SEE-GRID-SCI CE and BDII Hands-on Session Miloš Ivanović Research and Development Center for Bioengineering, Kragujevac Serbia The SEE-GRID-SCI initiative is co-funded by the European Commission under the FP7 Research Infrastructures contract no AEGIS Training for Site Administrators

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, Introduction OS installation & tunung Repository adjustment Java installation File system import/export gLite middleware packages installation SSH configuration gLite configuration Post-istallation tips Installed system testing

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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 sun-compat package! Virtual environment is a possible solution

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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 – touch /etc/ntp.drift /etc/ntp.drift.TEMP – chown ntp.ntp /etc/ntp.drift /etc/ntp.drift.TEMP – chkconfig ntpd on

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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.....

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, lcg-ca.repo [CA] name=CAs baseurl= enabled=1

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, glite.repo [glite-TORQUE_server] name=gLite Torque server baseurl= enabled=1 [glite-TORQUE_utils] name=gLite Torque utils baseurl= enabled=1 [glite-MPI_utils] name=gLite MPI utils baseurl= enabled=1 [lcg-CE] name=lcg CE baseurl= enabled=1 [glite-BDII] name=glite BDII baseurl= enabled=1

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, jpackage5.0.repo [main] [jpackage17-generic] name=JPackage 1.7, generic baseurl= enabled=1 protect=1 [jpackage17-generic-nonfree] name=JPackage 1.7, generic non-free baseurl= enabled=1 protect=1 [main] [jpackage5-generic] name=JPackage 5, generic baseurl= enabled=1 protect=1 [jpackage5-generic-nonfree] name=JPackage 5, generic non-free baseurl= enabled=1 protect=1

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, Repository adjustment Local repository at SCL has been available since November Configuration files for the majority of repos can be found at One should only copy appropriate *.repo files into /etc/yum.repos.d/, for example: – scl-glite-BDII.repo for BDII – scl-lcg-ca.repo for lcg-CA – scl-jpackage.repo for jpackage –... All necessary repos will be mirrored soon

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, Java installation Use latest Java 1.5! Follow advice from: or Alternative method is to install pre-built packages available at: using rpm -Uvh and rpm -Uvh 1jpp.i586.rpm

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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 / (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= Do 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

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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:link – yum install lcg-CE glite-BDII glite-TORQUE_server glite-TORQUE_utils glite-MPI_utils torque cri.slc4 maui-client-3.2.6p19_20.snap slc4 maui-server p19_20.snap slc4 maui-3.2.6p19_20.snap slc4 torque- server cri.slc4 torque-client cri.slc4

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, gLite configuration All grid sevices must be configured properly using YAIM tool. Official info available at Templates for input YAIM files can be taken from 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!

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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 – Example:./generate-pool-accounts-AEGIS-v4 seegrid seegrid >> 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.

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, gLite configuration Following /opt/globus/setup/globus/pbs.in should be replaced with 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

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, 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= GROUPCFG[prdseegrid] QDEF=qossam PRIORITY= GROUPCFG[sgmseegrid] QDEF=qossam PRIORITY= SRCFG[samreservation] TASKCOUNT=1 RESOURCES=PROCS:1 SRCFG[samreservation] PERIOD=INFINITY SRCFG[samreservation] GROUPLIST=prdseegrid,sgmseegrid SRCFG[samreservation] HOSTLIST=rti18.etf.bg.ac.yu SRCFG[samreservation] QOSLIST=qossam If maui.cfg is modified, restart it: /etc/init.d/maui restart

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, VO support SEEGRID VO – Install latest seegrid RPM available at AEGIS VO – Put into /etc/grid-security/vomsdir

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, Testing configured system Verify local batching system – qmgr -c "print server" Test if site properly provides info using GSTAT tool at GSTAT places delay of ~15mins, but up-to-date info can be obtained using simple ldap client: ldapsearch -x -H ldap:// :2170 -b mds-vo-name=,o=grid Useful CE and SE info: – lcg-infosites --vo seegrid ce – lcg-infosites --vo seegrid se

AEGIS Training for Site Administrators, Institute of Physics Belgrade, December 10-11, Helpful links 3_Guide 3_Guide GRID_MPI_Admin_Guide GRID_MPI_Admin_Guide kage kage