXPROC=1 PRIORITY=100000GROUPCFG[prdseegrid] QDEF=qossam PRIORITY=100000GROUPCFG[sgmseegrid] QDEF=qossam PRIORITY=100000SRCFG[samreservation] TASKCOUNT=1RESOURCES=PROCS:1SRCFG[samreservation] PERIOD=INFINITYSRCFG[samreservation] GROUPLIST=prdseegrid,sgmseegridSRCFG[samreservation] HOSTLIST=rti18.etf.bg.ac.yuSRCFG[samreservation] QOSLIST=qossam • If maui.cfg is modified, restart it:/etc/init.d/maui restart

  14. VO support • SEEGRID VO • Install latest seegrid RPM available athttp://www.irb.hr/users/vvidic/seegrid/ • AEGIS VO • Put http://voms.phy.bg.ac.yu/voms.phy.bg.ac.yu.119into /etc/grid-security/vomsdir • ........

  15. Testing configured system • Verify local batching system • qmgr -c "print server" • Test if site properly provides info using GSTAT tool athttp://egee017.cnaf.infn.it/gstat/seegrid/ • GSTAT places delay of ~15mins, but up-to-date info can be obtained using simple ldap client: ldapsearch -x -H ldap://<SITE_BDII_FQDN>:2170 -b mds-vo-name=<SITE-NAME>,o=grid • Useful CE and SE info: • lcg-infosites --vo seegrid ce • lcg-infosites --vo seegrid se

  16. Helpful links • http://wiki.egee-see.org/index.php/SG_GLITE-3_Guide • http://wiki.egee-see.org/index.php/SL4_WN_glite-3.1 • http://wiki.egee-see.org/index.php/SEE-GRID_MPI_Admin_Guide • https://twiki.cern.ch/twiki/bin/view/EGEE/GLite31JPackage • https://twiki.cern.ch/twiki/bin/view/LCG/YaimGuide400

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