ConfigureAmazonLinuxAMI

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How to configure an Amazon Linux AMI for EC2 to build Hyrax

This describes how to set up a vanilla Amazon Linux AMI virtual machine so that we can build the Hyrax data server.

Amazon Linux AMI versions

These instructions have been amended to cover:

• Amazon Linux AMI 2012.09

Initial configuration

Set up general build stuff that you need:

• yum install java-1.6.0-openjdk java-1.6.0-openjdk-devel
• yum install junit
• yum install ant
• yum install ant-junit.noarch
• yum install make
• yum install subversion
• yum install gcc-c++
• yum install flex
• yum install bison
• yum install curl-devel
• yum install libxml2-devel
• yum install libjpeg-devel
• yum install zlib-devel
• yum install readline-devel
• yum install libuuid-devel
• yum install openssl-devel

Other dependencies

• yum install libicu-devel

Autotools

• download the latest versions of autoconf, automake and libtool
• ./configure, make, make install

Building Hyrax from the shrew project

In a (ba)sh shell:

Check out the shrew project

svn co https://scm.opendap.org/sv/trunk/shrew

Change your working directory to the shrew directory.

cd shrew

Source the spath file

. spath

Build the dependancies

cd src/dependencies

make

Using the shrew top level Makefile

Change your working directory to the shrew directory.

cd $prefix

Copy the Makefile.am.master to Makefile.am

cp Makefile.am.master Makefile.am

Edit the Makefile.am to be certain that the various dependancies are correctly configured.

vim Makefile.am

(Since I am trying to get a new package up I edited this file, mostly I think you should just be able to make the copy and proceed.)

Engage the autotools process and see how far you get...

autoreconf -vif

./configure --prefix=$prefix

make

If the above fails then you need to build each Hyrax component by hand.'

Building by hand

Build and install libdap

cd $prefix/src/libdap

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the BES

cd $prefix/src/bes

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the dap-server module

cd $prefix/src/modules/dap-server

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the csv_handler module

cd $prefix/src/modules/csv_handler

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the fileout_gdal module

cd $prefix/src/modules/fileout_gdal

autoreconf -vif

./configure --prefix=$prefix --with-gdal=$prefix/deps/gdal-12.15.12

make install

Build and install the fileout_netcdf module

cd $prefix/src/modules/fileout_netcdf

autoreconf -vif

./configure --prefix=$prefix --with-netcdf=$prefix/deps/netcdf-4.1.2

make install

Build and install the fits_handler module

cd $prefix/src/modules/fits_handler

autoreconf -vif

./configure --prefix=$prefix --with-cfits=$prefix/deps/cfitsio

make install

Build and install the freeform_handler module

cd $prefix/src/modules/freeform_handler

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the gateway_module module

cd $prefix/src/modules/gateway_module

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the gdal_handler module

cd $prefix/src/modules/fileout_netcdf

autoreconf -vif

./configure --prefix=$prefix --with-gdal=$prefix/deps/gdal-12.15.12

make install

Build and install the hdf4_handler module

cd $prefix/src/modules/hdf4_handler

autoreconf -vif

./configure --prefix=$prefix --with-hdf4=$prefix/deps/hdf-4.2.8

make install

Build and install the hdf5_handler module

cd $prefix/src/modules/hdf5_handler

autoreconf -vif

./configure --prefix=$prefix --with-hdf5=$prefix/deps/hdf5-1.8.6

make install

Build and install the ncml_module module

cd $prefix/src/modules/ncml_module

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the netcdf_handler module

cd $prefix/src/modules/fileout_netcdf

autoreconf -vif

./configure --prefix=$prefix --with-netcdf=$prefix/deps/netcdf-4.1.2

make install

Build and install the xml_data_handler module

cd $prefix/src/modules/xml_data_handler

autoreconf -vif

./configure --prefix=$prefix

make install

Build and install the ugrid_functions module

cd $prefix/src/modules/ugrid_functions

autoreconf -vif

./configure --prefix=$prefix --with-gridfields=$prefix/deps/gridfields-1.0.1

make install

Building the ncml_handler when incompatible versions of ICU are resident on the system

1. Check to see what's on the machine in terms of ICU:

[root@ip-10-152-156-244 shrew]# rpm -qa | grep icu
libicu-4.2.1-9.9.amzn1.x86_64
libicu-devel-4.2.1-9.9.amzn1.x86_64
[root@ip-10-152-156-244 shrew]# 

(no need to be root)

So we can see that icu is there but it's the version 4 code and that is massively incompatible with the version 3 code. You probably knew all of that, I think we talked about it, but I just thought I'd show the useful 'rpm -qa' (query all) command.

1. Here's how to see where stuff is:

[ec2-user@ip-10-152-156-244 shrew]$ rpm -qil libicu-devel-4.2.1-9.9.amzn1.x86_64Name        : libicu-devel                 Relocations: (not relocatable)
Version     : 4.2.1                             Vendor: Amazon.com
Release     : 9.9.amzn1                     Build Date: Mon 09 Jan 2012 04:52:37 PM UTC
Install Date: Wed 30 Jan 2013 05:39:05 AM UTC      Build Host: build-31003.build 
Group       : Development/Libraries         Source RPM: icu-4.2.1-9.9.amzn1.src.rpm
.
.
.
Description :
Includes and definitions for developing with icu.
/usr/bin/icu-config
/usr/include/layout
/usr/include/layout/LEFontInstance.h
/usr/include/layout/LEGlyphFilter.h
/usr/include/layout/LEGlyphStorage.h
/usr/include/layout/LEInsertionList.h
/usr/include/layout/LELanguages.h
/usr/include/layout/LEScripts.h
/usr/include/layout/LESwaps.h
/usr/include/layout/LETypes.h
/usr/include/layout/LayoutEngine.h
/usr/include/layout/ParagraphLayout.h
/usr/include/layout/RunArrays.h
/usr/include/layout/loengine.h
/usr/include/layout/playout.h
/usr/include/layout/plruns.h
/usr/include/unicode
/usr/include/unicode/basictz.h
/usr/include/unicode/bms.h
/usr/include/unicode/bmsearch.h
.
.
.

1. So if configure looks for icu-config, it'll find the one for icu 4.x which our handler cannot use - at least not without some tweaking things. I think the includes are all different (nice, eh?)

4. Put our icu-3.6/bin dir on the PATH in front of everything: [ec2-user@ip-10-152-156-244 shrew]$ export PATH=/home/ec2-user/opendap/shrew/deps/icu-3.6/bin:$PATH

And configure works just fine

But when you try to start the server, massive library not found crap. That's because on linux you have to run ldconfig for a library to be found 'automatically'. As a convenience to users, icu left this step out…

5. Add our icu-3.6/lib dir to LD_LIBRARY_PATH [root@ip-10-152-156-244 shrew]# export LD_LIBRARY_PATH=/home/ec2-user/opendap/shrew/deps/icu-3.6/lib/ [root@ip-10-152-156-244 shrew]# besctl startStarting the BES OK: Successfully started the BES PID: 11975 UID: 0 [root@ip-10-152-156-244 shrew]#

Start tomcat and the server is up!

http://ec2-54-242-224-73.compute-1.amazonaws.com:8080/opendap/data/ncml/fnoc1_improved.ncml

Why we don't have this BS on CentOS is likely that they use icu-3.6 and even if we build our own version, it's not being used. In fact, the reason I had Michael use 3.6 and not 4.2 was that most linux distros came with 3.6.

Really, if we could just use TDS for aggregation, that would be fine with me! Oe maybe there's a better library out there now for the date stuff…