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STARDEV  December 2018

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Subject:

Shipping external libraries with Linux Build & removing $LD_LIBRARY_PATH

From:

Sarah Graves <[log in to unmask]>

Reply-To:

Starlink development <[log in to unmask]>

Date:

Tue, 18 Dec 2018 17:02:08 -1000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (118 lines)

Dear Starlink Developers,

There's been some discussion in the past about bundling the main
external libraries with our EAO Starlink Linux build so it works on
more installations, and also about applying a fixup to our linux build
so that LD_LIBRARY_PATH isn't needed (as we do on OSX).

To test this out, I've now done a build on a CentOS 6 container, and
copied in the relevant external libraries to create a Linux build that
should run on most modern Linux OSs. I've fixed up the RPATHs in the
libraries/binaries so they are all relative to $ORIGIN rather than
being absolute, and removed LD_LIBRARY_PATH from the setup scripts.

I've run some testing on an up-to-date ubuntu (18.10) VM and it seems
to run the basics of Starlink happily. You can download this build
from http://ftp.eao.hawaii.edu/starlink/test/starlink-ManyLinux2010-Beta1.tar.gz

I'd love to have testing, however minimal, done by other people. I do
have an example set of tests at
https://www.eao.hawaii.edu/~sgraves/StarlinkNOLDLibrary/starlink_test_script.sh,which
will download some tutorial data and run through some ORAC-DR and
simple bash commands (its a little slow). The ORAC-DR part runs the
gui's up. If anyone has a favourite bit of Starlink software you can
send me some example data and commands to add to the script.

Does anyone have any strong objections/problems with this as a method
of shipping Starlink on Linux?

I've put in fuller details at the bottom of this email, for those that
are interested.

Thanks,

Sarah


Specifics:

I ran the build on a CentOS6 container running in docker, installing
the minimal set of files required to do the build. An  example script
to prepare CentOS6 to build Starlink is  at
http://www.eao.hawaii.edu/~sgraves/StarlinkNOLDLibrary/setup-centos6-info.sh


I have copied in the following libraries to the build:

/usr/lib64/libXau.so.6
/usr/lib64/libXt.so.6
/lib64/libexpat.so.1
/usr/lib64/libgfortran.so.3
/lib64/libncurses.so.5
/usr/lib64/libpng12.so.0
/lib64/libselinux.so.1
/lib64/libtinfo.so.5
/lib64/libuuid.so.1
/usr/lib64/libxcb.so.1
/lib64/libz.so.1


I used pypi's manylinux-2010  spec (found at
https://www.python.org/dev/peps/pep-0571/ ) as an example for what
libraries I could assume would be found on most post-centos6 Linux
machines, and didn't copy in any of its whitelisted libraries.

I also ignored the libraries only required by Perl's SSLeay module, as
I am hesitant about shipping people such security-conscious libraries
as the ssl ones. I think this means that if they don't have openssl
etc installed (or have an incompatible version) then some of the
functions of Astro::Catalog won't work. The only standard bit of
software that I know about that uses Astro::Catalog::Query is parts of
the ORAC-DR UKIRT pipeline. I haven't tested this yet. This list of
missing libraries are:

libssl.so.10
libcrypto.so.10

(And their dependencies of course -- on centos6 this is mostly bunch
of krb stuff.)

I have fixed up the standard binaries, libraries and the Perl .so
files to have a RPATH pointing to the relative path to the
$STARLINK_DIR/lib directory. I used the patchelf utility to do this
(https://nixos.org/patchelf.html)

Licensing: I believe that all of the libraries I've copied in can be
redistributed -- they were all taken from libraries installable with a
simple yum command on a stock CentOS 6, without adding any special
repos. I've included a README_BUNDLED_LIBRARIES file indicating which
libraries were manually added in, and which package they came from.

I've removed the parts from the login/cshrc  and profile scripts that
set up the LD_LIBRARY_PATH, and also removed them from the
$GAIA_DIR/gaia.sh script. (Setting this variable in that script
weirdly caused Gaia to be unable to create the .skycat directory if it
didn't already exist, I'm not sure why.)

To ensure that developers don't *have* to run this fixup on their own
builds, if we move forward with this I'll set a variable
STAR_NOLDLIBRARY in the setup scripts, and then alter the login,
profile and gaia.sh scripts so that they check for that variable
before setting LD_LIBRARY_PATH. I'm also going to create a toplevel
buildscripts directory in the repo and put in the osx and linux fixup
scripts, as well as the build scripts we use at EAO and Graham's
example sourceme files.




--
Dr Sarah Graves
Scientific Programmer
East Asian Observatory/JCMT
[log in to unmask]

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