XNAT System Administration Chip Schweiss June 26, 2012

XNAT System Administration 1.System Requirements 2.Java, Tomcat & PostgreSQL Essentials 3.Scaling Vertically & Horizontally 4.An Automation Demonstration with VMware and Puppet 5.ZFS file system 6.Network Monitoring

XNAT System Requirements Highly dependent on size of data set and volume of users Highly dependent on size of data set and volume of users Minimum for a working build: Minimum for a working build: – 2 GB free RAM – Tomcat 6 on Java 6 – PostgreSQL 9.0 (9.1 not yet supported)

XNAT System Requirements Two Examples: 1.CNDA – A large instance with many users 2.XNAT Central – Small instance with light usage

CNDA – System Specifications Hosted on our VMware vSphere 5 cluster Hosted on our VMware vSphere 5 cluster – 3.46 GHz Core i7 hex core CPUs – 10 GbE – BlueArc 15k SAS pool NFS backing CNDA Virtual Machine CNDA Virtual Machine – 8 vCPU – 20 GB ram fully reserved – 20 GB vmdk Separate VM for PostgreSQL Separate VM for PostgreSQL

CNDA - System Specifications NAS File Storage 34 TB BlueArc NL-SAS + 34 TB BlueArc on DR site 34 TB BlueArc NL-SAS + 34 TB BlueArc on DR site 45 TB ZFS backup 45 TB ZFS backup Sun Grid Engine Processing Cluster core i7 2.4 GHz systems w/ 8 GB ram core i7 2.4 GHz systems w/ 8 GB ram 6 – 8 vCPU virtual machines w/ 16 GB ram 6 – 8 vCPU virtual machines w/ 16 GB ram Supporting VMs Shadow for database related processing Shadow for database related processing Files system shadow for cron triggered reporting Files system shadow for cron triggered reporting Development VMs Development VMs

XNAT Central – System Specifications XNAT Central Virtual Machine 4 vCPU 4 vCPU 4 GB ram 4 GB ram Separate PostgreSQL virtual machine NAS File Storage 2 TB BlueArc + 2 TB BlueArc DR 2 TB BlueArc + 2 TB BlueArc DR 3 TB ZFS Backup 3 TB ZFS Backup

Java, Tomcat & PostgreSQL Essentials Java & Tomcat: Memory settings Memory settings – Xmx Maximum memory allocation Maximum memory allocation – Xmn Minimum allocation Minimum allocation Set to 1/5 Xmx Set to 1/5 Xmx – Xms Initial heap size Initial heap size Set to 1/3 Xmx Set to 1/3 Xmx – XX:MaxPermSize Permanent memory allocation for classes & libraries Permanent memory allocation for classes & libraries Set to 256m for XNAT Set to 256m for XNAT

Java & Tomcat Additional configuration: Debugging w/ Eclipse Debugging w/ Eclipse-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8000 Running on port 80/443 with modjk server.xml: <Host name="localhost" appBase="/var/lib/tomcat6/webapps/empty" Running on port 80/443 with modjk server.xml: <Host name="localhost" appBase="/var/lib/tomcat6/webapps/empty" unpackWARs="true" autoDeploy="true" unpackWARs="true" autoDeploy="true" xmlValidation="false" xmlNamespaceAware="false"> xmlValidation="false" xmlNamespaceAware="false"> <Resource name="UserTransaction" auth="Container“ <Resource name="UserTransaction" auth="Container“ type="javax.transaction.UserTransaction" type="javax.transaction.UserTransaction" factory="org.objectweb.jotm.UserTransactionFactory“ factory="org.objectweb.jotm.UserTransactionFactory“ jotm.timeout="60"/> jotm.timeout="60"/>

DICOM Port Java on Linux does not support listening on ports < 1024 unless running as root IP Tables makes an easy work around: iptables –t nat –I PREROUTING –p tcp \ --dport 104 \ --dport 104 \ -j DNAT –-to-destination :8104 -j DNAT –-to-destination :8104

PostgreSQL Tuning Performance parameters: max_connections = 100 max_connections = 100 shared_buffers = xxxMB shared_buffers = xxxMB – ¼ memory available work_mem = xxxMB work_mem = xxxMB – Typically 50 to 80 MB maintenance_work_mem = xxxMB maintenance_work_mem = xxxMB – Typically 128 to 250 MB effective_cache_size = xxxMB effective_cache_size = xxxMB – ½ memory available

Scaling Vertically & Horizontally Reasons to Scale Vertically Reasons to Scale Vertically – More users – Higher activity level – Real-time processing Reasons to Scale Horizontally Reasons to Scale Horizontally – Pipeline processing – Scheduled jobs

Automated Demonstration Development, Test and Production Cycles VMware vSphere VMware vSphere Puppet Puppet ZFS ZFS

ZFS File System Developed by Sun Microsystems Developed by Sun Microsystems Highly scalable file system Highly scalable file system – Scales in performance with SSD read and write caches – Scales to Exabyte file system sizes Snapshots, compression, deduplication Snapshots, compression, deduplication Writeable clones of snapshots Writeable clones of snapshots Extremely efficient backups with ZFS send/receive Extremely efficient backups with ZFS send/receive Multiple OS support Multiple OS support – OpenIndiana: maintained fork of OpenSolaris – FreeBSD – ZFS on Linux – Oracle Solaris

Network Health Monitoring Preferred tools vCenter vCenter Nagios Nagios Pingdom Pingdom Spiceworks Spiceworks

Useful links Our ZFS Backup Server Our ZFS Backup Server Build Java RPMs for RHEL/Centos Build Java RPMs for RHEL/Centos Scale PostgreSQL horizontally Scale PostgreSQL horizontally Puppet Puppet Apache Redirect HTTP to HTTPS using mod_rewrite Apache Redirect HTTP to HTTPS using mod_rewrite OpenIndiana OpenIndiana ZFS on Linux ZFS on Linux Spiceworks Spiceworks VMware Perl Scripts VMware Perl Scripts