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All centralized astro-software (binaries and source) is placed under /cluster/apps/software

To use astro-software you should have these lines in your .bashrc so you will be able to see all the modulefiles for the configured workspaces and software.

if [ -d "/cluster/apps/software/_profile" ]; then
  if [ -z $SOFTWARE ]; then
    source "/cluster/apps/software/_profile/globals.bash"
  fi
fi
if [ -d "/cluster/apps/software/.profile.d" ]; then
  if [ -z $SOFTWARE ]; then
    source "/cluster/apps/software/.profile.d/globals.bash"
  fi
fi

If using c-shell instead, these lines should be added to your .cshrc:

if ( -d /cluster/apps/software/_profile ) then
    source /cluster/apps/software/_profile/globals.csh

Run first ml ASTRO to load the ASTRO workspace. This will set the environment and make available the ASTRO software modulefiles for loading.

#show available modules to load
[username@computername ~]$ ml av
----------------------------------------------- /cluster/apps/software/_profile/lmod/WORKSPACE -----------------------------------------
   ASTRO    CORE
----------------------------------------- /cluster/apps/spack/2022a/lmod/linux-fedora36-x86_64/Core ------------------------------------
# load the ASTRO module then show again the available modules
[username@computername ~]$ ml ASTRO
[username@computername ~]$ ml av
------------------------------------------- /cluster/apps/software/_profile/lmod/modulefiles/ASTRO -------------------------------------
   CALDB    conda+/ciao    conda+/fermi (D)    ds9/8.3    heasoft/6.30.1    heasoft/6.31 (D)    iraf/2.17
   starlink/fc36           starlink/2021A (D)  trm
---------------------------------------------- /cluster/apps/software/_profile/lmod/WORKSPACE ------------------------------------------
   ASTRO (L)    CORE
----------------------------------------- /cluster/apps/spack/2022a/lmod/linux-fedora36-x86_64/Core ------------------------------------
   anaconda3/2021.05    anaconda3/2022.05 (D)    gcc/10.2.0

For questions or software updates, contact Bogdan.

Anaconda

Some python packages are installed via anaconda (https://anaconda.cloud/package-categories/scientific). To load it type:

[username@computername ~]$ ml anaconda3
##################################################################################### 
#### Run "conda env list" to list all the environments
#### Load environment "conda activate env_name" where env_name is one from the list
#### Remember to run "conda deactivate" before unload/purge anaconda3
#### otherwise you will have to restart your shell to avoid possible issues
#################################################################################
[username@computername ~]$ init-conda[username@computername ~]$ conda env list
# conda environments:
#base                     /cluster/apps/software/anaconda3/2022.05
astroconda               /cluster/apps/software/anaconda3/2022.05/envs/astroconda
astrosource              /cluster/apps/software/anaconda3/2022.05/envs/astrosource
ciao                     /cluster/apps/software/anaconda3/2022.05/envs/ciao
fermitools               /cluster/apps/software/anaconda3/2022.05/envs/fermitools
iraf                     /cluster/apps/software/anaconda3/2022.05/envs/iraf
phoebe                   /cluster/apps/software/anaconda3/2022.05/envs/phoebe
posydon                  /cluster/apps/software/anaconda3/2022.05/envs/posydon
python-2.7               /cluster/apps/software/anaconda3/2022.05/envs/python-2.7
[username@computername ~]$ conda activate astrosource

# after finishing your tasks either exit the terminal or, you must deactivate the
# environment before unloading/purging the loaded modulefiles
(astrosource) [username@computername ~]$ conda deactivate
[username@computername ~]$ ml purge

heasoft: A Unified Release of the FTOOLS and XANADU Software Packages (https://heasarc.gsfc.nasa.gov/docs/software/heasoft/)
- Description:
  XANADU: High-level, multi-mission tasks for X-ray astronomical spectral, timing, and imaging data analysis (Xspec, Xronos, Ximage, qdp...)
  FTOOLS: General and mission-specific tools to manipulate FITS files (https://heasarc.gsfc.nasa.gov/lheasoft/ftools/ftools_subpacks.html)
  FITSIO: Core library responsible for reading and writing FITS files
  fv: General FITS file browser/editor/plotter with a graphical user interface
  XSTAR: Tool for calculating the physical conditions and emission spectra of photoionized gases
- To load it: ml ASTRO heasoft
  which also loads CALDB automatically
- Version installed (fversion): 6.31 (6.30)
- Acknowledgement:
  If FTOOLS has been useful in your research, please reference this site (http://heasarc.gsfc.nasa.gov/ftools) and use the ASCL reference for HEASoft [ascl:1408.004] or the ASCL reference for the original FTOOLs paper [ascl:9912.002]:
  Blackburn, J. K. 1995, in ASP Conf. Ser., Vol. 77, Astronomical Data Analysis Software and Systems IV, ed. R. A. Shaw, H. E. Payne, and J. J. E. Hayes (San Francisco: ASP), 367.

SAS: The Science Analysis Software (SAS) https://www.cosmos.esa.int/web/xmm-newton/what-is-sas.
- Description: The Science Analysis System (SAS) is a collection of tasks, scripts and libraries, specifically designed to reduce and analyze data collected by the XMM-Newton observatory.
  SAS pages at the XMM-Newton SOC: https://www.cosmos.esa.int/web/xmm-newton/sas
  XMM-Newton calibration information: https://www.cosmos.esa.int/web/xmm-newton/calibration
- To load: #ToDo
- Version installed: 21.0
- Acknowledgement:

caldb: HEASARC's calibration database (CALDB) system (https://heasarc.gsfc.nasa.gov/docs/heasarc/caldb/caldb_intro.html)
- Description: The HEASARC's calibration database (CALDB) system stores and indexes datasets associated with the calibration of high energy astronomical instrumentation.
- To load it: ml ASTRO CALDB
- Version installed: LAST UPDATE: 20220331
- Acknowledgement: see HEASOFT above.

ciao: Chandra Interactive Analysis of Observations (https://cxc.cfa.harvard.edu/ciao/)
- Description: CIAO is the software package developed by the Chandra X-Ray Center for analysing data from the Chandra X-ray Telescope. It can also be used with data from other Astronomical observatories, whether ground or space based.
- To load it: ml anaconda3 then conda activate ciao
  or from own module with: ml ASTRO conda+/ciao then conda activate ciao
- Version installed (ciaover): caldb_main 4.9.7, ciao 4.14.0, ciao-contrib 4.14.2, ds9 8.3, sherpa 4.14.0
- Acknowledgement: Fruscione et al. 2006, SPIE Proc. 6270, 62701V, D.R. Silvia & R.E. Doxsey, eds.

fermitools: Fermi-LAT Data Analysis Tools (https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/ https://github.com/fermi-lat/Fermitools-conda/wiki/The-Fermitools-and-Conda)
- Description: The Fermitools (also known as the Fermi ScienceTools) is a suite of data analysis software provided by the Fermi-LAT collaboration that is used in the analysis of data produced by the Fermi Gamma-Ray Space Telescope.
- To load it: ml anaconda3 then conda activate fermitools
  or from own module with: ml ASTRO conda+/fermitools
  there is a second environment called fermi
- Version installed (conda list fermi): fermipy 1.1.0, fermitools 2.2.0, fermitools-data 0.18
- Acknowledgement: FSSC https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/

starlink: Starlink Software Collection (https://starlink.eao.hawaii.edu/starlink/2021A)
- Description: The Starlink Software Collection provides access to a large number of Astronomical data reduction, analysis, and visualisation tools.
- To load it: ml ASTRO starlink then init-starlink
- Version installed: 2021A
- Acknowledgement: “The Starlink software (Currie et al 2014) is currently supported by the East Asian Observatory.” Currie et al. 2014 2014ASPC..485..391C.

TRM: Tom Marsh's ultracam and molly (and related) software packages (https://cygnus.astro.warwick.ac.uk/phsaap/software/ https://github.com/trmrsh)
- Description: molly: 1D spectrum analysis program. ultracam: aperture photometry pipeline. See all packages and documentation at /cluster/apps/software/trm/trm/html/
- To load it: ml ASTRO trm then init-starlink
- Version installed: molly v. 1.1.8, ultracam 8.1.17
- Acknowledgement: T. Marsh.

ds9: SAO Image ds9 (https://sites.google.com/cfa.harvard.edu/saoimageds9)
- Description: An image display and visualization tool for astronomical data.
- To load it: ml ASTRO ds9
- Version installed: 8.3
- Acknowledgement: SAOImageDS9 development has been made possible by funding from the Chandra X-ray Science Center (CXC), the High Energy Astrophysics Science Archive Center (HEASARC) and the JWST Mission office at Space Telescope Science Institute. To cite SAOImageDS9 in your paper, please use: 2003adass..295..489J

astroconda: Third-party add-on channel to provide easy access to STScI’s software packages (https://astroconda.readthedocs.io/en/latest/#)
- Description: AstroConda is a free Conda channel maintained (until Feb. 2023) by the Space Telescope Science Institute (STScI) in Baltimore, Maryland.
  This channel provides tools and utilities required to process and analyze data from the Hubble Space Telescope (HST), James Webb Space Telescope (JWST), and others.
- To load it: ml anaconda3 then conda activate astroconda
- Version installed: ?
- Acknowledgement: STScI

astrosource: Analysis script for sources with variability in their brightness (https://pypi.org/project/astrosource/).
- Description: automating optical astronomy measurement, calibration and analysis for variable stellar sources from provided photometry.
- To load it: ml anaconda3 then conda activate astrosource
- Version installed: 1.7.0 ?
- Acknowledgement: Written by Michael Fitzgerald and Edward Gomez. Fitzgerald et al. (2021)

iraf: Image Reduction and Analysis Facility (https://iraf-community.github.io/)
- Description: IRAF is the Image Reduction and Analysis Facility, a general purpose software system for the reduction and analysis of astronomical data. Development and maintenance of IRAF is discontinued since 2013.
- To load it: ml ASTRO iraf
- To set it up (first time only): setup-iraf
- To start iraf: init-iraf-ecl (which has the arrow and backspace keys working properly) or init-iraf-cl
- Version installed: 2.17
- Acknowledgement: The software was written by the National Optical Astronomy Observatories (NOAO) in Tucson, Arizona.

psrcat: ATNF pulsar catalog (https://www.atnf.csiro.au/research/pulsar/psrcat/)
- Description: The catalogue includes all published rotation-powered pulsars, including those detected only at high energies. It also includes Anomalous X-ray Pulsars (AXPs) and Soft Gamma-ray Repeaters (SGRs) for which coherent pulsations have been detected. However, it excludes accretion-powered pulsars such as Her X-1 and the X-ray millisecond pulsars, for example, SAX J1808.4-3658.
- To run it: psrcat
- Version installed (psrcat -v): Software version: 1.50. Catalogue version number = 1.70
- Acknowledgement: If you make use of the ATNF Pulsar Catalogue in a publication, we request that you acknowledge the source of the information by referencing the paper: Manchester, R. N., Hobbs, G. B., Teoh, A. & Hobbs, M., Astron. J., 129, 1993-2006 (2005) (astro-ph/0412641), which gives a full description of the catalogue, and by quoting the web address http://www.atnf.csiro.au/research/pulsar/psrcat.

NE2001 and ymw16: Dispersion measure (pulsar) distance models.
- Description: Two common models for the Galactic distribution of free electrons. Both YMW16 and NE2001 can convert from pulse dispersion measure (DM, in pc/cm^3) to distance (in pc or kpc), or vice-versa, using the corresponding electron density models.
- To load/start it use NE2001 and ymw16 commands
- Version installed: 2001 and 2017, static.
- Acknowledgements:

NE2001: Cordes & Lazio (2002) https://arxiv.org/abs/astro-ph/0207156
See also: /cluster/apps/software/ASTRO/ne2001/src.NE2001/code.ps

YMW16: Yao, Manchester and Wang, 2017, Astrophys. J., 835, 29; arXiv:1610.09448
See also: /cluster/apps/software/ymw16/src/README

See also: https://apps.datacentral.org.au/pygedm/
/cluster/apps/software/ASTRO/pygedm/README.md

tempo2: Pulsar timing software (https://bitbucket.org/psrsoft/tempo2/src/master/; see also http://www.pulsarastronomy.net/wiki/Software/PSRSoft)
- Description: Tempo2 is a high precision pulsar timing tool. See user manual at https://www.jb.man.ac.uk/research/pulsar/Resources/tempo2_manual.pdf
- To load it: ml ASTRO
- Version installed: 2023.05.1
- Acknowledgement: Hobbs et al. (2006). TEMPO2 is a software package for pulsar timing, developed at the ATNF mainly by George Hobbs and Russell Edwards. Significant enhancements have also been made by Joris Verbiest.

ATLAS: Stellar atmosphere models (..)
- Description: blah... See online documentation at blah...
- To load it: any modules?
- To use it see README: path here (must be in group 'physlinux_manuelli')

/work/olsen/_group/astroparticle/Icarus-grids/

- Data files and spectra here: path
- Icarus photometric grids here:
  The full ATLAS9 grid is at /work/olsen/_group/astroparticle/Icarus-grids/Grids/photo_grids/ATLAS9/h5data
  , along with some of the filter specific grids.
- Version installed: ATLAS9

HDFview: HDF (5&4) file viewer.
- Description: HDFView software consists of the HDFView utility and the Java HDF Object Package. HDFView is a visual tool written in Java for browsing and editing HDF (HDF5 and HDF4) files. HDFView uses the Java HDF Object Package, which implements HDF4 and HDF5 data objects in an object-oriented form. Using a recent version of HDFView (at least 3.4.99), you can:
  - View a file hierarchy in a tree structure
  - Create new files, add or delete groups and datasets
  - View and modify the content of a dataset
  - Add, delete and modify attributes
- To load it (via anaconda): ml anaconda3; hdfview
- Version installed: 2.14
- Acknowledgement (and more recent versions): https://www.hdfgroup.org/download-hdfview/