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Student Challenge

Contents

Build Lifemapper Biodiversity Infrastructure

Use VirtualBox Rocks Cluster images to install and run Lifemapper on your laptop. The main steps are :

  1. Install VirtualBox on your laptop
  2. Download VM image for cluster frontend
  3. Import VM into VirtualBox. Change VM settings for shared folders based on your laptop folders availability. Change VM settings for Virtual memory based on your laptop memory. The VM is set for 2Gb (and works with 2Gb), a better setting is 4Gb.
  4. Download lifemapepr-server ISO image. Make it available in the folder on your laptop that will be used as a shared folder by your VM.
  5. Start VM and login as root
  6. Install Lifemapper server roll - see section below
  7. Start using Lifemapper server roll - see section below

Downloads

All the downloads that you need for the challenge are av ailable from the PRAGMA 27 Challenge site and include

  1. rocks611.ova - cluster frontend virtual image
  2. lifemapper-server-6.1.1-0.x86_64.disk1.iso - lifemapper-server roll. This is an ISO image that inlcudes all needed lifemapepr server software and configuration.
  3. Instructions about VirtualBox installation and setup.

Optional

  1. rocks611-compute-0-0.ova - cluster compute node virtual image. This image is not needed for lifemapepr server to work but gives one an opportunity to explore the whole cluster setup.

Install Lifemapper roll

A roll can be added to the existing frontend. Assume that your downloaded lifemapper-server ISO is available in the folder that is mounted as data1. This means that on the VM the directory with the ISO is /media/sf_data1

Check the ISO md5sum signature:

# md5sum /media/sf_data1/lifemapper-server-6.1.1-0.x86_64.disk1.iso

The output should be:

fe77b42373910eafc3db243aca70d596 /media/sf_data1/lifemapper-server-6.1.1-0.x86_64.disk1.iso

If you see a different signature it means the ISO is corrupted and needs to be downloaded anew.

Execute all commands below to install the roll:

# rocks add roll /media/sf_data1/lifemapper-server-6.1-0.x86_64.disk1.iso
# rocks enable roll lifemapper-server
# (cd /export/rocks/install; rocks create distro)
# yum clean all
# rocks run roll lifemapper-server > add-roll.sh

The last command creates a script add-roll.sh in your current directory. The scirpt contains all the commands that will be executed on the system to install the roll software. Examine the scirpt and then run it :

# bash add-roll.sh  > add-roll.out 2>&1

After the command is finished, examine the add-roll.out file for errors and then reboot your frontend:

# reboot

The reboot is needed to run a few initialization commands. After the frontend boots up login as root and check the /tmp/lifemapper-config.log file to check the status of initialization commands.

Using Lifemapper roll

After the roll install is completed the frontend is ready and configured as for Lifemapepr LmDbServer and LmWebServer components. To use the roll and run lifemapper-specific commands for pipeline initialization and data seeding, see Using Lifemapper

Info: where installed roll components are

This section outlines where installed lifemapper servers components are installed and where to expect log files.

  1. Created user lmwriter
  2. Add user apache to lmwriter group
  3. Created rocks attributes LM_dbserver and LM_webserver, both set to true. Currently dbserver and webserver are installed on the same host - setting true means host's FQDN is used for configurations where needed. These attributes will be used in the future for possible separation of servers to different hosts.
  4. /opt/lifemapper - prerequisites and lifemapper code
  5. /opt/lifemapper/rocks - scripts, templates, etc for installation management. Reequires root access for most.
  6. /opt/python/lib/python2.7/site-packages - python prerequisites
  7. /etc/ld.so.conf.d/lifemapper-server.conf - dynamic linker bindings
  8. /etc/httpd/conf.d/lifemapper.conf - apache configuration
  9. /etc/profile.d/lifemapper.[sh,csh] - environment settings for all users
  10. /etc/yum.repos.d - epel and pgdg yum repos
  11. cmake, screen, fribidi, hdf4*, hdf5*, mapserver, readline-devel, byacc, giflib-devel, bitstrieam-vera-*fonts*, json-c, uuid - in usual system directories /usr/bin, /usr/lib, /usr/include, etc. as required by each RPM. Use rpm -ql X to find all files for a package X.
  12. Postgres
    • Created user/group postgres
    • /usr/pgsql-9.1 and /usr/share/doc - postgres and postgis_2
    • /var/run/postgresql/ - postgres daemon socket files
    • /etc/init.d/postgresql* - init script
    • /var/lib/pgsql/ - database, backups, log, pid
    • /etc/sysctl.d/postgresd - modification for memory usage
  13. Pgbouncer
    • Created user/group pgbouncer, add user pgbouncer to postgres group
    • /etc/pgbouncer/ - authentication
    • /etc/logrotate.d/pgbouncer - logrotate script
    • /etc/sysconfig/pgbouncer, /usr/share/* - pbbouncer. Use rpm -ql pgbouncer to list all files.
    • /var/run/postgresql/ - pgbouncer socket file
    • /etc/init.d/pgbouncer - init script
    • /var/log/pgbouncer.log - log
    • /var/run/pgbouncer.pid - pid
  14. /state/partition1/lmserver/ - mounted as /share/lmserver/
    • /share/lmserver/data/ - ClimateData/, ESRIDATA/, image/, models/, species/.
    • /share/lmserver/log/ - pipeline logs. Alos available via link /opt/lifemapper/log
  15. /var/lib/lm2/ - pylucene index and sessions
  16. /var/www/tmp/ - for mapserver temp files