Libdap On Leopard

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libdap on OS-X 10.5.3 (Leopard)

PowerPC

June 5th, 2008

Installed Leopard (OS-X 10.5) n a newly formatted disk.

System: PowerMac quad core G5, 6GB RAM


Installed:

  • bison: /usr/local/bin/bison
version: bison (GNU Bison) 2.3
  • libtool: /usr/local/bin/libtool
version: ltmain.sh (GNU libtool) 1.5.26 (1.1220.2.492 2008/01/30 06:40:56)
  • autoconf: /usr/local/bin/autoconf
version: autoconf (GNU Autoconf) 2.62
  • automake: /usr/local/bin/automake
version: automake (GNU automake) 1.10.1
  • m4: /usr/local/bin/m4
version: m4 (GNU M4) 1.4.11


In the top level of libdap ran:

gnulib-tool --import --dir=. --lib=libgnu --source-base=gl --m4-base=gl/m4 --doc-base=--dir=. --aux-dir=conf --lgpl --libtool --macro-prefix=gl regex
autoreconf
./configure
make
make check

libdap fails 3 tests:

  • FAIL: test.yb
  • FAIL: test.yd
  • FAIL: test.yg

But I think that happened under Tiger (10.4.x) too.

Same results for trunk and 3.8.0 source release.

Update

Looks like all tests pass now! http://scm.opendap.org/trac/ticket/1146

MacBook Pro

October 26th, 2008

Installed Leopard (OS-X 10.5) on a newly formatted disk.

System: MacBook Pro, 2.53GHz Core 2 Duo, 4GB RAM.


Installed:

  • bison: /usr/local/bin/bison
version: bison (GNU Bison) 2.3
  • libtool: /usr/local/bin/libtool
version: ltmain.sh (GNU libtool) 2.2.6b from source
  • autoconf: /usr/local/bin/autoconf
version: autoconf (GNU Autoconf) 2.65 from source
  • automake: /usr/local/bin/automake
version: automake (GNU automake) 1.11 from source
  • m4: /usr/local/bin/m4
version: m4 (GNU M4) 1.4.13 from source
  • subversion: /usr/local/bin/svn
version: subversion-1.5.2 from Collab.net binary
  • dejagnu: /usr/local/bin/runtest (and others)
version: dejagnu-1.4.4 from source
  • cppunit: /usr/local
version: cppunit-1.12.1 from source

In the top level of libdap ran:

autoreconf
./configure
make
make check

And it failed one test: 

..F...


!!!FAILURES!!!
Test Results:
Run:  5   Failures: 1   Errors: 0


1) test: DODSFilterTest::get_das_last_modified_time_test (F) line: 195 DODSFilterTest.cc 
assertion failed
- Expression: df3->get_das_last_modified_time() == st.st_mtime


FAIL: DODSFilterTest
installed it anyway...
  • szip: /usr/local
version: szip-2.1 from source (./configure --prefix=/usr/local)
  • zlib: /usr/local
version: zlib-1.2.3 from source
  • jpeg lib: /usr/local
version: jpeg-6b from source (ftp://ftp.uu.net/graphics/jpeg/jpegsrc.v6b.tar.gz)
[note: jpeg-7 is now shipping, but hdf as of hdf4.2r4 won't pass tests with it! If you need 7, best to install it in it's own dir and NOT /usr/local ... (mjohnson 1 oct 2009)]
Notes:
- Doing a make install will only install the executable files. To install the libraries do the following:
cp libjpeg.a /usr/local/lib
cp *.h /usr/local/include
- You must install the jpeg library and includes in /usr/local or the ./configure script for the hdf4_handler won't find it.
  • netcdf: /usr/local
version netcdf-3.6.3 from source (./configure --prefix=/usr/local)
  • HDF4: /usr/local
version: HDF4.2r3 from source, (./configure --disable-fortran --with-jpeg=/usr/local --with-szlib=/usr/local --prefix=/usr/local)
Updated
Configure with: ./configure --disable-fortran --with-szlib=/usr/local --disable-netcdf --enable-production --enable-shared
If you don't configure this correctly it's possible to install the HDF4 version of netcdf on top of the regular version and that will make all kinds of trouble.
Notes on libjpeg and hdf4.2r4 [mjohnson 1 oct 2009]: HDF4.2r4 won't pass tests with jpeg-7, the new dist. If you have it installed, you need to remove it and install jpeg-6b. Also, 4.2r4 fails to build with --enable-shared.



  • hdf5: /usr/local
version hdf5-1.8.1 from source (./configure --prefix=/usr/local --with-szlib=/usr/local --enable-cxx)

Continuing in the xmlrequest branch I checked out, built, and installed:

  • bes
  • dap-server
  • freeform_handler
  • hdf4_handler
  • hdf5_handler
  • netcdf_handler


Building Hyrax-1.6.2 Package Installer(s) for OS-X 10.5 (Leopard)

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 throughout this section as $prefix.


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 the story:

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

Downloads

  • hdf-4.2r3.tar.gz
  • hdf5-1.8.1.tar.gz
  • icu4c-3_6-src.tgz
  • jpegsrc.v6b.tar.gz
  • netcdf-3.6.3.tar.gz
  • szip-2.1.tar.gz*
  • zlib-1.2.3.tar.gz

Builds

In order:

szip

Required by: HDF4, hdf4_handler

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.

szip-2.1.tar.gz*
./configure --prefix=$prefix/deps/hdf-4.2.5
make
make check
make install
zlib

Required by: HDF4, hdf4_handler

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.

zlib-1.2.3.tar.gz
./configure --prefix=$prefix/deps/hdf-4.2.5
make
make check
make install
jpeg

Required by: HDF4, hdf4_handler

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.

jpegsrc.v6b.tar.gz
./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 $prefix/include
hdf5
hdf5-1.8.5-patch1.tar.gz
./configure --prefix=$prefix/deps/hdf5-1.8.5-patch1
make
make check
make install
netcdf
netcdf-3.6.3.tar.gz
./configure --prefix=$prefix/deps/netcdf-3.6.3
make
make check
make install
hdf4
hdf-4.2.5.tar.gz
./configure --prefix=$prefix/deps/hdf-4.2.5 --disable-fortran --with-szlib=$prefix/deps/hdf-4.2.5 --with-netcdf=$prefix/deps/netcdf-3.6.3 --enable-production --enable-shared -with-jpeg=$prefix/deps/hdf-4.2.5
make
make check
make install
icu
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-source-directory>/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, then

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

PackageMaker

  • When I built the package I got a large number warnings that the target install location had different owner/group than the install source.
  • I used chown and chgrp to change to install source files and folders to the same user as the target directories. This caused PackageMaker to hang permanently. Required a force quit (kill -9). This was repeatable.
  • I changed back the ownership of the files to my user and group.
  • In the contents "tab" on the Package I attempted to set the Owner and group to root / wheel.
  • I still got the same warnings when building the package.
  • I tested it on another mac
    • It unpacked to /usr/local/ as directed.
    • The files were all owned by root/wheel


Hyrax

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, 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.

libdap

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

bes

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

dap-server

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

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!

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

freeform_handler

./configure --prefix=$prefix
make
make check
make install

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!

./configure --prefix=$prefix --with-hdf4=$prefix/deps/hdf-4.2.5
make
make check
make install

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!

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

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!

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

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!


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