Difference between revisions of "Hyrax Package for OS-X"

From OPeNDAP Documentation
(hdf4)
(Build some code)
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=== Build some code ===
 
=== Build some code ===
  
Run the following commands:
+
To build the OS/X packages for the entire C/C++ part of the server,
 +
run the following commands:
 
;autoreconf : This rebuilds ''configure'' from ''configure.ac'' and ''Makefile.in'' from ''Makefile.am''
 
;autoreconf : This rebuilds ''configure'' from ''configure.ac'' and ''Makefile.in'' from ''Makefile.am''
 
;./configure --prefix=$prefix : This builds ''Makefile'' from ''Makefile.in'' using the value of '''$prefix''' for the autoconf directory ''prefix''  
 
;./configure --prefix=$prefix : This builds ''Makefile'' from ''Makefile.in'' using the value of '''$prefix''' for the autoconf directory ''prefix''  
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:NB: Add to the top-level Makefile.am to make the olfs/tomcat pkg
 
:NB: Add to the top-level Makefile.am to make the olfs/tomcat pkg
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 +
What you wind up with is an OS/X Package for the dependencies, libdap, bes, and each of the handlers in their respective ''src/...'' directories. In a subsequent step these will be loaded into a Metapackage by hand, but there's one more thing to do...
 +
 +
=== Build the OLFS package ===
 +
 +
The OLFS package should combine the current release of the OLFS with an appropriate version of tomcat. To do this, for now, work from the command line executing command by hand (and leave the OLFS-<version>.pkg around for use later). Here's a synopsis of the process: First grab a copy of tomcat and put the '''opendap.war''' file in it's ''webapps'' directory. Once that's done, copy that into a directory tree structure that mirrors the destination structure for the server. Here's how to do that:
 +
 +
 +
 +
 +
Tar up that entire directory tree and store the result in an archive I'll call ''olfs.tar''. Now make a new directory tree that mirrors the pathname of $prefix using ''mkdir -p macosx/$prefix''. Neat huh? Now
 +
 +
Run the following commands by hand.
  
 
== Notes ==
 
== Notes ==

Revision as of 18:30, 14 January 2011

1 Overview

The goal of this build was to produce a set of OS-X package installers for Hyrax. This includes bundling all of the Hyrax dependancies in an installer. In addition, all of the installed files (Hyrax and dependancies) should be confined to a single directory (tree) for the release. For this release I chose /usr/local/opendap./servers/hyrax-1.6.2. This abbreviated is throughout this section as $prefix.

1.1 Development System

Operating System
OS-X 10.5.8
Hardware
MacBook Pro, 2.53GHz Intel Core 2 Duo, 4GB RAM

2 Building Hyrax Dependancies

In an effort to build a binary distribution for Hyrax I built all of our dependancies from source and rolled them up with PackageMaker. Here's an ordered list what got built and installed. Note that with some noted exceptions, each of the dependancies gets installed into its own directory.


2.1 szip

Required by: HDF4, hdf4_handler
File: szip-2.1.tar.gz*

The hdf4_handlers configure script does not provide options to allow the location of szip to be specified. When the hdf4_handlers configure script is run it looks in the --with-hdf4 location of szip, after that it looks in the usual places. In order to ensure that the correct szip (the one sent with the installer) was located we needed to install the szip library into the HDF4 library location.

Build process
./configure --prefix=$prefix/deps/hdf-4.2.5
make
make check
make install

2.2 zlib

Required by: HDF4, hdf4_handler
File: zlib-1.2.3.tar.gz

The hdf4_handlers configure script does not provide options to allow the location of zlib to be specified. When the hdf4_handlers configure script is run it looks in the --with-hdf4 location of zlib, after that it looks in the usual places. In order to ensure that the correct zlib (the one sent with the installer) was located we needed to install the zlib library into the HDF4 library location.

Build process
./configure --prefix=$prefix/deps/hdf-4.2.5
make
make check
make install

2.3 jpeg

Required by: HDF4, hdf4_handler
File: jpegsrc.v6b.tar.gz

The hdf4_handlers configure script does not provide options to allow the location of jpeg to be specified. When the hdf4_handlers configure script is run it looks in the --with-hdf4 location of jpeg, after that it looks in the usual places. In order to ensure that the correct jpeg (the one sent with the installer) was located we needed to install the jpeg library into the HDF4 library location.

Build process
./configure --prefix=$prefix/deps/hdf-4.2.5
make
make check
mkdir -p /usr/local/opendap/servers/hyrax-1.6.2/bin
mkdir -p /usr/local/opendap/servers/hyrax-1.6.2/man/man1
make install
cp libjpeg.a $prefix/lib
cp *.h $prefix/include

2.4 hdf5

Required by: hdf5_handler
File: hdf5-1.8.5-patch1.tar.gz

Build process
./configure --prefix=$prefix/deps/hdf5-1.8.5-patch1
make
make check
make install

2.5 netcdf

Required by: netcdf_handler
File: netcdf-3.6.3.tar.gz

Build process
./configure --prefix=$prefix/deps/netcdf-3.6.3
make
make check
make install

2.6 hdf4

Required by: hdf4_handler
File: hdf-4.2.5.tar.gz

Build process
./configure --disable-fortran --enable-production --enable-shared --disable-netcdf --prefix=$prefix/deps/hdf-4.2.5 --with-szlib=$prefix/deps/hdf-4.2.5 -with-jpeg=$prefix/deps/hdf-4.2.5 --with-netcdf=$prefix/deps/netcdf-3.6.3
make
make check
make install

2.7 hdf-eos2

Required by: hdf4_handler
File: HDF-EOS2.17v1.00.tgz

Build process
./configure --disable-fortran --enable-production --enable-shared --enable-install-include --prefix=$prefix/deps/hdf-4.2.5 --with-jpeg=$prefix/deps/hdf-4.2.5 --with-szlib=$prefix/deps/hdf-4.2.5 --with-zlib=$prefix/deps/hdf-4.2.5 --with-hdf4=$prefix/deps/hdf-4.2.5
make
make check
make install

2.8 icu

Required by: ncml_handler
File: icu4c-3_6-src.tgz

At run time ICU dependents failed to link correctly. Using otool -L we could see in our libraries all of the ICU dependancies were shown like:

libicui18n.dylib.36 (compatibility version 36.0.0, current version 36.0.0)

When all the other libs had a full path like this:

/usr/local/opendap/servers/hyrax-1.6.2/lib/libbes_dap.3.dylib (compatibility version 5.0.0, current version 5.5.0)

The ICU build was producing only dynamic libraries where the links were only to the package name (no path). This also caused programs linking to one of theICU libs to get "path free" links.

James found the following in the last reply to this thread: http://bugs.php.net/bug.php?id=34089 (Thanks James!)

The icu build system produces MAC platform libraries with an install name which does not include a path, this can be seen by running "otool -L" on any of the libraries or anything you build that links against any of the libraries.
My solution was to edit icu's darwin config file found at "<icu_distribution_dir>/source/config/mh-darwin"
By changing line 28 from:
LD_SONAME = -Wl,-compatibility_version -Wl,$(SO_TARGET_VERSION_MAJOR) -Wl,-current_version -Wl,$(SO_TARGET_VERSION) -install_name $(notdir $(MIDDLE_SO_TARGET))
To:
LD_SONAME = -Wl,-compatibility_version -Wl,$(SO_TARGET_VERSION_MAJOR) -Wl,-current_version -Wl,$(SO_TARGET_VERSION) -install_name $(libdir)/$(notdir $(MIDDLE_SO_TARGET))

I made the recommended change and everything worked great.

Build process
./runConfigureICU MacOSX --prefix=$prefix/deps/icu-3.6
make
make check
make install

3 Building Hyrax C++ (libdap, bes, handlers and modules)

URL: http://scm.opendap.org/svn/branch/shrew/hyrax_1.6.2_release
Revision: 23904

Summary
I patched all of the Makefile.am targets for the OS-X packages (make pkg). I found numerous problems with small details such as incorrect package names for PackageMaker and failure to preserve configure options in the package build. The code works now, but there are soma caveats for some of the packages. Details in each section below.

3.1 libdap

Build process
./configure --prefix=$prefix
make pkg
make check
make install

3.2 bes

Build process
./configure --prefix=$prefix
make pkg
make check
make install

3.3 dap-server

Build process
./configure --prefix=$prefix
make pkg
make check
make install

3.4 fileout_netcdf

The configure command accepts:

--with-netcdf=ARG netcdf directory
--with-netcdf-include=ARG netcdf include directory
--with-netcdf-libdir=ARG netcdf library directory

However for OS-X packages ONLY --with-netcdf will work!

Build process
./configure --prefix=$prefix --with-netcdf=$prefix/deps/netcdf-3.6.3
make pkg
make check
make install

3.5 freeform_handler

Build process
./configure --prefix=$prefix
make pkg
make check
make install

3.6 hdf4_handler

The configure command accepts:

--with-hdf4=ARG hdf4 directory
--with-hdf4-include=ARG hdf 4 include directory
--with-hdf4-libdir=ARG hdf 4 library directory

However for OS-X packages ONLY --with-hdf4 will work!

Build process
./configure --prefix=$prefix --with-hdf4=$prefix/deps/hdf-4.2.5 --with-hdfeos2=$prefix/deps/hdf-4.2.5
make pkg
make check
make install

3.7 hdf5_handler

The configure command accepts:

--with-hdf5=ARG hdf5 directory
--with-hdf5-include=ARG hdf5 include directory
--with-hdf5-libdir=ARG hdf5 library directory

However for OS-X packages ONLY --with-hdf5 will work!

Build process
./configure --prefix=$prefix --with-hdf5=$prefix/deps/hdf5-1.8.5-patch1
make pkg
make check
make install

3.8 nectdf_handler

The configure command accepts:

--with-netcdf=ARG netcdf directory
--with-netcdf-include=ARG
netcdf include directory
--with-netcdf-libdir=ARG
netcdf library directory

However for OS-X packages ONLY --with-netcdf will work!

Build process
./configure --prefix=$prefix --with-netcdf=$prefix/deps/netcdf-3.6.3
make pkg
make check
make install

3.9 ncml_handler

The configure command accepts:

--with-icu-prefix=PREFIX
Prefix where icu is installed (optional)
--with-icu-exec-prefix=EPREFIX
Exec prefix where icu is installed (optional)

However for OS-X packages ONLY --with-icu-prefix will work!

Build process
./configure --prefix=$prefix--with-icu-prefix=$prefix/deps/icu-3.6
make pkg
make check
make install

4 Building Hyrax Java (olfs)

This required no additional code building.

4.1 Tomcat

I got the latest apache Tomcat (6.0.29) from http://tomcat.apache.org/download-60.cgi

Build process
cd $prefix
tar -xvf $downloads/apache-tomcat-6.0.29.tar.gz
find . -exec xattr -d com.apple.quarantine {} \; -print
Because I used Safari to grab the tomcat archive file and Finder to open it OS-X marked everything in the file system with the com.apple.quarantine extended file attribute. This causes OS-X to produce the This is a web downloaded file, are you sure you want to do this user dialogs when it is first run. You can see this using an ls -l command. The presence of extended attributes is denoted by a trailing @ sign at the end of the permissions string.
For example
drwxr-xr-x@ 9 ndp staff 476 Dec 3 14:59 apache-tomcat-6.0.29
I removed this using find and the xattr command:
find . -exec xattr -d com.apple.quarantine {} \; -print

4.2 OLFS

I downloaded OLFS-1.7.1 from http://www.opendap.org/pub/olfs/olfs-1.7.1-webapp.tgz and unpacked it. From the bundle I took the opendap.war file and copied it to $prefix/tomcat/webapps

Build process
cd $prefix
cp $downloads/olfs-1.7.1-webapp/opendap.war tomcat/webapps

5 Shell Scripts

I also added a shell script that can be used to configure the users shell so that they can easily control Hyrax. There is both a bash and a c-shell version in the top distribution directory.

6 PackageMaker

6.1 Hyrax Dependancies

In order to bundle the dependancies into an OSX package I used the pattern established by James in http://scm.opendap.org/svn/trunk/libdap/Makefile.am where he used the automake DESTDIR property to deploy the linked libraries to a directory of his choosing. I also created an OSX_Resources directory based on James' work and used it to generate the dependancies package.

Build process
cd $project_dir
mkdir -p macosx/$prefix
cd $prefix
tar -cv $project_dir/deps.tar deps
cd $project_dir/macosx/$prefix
tar -xvf project_dir/deps.tar
cd $project
/Developer/usr/bin/packagemaker --root macosx --id org.opendap.hyrax_dependancies-1.6.2 --title "Hyrax-1.6.2 dependancies" --version "1.6.2" --out hyrax-1.6.2-depends.pkg --resources OSX_Resources

6.2 Hyrax C++ (libdap, bes, modules and handlers)

All of the C++ components have a OS-X package target. I did have to make modifications to the production rules (Makefile.am) and some of the OSX_Resources for every one of these. They are all pretty clean now.

Things to do
Most of the OSX_Resources/InstallationCheck scripts have hardwired PATH environments that point to this (hyrax-1.6.2) install. The production rules need to be tweaked to make this dependent on the build prefix.

6.3 Hyrax Java (The OLFS)

In order to bundle the dependancies into an OSX package I used the pattern established by James in http://scm.opendap.org/svn/trunk/libdap/Makefile.am where he used the automake DESTDIR property to deploy the linked libraries to a directory of his choosing. I also created an OSX_Resources directory based on James' work and used it to generate the dependancies package.

Basically I grabbed the tomcat tree (with the olfs opendap.war file in place) from $prefix, popped it into the macosx directory in my olfs package project and called packagemaker.

Build process
cd $project_dir
mkdir -p macosx/$prefix
cd $prefix
tar -cv $project_dir/olfs.tar apache-tomcat-6.0.29
cd $project_dir/macosx/$prefix
tar -xvf project_dir/olfs.tar
cd $project
/Developer/usr/bin/packagemaker --root macosx --id org.opendap.olfs-1.7.1 --title "OPeNDAP olfs-1.7.1" --version "1.7.1" --out olfs-1.7.1.pkg --resources OSX_Resources

6.4 Hyrax-1.6.2

6.4.1 Meta-Package

Once I was able to build all all of the component packages I was able to use the PackageMaker GUI to build a meteapackage that combined all of the previously packaged components. I allowed the user to choose which handlers they wish to install.

6.4.2 OneBigPackage

I was also able to use the PackageMaker GUI to build a single package based on the body of installed code in $prefix.



7 Using Shrew

Based on the work that Nathan did, I've modified the shrew project to accommodate most of this process. It's almost automatic...

NB: This is not actually in svn/trunk/shrew but rather in the shrew branch for hyrax_1.6.2_release and will be merged back to the trunk copy of shrew when the kinks are all worked out.

7.1 Preconditions

A completely up to date checkout

7.2 Options

You can use these targets to build a set of dependencies that are then used to build the various handlers and/or you can build a set of OS/X packages that can be combined into a single, huge, metapackage. There may be some utility in just doing the former, but this process has been developed with the idea that it will be used to make an OS/X metapackage for Hyrax.

7.3 Set environment variables

You must set $prefix, $PATH and $CATALINA_HOME for this all to work.

7.3.1 $prefix

Set $prefix to the full path of the desired installation location. This should be /usr/local/opendap/servers/hyrax-<version>. We chose this because we want to make sure several things are true:

  • When the build is done, components of the server must be linked to the libraries they use and those same libraries must be in the same place when the server is run.
  • Since OS/X's various installers don't have an uninstall option, putting the entire server in one place makes it easy to remove
  • We're Unix nerds and we like things to be in /usr/local ;-)

7.3.2 $PATH

Set $PATH to $prefix/bin:$PATH

7.3.3 $CATALINA_HOME

Set $CATALINA_HOME to $prefix/apache-tomcat-6.0.29

NB: I think the process described here installs a tomcat for you, but maybe not. If not, edit this to say that you need to put Tomcat into the place referenced by $CATALINA_HOME

7.4 Build some code

To build the OS/X packages for the entire C/C++ part of the server, run the following commands:

autoreconf 
This rebuilds configure from configure.ac and Makefile.in from Makefile.am
./configure --prefix=$prefix 
This builds Makefile from Makefile.in using the value of $prefix for the autoconf directory prefix
make depends-pkg 
Build the dependencies, install them in $prefix and then make an OSX package to be used later
make world 
Make the server and install the bits and pieces in $prefix. This makes sure that the modules all link against the correct versions of the libraries (but it depeends on having $PATH set as described above.
make pkg 
Given that the code is all built and installed (and this includes the OLFS), make OSX packages for all the pieces. The packages will be stored in the different directories, but that doesn't matter so long as you followed the advice above about starting out in you OSX home directory and not /usr/local/src, or some other place that OSX file chooser dialogs won't find.
NB: Fix the pkg targets so that the package is not erased byt eh .dmg target
NB: Add to the top-level Makefile.am to make the olfs/tomcat pkg

What you wind up with is an OS/X Package for the dependencies, libdap, bes, and each of the handlers in their respective src/... directories. In a subsequent step these will be loaded into a Metapackage by hand, but there's one more thing to do...

7.5 Build the OLFS package

The OLFS package should combine the current release of the OLFS with an appropriate version of tomcat. To do this, for now, work from the command line executing command by hand (and leave the OLFS-<version>.pkg around for use later). Here's a synopsis of the process: First grab a copy of tomcat and put the opendap.war file in it's webapps directory. Once that's done, copy that into a directory tree structure that mirrors the destination structure for the server. Here's how to do that:



Tar up that entire directory tree and store the result in an archive I'll call olfs.tar. Now make a new directory tree that mirrors the pathname of $prefix using mkdir -p macosx/$prefix. Neat huh? Now

Run the following commands by hand.

8 Notes

These things would complete the hyrax configuration as part of the installation process:

  1. If possible we should ask for user and group names in the install process.
  2. We should create the logs directory as part of the install and configure the bes to use it.