separation from lifemapper roll

Makefile

@@ -0,0 +1,64 @@
+#
+# $Id$
+#
+# @Copyright@
+# 
+# 				Rocks(r)
+# 		         www.rocksclusters.org
+# 		         version 5.6 (Emerald Boa)
+# 		         version 6.1 (Emerald Boa)
+# 
+# Copyright (c) 2000 - 2013 The Regents of the University of California.
+# All rights reserved.	
+# 
+# Redistribution and use in source and binary forms, with or without
+# modification, are permitted provided that the following conditions are
+# met:
+# 
+# 1. Redistributions of source code must retain the above copyright
+# notice, this list of conditions and the following disclaimer.
+# 
+# 2. Redistributions in binary form must reproduce the above copyright
+# notice unmodified and in its entirety, this list of conditions and the
+# following disclaimer in the documentation and/or other materials provided 
+# with the distribution.
+# 
+# 3. All advertising and press materials, printed or electronic, mentioning
+# features or use of this software must display the following acknowledgement: 
+# 
+# 	"This product includes software developed by the Rocks(r)
+# 	Cluster Group at the San Diego Supercomputer Center at the
+# 	University of California, San Diego and its contributors."
+# 
+# 4. Except as permitted for the purposes of acknowledgment in paragraph 3,
+# neither the name or logo of this software nor the names of its
+# authors may be used to endorse or promote products derived from this
+# software without specific prior written permission.  The name of the
+# software includes the following terms, and any derivatives thereof:
+# "Rocks", "Rocks Clusters", and "Avalanche Installer".  For licensing of 
+# the associated name, interested parties should contact Technology 
+# Transfer & Intellectual Property Services, University of California, 
+# San Diego, 9500 Gilman Drive, Mail Code 0910, La Jolla, CA 92093-0910, 
+# Ph: (858) 534-5815, FAX: (858) 534-7345, E-MAIL:[email protected]
+# 
+# THIS SOFTWARE IS PROVIDED BY THE REGENTS AND CONTRIBUTORS ``AS IS''
+# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+# PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS
+# BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
+# BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
+# OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN
+# IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+# 
+# @Copyright@
+#
+# $Log$
+#
+
+-include $(ROLLSROOT)/etc/Rolls.mk
+include Rolls.mk
+
+default: roll

README.md

@@ -1,4 +1,45 @@
-lifemapper-server
-=================
+LifeMapper Server roll
+=======================
+
+This roll installs lmserver and lmweb parts of Lifemapper
+
+Installing LMserver
+-------------------
+
+**Prerequisites**  
+  * *install repos from RPM:* elgis, pgdg91
+  * *yum base repo:* cmake, subversion, sqlite-devel, giflib-devel, byacc, readline-devel 
+  * *yum rpmforge repo:* hdf4, hdf4-devel, hdf5, hdf5-devel
+  * *yum epel repo:* fribidi, json-c
+  * *yum elgis repo:* mapserver 
+  * *yum pgdg91 repo:* postgresql91, postgresql91-devel, postgis2_91, pgbouncer
+  * *build from source:* libspatialindex, geos, ant, mod_python, gdal
+  * *build python modules from source:* numexpr, Cheetah, CherryPy, Cython, pytables, egenix-mxDateTime, setuptools, rtree, pylucene, psycopg2, MySQL-python, faulthandler
+
+  **repos download:**  
+    wget http://yum.postgresql.org/9.1/redhat/rhel-6-x86_64/pgdg-centos91-9.1-4.noarch.rpm  
+    wget http://elgis.argeo.org/repos/6/elgis-release-6-6_0.noarch.rpm  
+
+  **source download:**  
+    wget http://download.osgeo.org/geos/geos-3.4.2.tar.bz2  
+    wget http://www.cython.org/release/Cython-0.20.tar.gz  
+    wget http://sourceforge.net/projects/pytables/files/pytables/3.1.0/tables-3.1.0rc2.tar.gz  
+    wget http://download.osgeo.org/libspatialindex/spatialindex-src-1.8.1.tar.gz  
+    wget http://www.poolsaboveground.com/apache/lucene/pylucene/pylucene-4.5.1-1-src.tar.gz  
+    wget http://download.cherrypy.org/cherrypy/3.1.2/CherryPy-3.1.2.tar.gz  
+    wget http://mirror.metrocast.net/apache//ant/source/apache-ant-1.9.3-src.tar.gz  
+    wget http://dist.modpython.org/dist/mod_python-3.5.0.tgz  
+    wget --no-check-certificate https://pypi.python.org/packages/source/n/numexpr/numexpr-2.3.tar.gz  
+    wget --no-check-certificate https://downloads.egenix.com/python/egenix-mx-base-3.2.7.tar.gz  
+    wget --no-check-certificate http://pypi.python.org/packages/source/s/setuptools/setuptools-2.1.tar.gz  
+    wget --no-check-certificate  https://pypi.python.org/packages/source/R/Rtree/Rtree-0.7.0.tar.gz  
+    wget --no-check-certificate  https://pypi.python.org/packages/source/p/psycopg2/psycopg2-2.5.2.tar.gz  
+    wget --no-check-certificate https://pypi.python.org/packages/source/M/MySQL-python/MySQL-python-1.2.5.zip  
+    wget --no-check-ertificate https://pypi.python.org/packages/source/C/Cheetah/Cheetah-2.4.4.tar.gz  
+    wget --no-check-certificate https://pypi.python.org/packages/source/f/faulthandler/faulthandler-2.3.tar.gz  
+    wget --no-check-certificate https://pypi.python.org/packages/source/R/Rtree/Rtree-0.7.0.tar.gz
+
+  **RPMs download:**  
+    wget ftp://ftp.pbone.net/mirror/atrpms.net/el6-x86_64/atrpms/stable/bitstream-vera-sans-fonts-1.10-18.el6.noarch.rpm  
+    wget ftp://ftp.pbone.net/mirror/atrpms.net/el6-i386/atrpms/stable/bitstream-vera-fonts-common-1.10-18.el6.noarch.rpm  
 
-Lifemapper lmserver and lmweb 

bootstrap.sh

@@ -0,0 +1,34 @@
+#!/bin/bash
+
+# Create prerequisites for building  lmserver dependencies
+
+. /opt/rocks/share/devel/src/roll/etc/bootstrap-functions.sh
+
+# add pgdg repo: need for installing postgresql and postgis2 rpms
+(cd src/RPMS; rpm -i pgdg-centos91-9.1-4.noarch.rpm)
+
+# for mapserver
+yum --enablerepo base install cmake
+(cd src/RPMS; \
+	rpm -i elgis-release-6-6_0.noarch.rpm; \
+	rpm -i bitstream-vera-fonts-common-1.10-18.el6.noarch.rpm; \
+	rpm -i bitstream-vera-sans-fonts-1.10-18.el6.noarch.rpm;\
+)
+echo "/usr/java/latest/jre/lib/amd64" > /etc/ld.so.conf.d/lifemapper-server.conf
+echo "/usr/java/latest/jre/lib/amd64/server" >> /etc/ld.so.conf.d/lifemapper-server.conf
+/sbin/ldconfig
+
+# for building PyLucene 
+compile_and_install ant
+(cd src/pylucene;  make install_jcc)
+
+# for building pytables 
+compile_and_install cython 
+compile_and_install numexpr 
+yum --enablerepo rpmforge install hdf5 hdf5-devel
+
+# for building psycopg
+compile_and_install gdal
+/sbin/ldconfig
+yum install postgresql91
+

graphs/default/lifemapper-server.xml

@@ -0,0 +1,38 @@
+<?xml version="1.0" standalone="no"?>
+
+<graph>
+
+	<description>
+
+	The lifemapper Roll
+
+	</description>
+
+	<copyright>
+	Copyright (c) 2000 - 2012 The Regents of the University of California.
+	All rights reserved. Rocks(r) v5.5/v6.0 www.rocksclusters.org
+
+	</copyright>
+
+	<changelog>
+	$Log$
+	</changelog>
+
+
+	<!-- for lmserver -->
+        <edge from="server" to="lifemapper-lmserver" cond="lmserver"/>
+        <edge from="server" to="lifemapper-server-base" cond="lmserver"/>
+
+        <order head="lifemapper-server-base">
+                <tail>lifemapper-lmserver</tail>
+        </order>
+
+	<!-- for lmweb -->
+        <edge from="server" to="lifemapper-lmweb" cond="lmweb"/>
+        <edge from="server" to="lifemapper-server-base" cond="lmserver"/>
+
+        <order head="lifemapper-server-base">
+                <tail>lifemapper-lmweb</tail>
+        </order>
+
+</graph>

nodes/lifemapper-lmserver.xml

@@ -0,0 +1,43 @@
+<?xml version="1.0" standalone="no"?>
+
+<kickstart>
+
+
+	<description>
+	Lifemapper-server roll.
+	LMserver installation 
+	</description>
+
+	<copyright>
+	Copyright (c) 2000 - 2012 The Regents of the University of California.
+	All rights reserved. Rocks(r) v5.5/v6.0 www.rocksclusters.org
+
+	</copyright>
+
+	<changelog>
+	$Log$
+	</changelog>
+
+        <package>mysql</package>
+        <package>mysql-devel</package>
+        <package>opt-MySQL-python</package>
+        <package>libxslt</package>
+        <package>lifemapper-spatialindex</package>
+
+<post>
+
+#yum install postgis2_91
+#yum --enablerepo epel fribidi
+#yum install mapserver
+
+# set mode to strict (2) to prevent postgres being killed  by OOM 
+/sbin/sysctl -w vm.overcommit_memory=2
+
+# may need this later for postgres tuning 
+# rocks set network mtu public 9000
+# rocks sync host network `hostname -s`
+
+
+</post>
+
+</kickstart>

nodes/lifemapper-lmweb.xml

@@ -0,0 +1,39 @@
+<?xml version="1.0" standalone="no"?>
+
+<kickstart>
+
+
+	<description>
+	Lifemapper-server roll.
+	LMweb install 
+	</description>
+
+	<copyright>
+	Copyright (c) 2000 - 2012 The Regents of the University of California.
+	All rights reserved. Rocks(r) v5.5/v6.0 www.rocksclusters.org
+
+	</copyright>
+
+	<changelog>
+	$Log$
+	</changelog>
+
+	<package>lifemapper-mod_python</package>
+	<package>lifemapper-ant</package>
+	<package>opt-cherrypy</package>
+	<package>opt-cheeta</package>
+	<package>opt-pylucene</package>
+
+<post>
+
+mkdir -p /var/lib/lm
+mkdir -p /var/lib/lm/sessions
+mkdir -p /var/lib/lm/luceneIndex
+mkdir -p /var/lib/lm/.python-eggs
+chgrp -R lmwriter /var/lib/lm
+chmod -R g+ws     /var/lib/lm
+
+
+</post>
+
+</kickstart>

nodes/lifemapper-server-base.xml

@@ -0,0 +1,96 @@
+<?xml version="1.0" standalone="no"?>
+
+<kickstart>
+
+
+	<description>
+	Lifemapper-server roll. 
+	LMserver and LMweb servers common install 
+	</description>
+
+	<copyright>
+	Copyright (c) 2000 - 2012 The Regents of the University of California.
+	All rights reserved. Rocks(r) v5.5/v6.0 www.rocksclusters.org
+
+	</copyright>
+
+	<changelog>
+	$Log$
+	</changelog>
+
+        <!-- RPM repos needed for postgresql,postgis,mapserver -->
+	<package>pgdg-centos91</package>
+	<package>elgis-release</package>
+
+	<!-- packages available on the system -->
+	<package>sqlite</package>
+	<package>flex</package>
+	<package>libxslt</package>
+
+	<!-- mapserver prereq -->
+	<package>bitstream-vera-fonts-common</package>
+	<package>bitstream-vera-sans-fonts</package>
+
+	<!-- packages build from source -->
+	<package>lifemapper-proj</package>
+	<package>lifemapper-geos</package>
+	<package>lifemapper-gdal</package>
+	<package>lifemapper-tiff</package>
+	<package>lifemapper-mod_python</package>
+
+	<package>opt-setuptools</package>
+	<package>opt-numexpr</package>
+	<package>opt-cython</package>
+	<package>opt-pytables</package>
+	<package>opt-egenix-mx-base</package>
+	<package>opt-psycopg2</package>
+	<package>opt-faulthandler</package>
+
+	<package>roll-lifemapper-usersguide</package>
+
+<post>
+
+<file name="/etc/ld.so.conf.d/lifemapper-server.conf">
+/opt/lifemapper/lib
+/usr/java/latest/jre/lib/amd64
+/usr/java/latest/jre/lib/amd64/server
+/opt/python/lib
+</file>
+
+yum --enablerepo base     install giflib-devel
+yum --enablerepo base     install byacc
+yum --enablerepo base     install readline-devel
+yum --enablerepo base     install subversion
+yum --enablerepo rpmforge install hdf4 hdf4-devel 
+yum --enablerepo rpmforge install hdf5 hdf5-devel
+yum --enablerepo base install cmake
+
+yum --enablerepo base update openssl
+yum install postgresql91
+yum install postgresql91-devel
+yum install pgbouncer
+yum --enablerepo epel install json-c.x86_64
+yum install postgis2_91
+
+yum --enablerepo epel fribidi
+yum install mapserver
+
+GID=`grep lmwriter: /etc/group`
+if [ "$GID" == "" ] ; then
+    /usr/sbin/groupadd -g 502 lmwriter
+fi
+
+/usr/sbin/groupadd -g 501 lmreader
+rocks sync users
+
+mkdir -p /state/partition/lm/logs
+chgrp -R lmwriter /state/partition1/lm
+chmod -R g+ws /state/partition1/lm
+
+
+</file>
+
+
+</post>
+
+</kickstart>

version.mk

@@ -0,0 +1,5 @@
+ROLLNAME	= lifemapper-server
+RELEASE		= 0
+COLOR		= orchid
+
+REDHAT.ROOT	= $(CURDIR)