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This file describes the installation process for yaxx. Yaxx is a Perl script that facilitates batch spectral processing of X-ray data using Perl open source tools and commonly available astronomical software (CIAO, SAS, HEASOFT).
Yaxx has been successfully tested on these operating systems:
The build and installation process requires approximately 200 Mb of free disk space (due mostly to a few perl modules used by yaxx). After installation and testing, one can remove the top-level build and pkgs directories to free up around 110 Mb of disk space.
Perl version 5.8.0 or newer. All non-standard packages used by yaxx are included in this distribution.
CIAO version 3.4 or later. You also need to have the CIAO contributed scripts installed as well as the latest version of the Chandra calibration database.
For the default Chandra and XMM threads the spectral fitting step requires the use of CIAO 3.4 Sherpa and is not compatible with CIAO 4.0. However if spectral fitting is not required then the thread processing step fit_spectral_models can be removed and the thread can be run using CIAO 4.0.
This is required if LaTeX-generated postscript fit summaries are desired.
To install and test yaxx, do the following steps.
Make sure your perl has version 5.8.0 or newer by checking the output of entering 'perl -v' at your command prompt:
perl -v
Yaxx can be installed from source (which involves building all of the dependent perl modules), or from pre-built binary distributions. At this time the binary distributions have only been tested locally so this is somewhat experimental. However, if your platform is reasonably close to the build architecture then this should work and save time.
The downloads are available at http://cxc.harvard.edu/contrib/yaxx/downloads/. The source distribution is named yaxx-<version>.tar.gz while binary distributions are named yaxx-<version>-<platform>.tar.gz.
Change dir to the directory where you want the yaxx installation to reside. The only requirement is that sufficient disk space be available. For example if you do:
cd /path/to/install
then the yaxx package will be installed in /path/to/install/yaxx/.
Untar the yaxx tar file by doing one of the following (for source or binary respectively):
gunzip --stdout yaxx-<version>.tar.gz | tar xvf - gunzip --stdout yaxx-<version>-<platform>.tar.gz | tar xvf -
This will create a 'yaxx-<version>' directory and put the contents there.
ln -s yaxx-<version> yaxx cd yaxx
Yaxx depends on external analysis packages such as CIAO (required) and SAS and HEAsoft (for XMM). To minimize potential package conflicts, yaxx does the analysis environment initialization internally (in the correct order) and expects that the user has not done any initialization. It is necessary therefore to tell yaxx how to initialize each of the analysis packages, typically by sourcing an initialization script.
The environment setup is specified in the environment parameter within the System configuration file yaxx.cfg in the top-level yaxx installation directory. More information about configuration files is available in the reference manual. Edit this file and change the environment parameters to be appropriate for your system setup. The initial installation and testing uses the Chandra analysis thread, which only requires setting the CIAO environment:
<environment CIAO> shell csh script source /soft/ciao/bin/ciao.csh <<--- CHANGE THIS </environment>
Users doing XMM analysis will have to adjust the HEAsoft and SAS enviroments as well.
Skip this step if installing from binary.
This is the longest step and can take over an hour on a Solaris machine, but on a modern linux box it should finish within 20 minutes. At the command prompt enter:
make
This runs the perl script install_yaxx.pl which puts the necessary perl modules in the yaxx-perl directory of the source distribution.
If any library or module fails to compile or pass its internal tests, the install script will ask if you want to quit or continue. See the Known Issues section if this occurs. Depending on the severity of the failure, it may be possible to push through and still have a working system. Please email the developer with details and a copy of the installation log install.log if any modules do not compile.
Test yaxx by doing:
make test
You should see that yaxx does not stop with any error messages and finishes with the message (except for the time):
<2006-Nov-05 18:44:04> *** SUCCESS for Obsid=3102 Ccdid=ACIS-S3 Srcid=1 Creating HTML report index
If the test step does not succeed, please email the developer with details and a copy of the log file which is created in Test/install/Log. Note that on some systems the make program may indicate a failure, but if yaxx ends with the above message then everything should be OK.
The final product is a report (Test/install/obs3102/src1/report.ps) which summarizes the fitting. There will also be a file Test/install/report_index.html which can be viewed with your favorite web browser, e.g.
firefox Test/install/report_index.html
The 'make' step also creates a customized shell script 'yaxx' in the source directory which should be used to actually start yaxx for analysis. Copy this file to a directory which is in your PATH (e.g. ~/bin) and do 'rehash' (if you are running csh or tcsh).
A less desirable but valid option is to make an alias and put this in your shell initialization script (e.g. ~/.cshrc):
alias yaxx /path/to/install/yaxx/yaxx
One issue arose because the compiler suite had been upgraded without recompiling the system Perl. This can lead to obscure errors when building the modules.
This came up on two Solaris systems. In these cases the issue was resolved without having to recompile perl by reverting to an older compiler with a command similar to:
set path = ( /opt/SUNWspro_6.1/bin $path )
Details will vary with your installation.
On one linux machine (Fedora Core 4 with Perl 5.8.6) the Compress::Zlib library failed a self-test. The installation process was continued with no further issues and was ultimately successful.