Scientific Software in /usr/local/hssoft

This directory is mounted on Ubuntu 16 hosts.
 
Instructions for using installed software is given in alphabetic order.
 

AIPS

Dieter Engels

 

The Astronomical Image Processing System AIPS is a software package for calibration, data analysis, image display, plotting, and a variety of ancillary tasks on Astronomical Data. It comes from the National Radio Astronomy Observatory. It is primarily for Radio Astronomy. There are a manual AIPS Cookbook and FAQ (answers to Frequently Asked Questions) available.

To use AIPS at the Hamburger Sternwarte you require an AIPS User number and reserved disk space allocated. Contact Dieter Engels.

Anaconda

Wolfram Schmidt

 

This package is obsolete. For Ubuntu 18.04+ users, a current version is available under /hsopt. For Ubuntu 14/16 users, we recommend to create your own Anaconda under /data.

The free Python distribution Anaconda includes many popular Python packages for scientific data analysis and visualization (the yt package for postprocessing astrophysical simulation data is also installed). Anaconda also features Jupyter notebooks, which allow you to run Python from graphical notebooks via a web browser on local or remote hosts.

To install and update packages, simply run

  conda_install.sh <package>

  conda_update.sh <package>

Please do not use the native install or update commands (this might result in permission conflicts with other users)!

To use the Anaconda-based Python, IPython, and Jupyter, add the following line to your .bashrc file:

  export PATH="/usr/local/hssoft/anaconda3/bin:$PATH"

AtomDB

Jan Robrade

 

APEC (Atomic Plasma Emission Code). X-Ray database (Homepage), for use with IDL.

Binning Algorithms

Rainer Wichmann

 

Contour and adaptive binning algorithms written by Jeremy Sanders. As its name says, the adaptive binning algorithm adaptively bins X-ray data. The contour binning algorithm has a similar purpose, but the binning is done following the surface brightness contours. The codes are intended primarily for Chandra data. While they work with other instruments, the resulting bins should not be narrower than the instrument's PSF. To run the codes, add /usr/local/hssoft/jsbinning/bin to your path:

  export PATH="/usr/local/hssoft/jsbinning/bin:$PATH" # bash

CalDB

Jan Robrade

 

Calibration database for Chandra data, required by the CIAO software.

CalFUSE

Hans Moritz Guenther

 

CalFUSE is the pipeline for data from the FUSE satellite. To set the required environment variables:

. /hslocal/local/hssoft/CalFUSE/v3.2/bin/cfsetup.sh        # bash
source /hslocal/local/hssoft/CalFUSE/v3.2/bin/cfsetup.csh  # tcsh

User guide and other information can be found on the website http://fuse.pha.jhu.edu/analysis/calfuse.html .

CASA

Dieter Engels

 

The Common Astronomy Software Applications (CASA) package is a set of C++ tools bundled together under an iPython interface as a set of data reduction tasks. Its primary goal is supporting the data post-processing needs of the next generation of radio astronomical telescopes such as the ALMA and EVLA projects. It comes from a collaboration led be the National Radio Astronomy Observatory.

To use CASA at the Hamburger Sternwarte you have to add to your PATH: /usr/local/hssoft/CASA/casapy-24.0.8115-001/casapy and start CASA by typing "casapy".

Chianti

Jan Robrade

 

Atomic database (Homepage), for use with IDL. In idl_startup.pro:

defsysv,'!xuvtop','/usr/local/hssoft/chianti/dbase/' 
defsysv,'!ioneq_file',!xuvtop+'ioneq/mazzotta_etal.ioneq'
defsysv,'!ioneq_file',!xuvtop+'ioneq/arnaud_rothenflug.ioneq'
defsysv,'!abund_file',!xuvtop+'abundance/cosmic.abund'

CIAO

Jan Robrade

 

Chandra Interactive Analysis of Observations, for analysing Chandra data. More information on the homepage.
To set required environment variables (csh, tcsh):

source /usr/local/hssoft/ciao/bin/ciao.csh

(bash):

source /usr/local/hssoft/ciao/bin/ciao.bash

(ksh):

source /usr/local/hssoft/ciao/bin/ciao.ksh

Cloudy

Rainer Wichmann

 

Cloudy ist ein Programm zur Simulation astrophysikalischer Plasmen und ihrer Spektren (Homepage). Zum Starten:

(ksh, bash):

. /usr/local/hssoft/cloudy/c10.00/sourcecl.sh
cloudy < Inputdatei > Outputdatei

(csh, tcsh):

source /usr/local/hssoft/cloudy/c10.00/sourcecl.csh
cloudy < Inputdatei > Outputdatei

Anleitungen sind im Verzeichnis /usr/local/hssoft/cloudy/c10.00/docs zu finden. Die vorherige Version steht weiterhin im Verzeichnis /usr/local/hssoft/cloudy/c08.00/bin_32 (32 bit) bzw. /usr/local/hssoft/cloudy/c08.00/bin_64 (64 bit) zur Verfügung.

CORA

Rainer Wichmann

 

Cora ist ein interaktives Programm zum Fitten von Emissionslinien. Es benutzt die Poisson-Statistik, und ist daher auch für Spektren mit kleinen Zählraten geeignet. Zum Starten:

(csh, tcsh):

setenv PATH $PATH":/usr/local/hssoft/cora/bin"
cora

(ksh, bash):

export PATH=$PATH":/usr/local/hssoft/cora/bin"
cora

DS9

Rainer Wichmann

 

FITS viewer. May be used standalone, but can also communicate with other software.

Eclipse

Günter Wiedemann

 

eclipse provides Unix command line utilities to work with FITS headers and data without the need of invoking software packages like IRAF.

Usage: first call /usr/local/hssoft/eclipse/eclipse-4.7.0/bin/e_setup, which creates a file $HOME/.eclipse-rc that you need to source in your shell:
(ksh, bash: . .eclipse-rc, csh, tcsh: source .eclipse-rc).
ESO provides a Eclipse User's Guide

The command line utilities (e.g. dfits to list the header) are actually more or less a byproduct of the eclipse software:

"eclipse is a library written in ANSI C, offering services dedicated to astronomical data processing. There are services to read/write FITS files, to perform image processing, 3d filtering, compute photometry, image quality, statistics, manipulate image files, etc. These services are all accessible to the C programmer directly, the documentation is contained within the source code in the header files."

ESO Pipeline

Rainer Wichmann

 

The ESO Reduction Pipeline is an ESO product, documentation available from ESO.

cp -a /usr/local/hssoft/eso_pipelines/gasgano $HOME/
export CPLDIR=/usr/local/hssoft/eso_pipelines
export PATH=$PATH:/usr/local/hssoft/eso_pipelines/bin
export PATH=$PATH:$HOME/gasgano/bin
export LD_LIBRARY_PATH=/usr/local/hssoft/eso_pipelines/lib

Funtools

Rainer Wichmann

 

Funtools is a set DS9-compatible basic tools for analyzing astronomical FITS images, event files, and tables. More information can be found at: https://www.cfa.harvard.edu/~john/funtools/

GCC

Rainer Wichmann

 

The current version of the gcc compiler: /usr/local/hssoft/gcc/current/bin/(gcc|gfortran|g++)

GDL

Rainer Wichmann

 

GNU Data Language is a free clone of IDL, with identical syntax. However, not all IDL functions are implemented (yet), thus your mileage may vary.

Comparison GDL vs. IDL Also see the file NEWS in /usr/local/hssoft/gdl/gdl-<version>/

Usage: source the script 'setup.sh' (ksh/bash), then start GDL with the command 'gdl'.

. /usr/local/hssoft/gdl/setup.sh
gdl

GRACE

Rainer Wichmann

 

Grace is a WYSIWYG (What You See Is What You Get) 2D plotting tool for the X window system. There's a user guide and a tutorial available. Required for SAS.

GRTensor II

Rainer Wichmann

 

A Maple extension, mainly for general relativity (see www.grtensor.org). Tu use it, copy /usr/local/hssoft/grtensor/grii/mapleinit.sample to ~/.mapleinit (or add, if you already have a  ~/.mapleinit). In Maple then enter the following command:

grtw();

GILDAS

Dieter Engels

 

GILDAS, the "Grenoble Image and Line Data Analysis Software", is a collection of software developped by the Observatoire de Grenoble and IRAM, oriented towards radioastronomical applications in the mm- and submm-range.

To use GILDAS software make the setup as described in /hslocal/local/hssoft/gildas/Readme. Manuals are available from the GILDAS homepage.

HEADAS/HEASOFT

Jan Robrade

 

"A Unified Release of the FTOOLS and XANADU Software Packages." Includes XSPEC. To start:

  • bash, ksh:
    export HEADAS="/usr/local/hssoft/headas"
    . $HEADAS/headas-init.sh
    
  • tcsh, csh:
    setenv HEADAS "/usr/local/hssoft/headas"
    source $HEADAS/headas-init.csh
    

Required by the SAS software.

IDL

Volkmar Niemann

 

Interactive Data Language. The license server is at the RRZ, in case of service interruptions only the IDL demo version is available. To notify the RRZ of service interruptions: Fon. 8:30-20:30: (040) 42838 7790, email see Serviceline. The demo version runs for a maximum of 7 minutes and cannot save sessions, print, or write out text files. However, it is possible to save plots as postscript files.

 

Numerical issue:
> print,format='(D15.6)', double(54237.53562)
> 54237.535156
  However, if you add a 'd' at the end of the number:
> print,format='(D15.6)', 54237.53562d
> 54237.53562

 

To start ( bash | ksh ) (current default version):

. /usr/local/bin/hs_idl.(sh|ksh)
idl

Please note: idlde shortcuts may not work if 'Num Lock' is active.

A sample idl_startup.pro can be found in ~st2j207/idl_startup.pro

Emacs-Support: in $HOME/.emacs add this:

(autoload 'idlwave-mode "idlwave" "IDLWAVE Mode" t)
(autoload 'idlwave-shell "idlw-shell" "IDLWAVE Shell" t)
(setq auto-mode-alist
 (cons '("\\.pro\\'" . idlwave-mode) auto-mode-alist))
;; Syntax Highlighting
(add-hook 'idlwave-mode-hook 'turn-on-font-lock)

ICC/IFC

Andreas Schweitzer

 

The Intel Compiler should provide best performance for Intel computers (surprise!). There are Fortran and C/C++ compilers. For more or less helpful information see /usr/local/hssoft/intel/README.HS.

Versions 8.0 and 7.1 are installed:

Fortran 8.0 (bash, ksh):

. /usr/local/hssoft/intel/fc_80/bin/ifortvars.sh

or (chs, tcsh):

source /usr/local/hssoft/intel/fc_80/bin/ifortvars.csh

C/C++ 8.0 (bash, ksh):

. /usr/local/hssoft/intel/cc_80/bin/iccvars.sh          

or (chs, tcsh):

source /usr/local/hssoft/intel/cc_80/bin/iccvars.csh

Fortran/C 7.1 (bash, ksh):

. /usr/local/hssoft/intel/compiler70/ia32/bin/ifcvars.sh

or (chs, tcsh):

source /usr/local/hssoft/intel/compiler70/ia32/bin/ifcvars.csh

IRAF

Rainer Wichmann

 

Image Reduction and Analysis Facility. Like MIDAS, it does almost everything except brewing coffee. Use the command startiraf for starting.

Documentation, FAQ and online help pages available on the IRAF Homepage.

MAPLE

Rainer Wichmann

 

Maple 17 provides users with two worksheet interfaces (graphical user interfaces) and a command-line (text-based) interface. By default, worksheets open in the enhanced and more modern Standard Worksheet. The Classic Worksheet, available on Windows and Linux platforms, has the traditional Maple worksheet look and uses less memory.

Standard Worksheet Maple

To start Standard Worksheet Maple 17, modify your command search path to contain your Maple 17 directory (/usr/local/hssoft/maple/bin) and execute xmaple or execute the full path (/usr/local/hssoft/maple/bin/xmaple).

Classic Worksheet Maple

To start Classic Worksheet Maple 17, modify your command search path to contain your Maple 17 directory (/usr/local/hssoft/maple/bin) and execute maple -cw or execute the full path (/usr/local/hssoft/maple/bin/maple -cw).

Command-line Maple

The Command-line version of Maple has a text-based user interface. While allowing complete access to the mathematical engine, the Command-line version of Maple requires less system resources. To start Command-line Maple, modify your command search path to contain your Maple 17 directory (/usr/local/hssoft/maple/bin) and execute maple or execute the full path (/usr/local/hssoft/maple/bin/maple).

Matlab

Rainer Wichmann

 

Matlab is a technical computing environment for high-performance numeric computation and visualization

/usr/local/hssoft/matlab/bin/matlab

MIDAS

Hans-Jürgen Hagen

 

Munich Image Data Analysis System. Like IRAF, only different. To start, use the command inmidas.

In case of display issues (black display window)  Grafikfenster) it may help to put the following line into $HOME/midwork/login.prg
ini/dis ? ? ? ? RGBQ

If you want to use EXSAS (for ROSAT X-ray data), please note that not every MIDAS version is compatible with every EXSAS version. Working combinations are:  MIDAS 01FEB / EXSAS 01APR. For tcsh users, add in .tcshrc :

# MIDAS setup
setenv MIDASHOME /usr/local/hssoft/midas
setenv MIDVERS 01FEB
source $MIDASHOME/exsas/01APR_EXP/EXSAS.csh

For bash users, add in .bashrc

MIDASHOME=/usr/local/hssoft/midas; export MIDASHOME
MIDVERS=01FEB; export MIDVERS
. $MIDASHOME/exsas/01APR_EXP/EXSAS.bash

Online documentation on the MIDAS Homepage.

Numarray

Rainer Wichmann

 

Numerische Erweiterung für Python, wird für GDLgebraucht. Wer es benutzen will, sollte /usr/local/hssoft/numarray in seiner PYTHONPATH Umgebungsvariablen haben.

P2PP

Rainer Wichmann

 

For usage information see P2PP User Manual at ESO

You may want to have a file $HOME/.p2pp.cf in your home directory, with the following content:

CACHE.FOLDER    "/home/hslxrsrv3/USERNAME/p2pp-2-cache"
IMPEX.FOLDER    "/home/hslxrsrv3/USERNAME/impex"
INSTRUMENTS.IPVERSIONING.IPCACHE.FOLDER "/home/hslxrsrv3/USERNAME/p2pp-2-cache/instruments"

Version 3.4.0 may be called like:

export JAVA_HOME=/usr/local/hssoft/jre7_32/
/usr/local/hssoft/p2pp/bin/p2pp

Older versions: /usr/local/hssoft/p2pp-X.Y/bin/p2pp

PGPLOT

Rainer Wichmann

 

Vektor plotting library for C und Fortran. For help see online manual. To compile a C program:

gcc -I/usr/local/hssoft/pgplot -c programm.c
g77 -O -o progamm programm.o -L/usr/local/hssoft/pgplot -L/usr/X11R6/lib -lcpgplot -lpgplot -lX11
oder für Tk/Tcl:
g77 -o programm programm.o -L/usr/local/hssoft/pgplot -ltkpgplot -lcpgplot -lpgplot -L/usr/lib -ltk8.4 -ltcl8.4 -L/usr/X11R6/lib -lX11 -ldl

To start a PGPLOT program, /usr/local/hssoft/pgplot has to be in the environment variable LD_LIBRARY_PATH, and the environment variable PGPLOT_DIR=/usr/local/hssoft/pgplot needs to be set:

export PGPLOT_DIR=/usr/local/hssoft/pgplot
export LD_LIBRARY_PATH="/usr/local/hssoft/pgplot:$LD_LIBRARY_PATH"

or (csh)

setenv PGPLOT_DIR /usr/local/hssoft/pgplot
setenv LD_LIBRARY_PATH "/usr/local/hssoft/pgplot:$LD_LIBRARY_PATH"

PINTofALE

Jan Robrade

 

PINTofALE is a package of IDL routines for analysing and simulating X-ray spectra incorporating several atomic databases (CHIANTI 4.2, APED, SPEX).

For usage, see /usr/local/hssoft/PINTofALE/README

SAS

Jan Robrade

 

Explanations, threads, etc. can be found here.

SAS runs with the following setup (important: set the LANG environment variable!):

  • bash, ksh:
    export LHEASOFT=/usr/local/hssoft/lheasoft/Linux_2.2_i686
    . $LHEASOFT/lhea-init.sh
    export GRACE_HOME=/usr/local/hssoft/grace/grace
    export SAS_DIR=/usr/local/hssoft/sas/xmmsas
    export SAS_PATH=$SAS_DIR
    export SAS_CCFPATH=/usr/local/hssoft/sas/ccf/
    . $SAS_DIR/sas-setup.sh
    export PATH=$PATH:/usr/local/hssoft/xpa2.1.3/bin/:/usr/local/hssoft/ds9_new/:$GRACE_HOME/bin/
    export LANG=C
    export XPA_METHOD=local
    
  • tcsh, csh sollte entsprechend funktionieren:
    setenv LHEASOFT /usr/local/hssoft/lheasoft/Linux_2.2_i686
    source $LHEASOFT/lhea-init.csh
    setenv GRACE_HOME /usr/local/hssoft/grace/grace
    setenv SAS_DIR /usr/local/hssoft/sas/xmmsas
    setenv SAS_PATH $SAS_DIR
    setenv SAS_CCFPATH /usr/local/hssoft/sas/ccf/
    . $SAS_DIR/sas-setup.sh
    setenv PATH $PATH:/usr/local/hssoft/xpa2.1.3/bin/:/usr/local/hssoft/ds9_new/:$GRACE_HOME/bin/
    setenv LANG C
    setenv XPA_METHOD local
    

SExtractor

Rainer Wichmann

 

SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it performs rather well on moderately crowded star fields.

For running it just type

/usr/local/hssoft/SEXtractor/sextractor-2.5.0/bin/sex
or (older Versions):/usr/local/hssoft/SEXtractor/sextractor-2.4.4/bin/sex/usr/local/hssoft/SEXtractor/sextractor-2.4.3/bin/sex

More information: http://terapix.iap.fr/rubrique.php?id_rubrique=91/

SMART

Felix Bunzel

 

SMART, developed by the Spitzer IRS team at Cornell, is an IDL-based software tool for processing Spitzer IRS observations. It allows the user to perform a wide variety of processing and analysis tasks in real time.

To use the SMART software copy the four *.idl files located at /hslocal/local/hssoft/smart/smart_bin/ as well as the script smart that can be found at /hslocal/local/hssoft/smart/smart/ to your smart-user-directory in your home directory. Set the path to your smart-user-directory in your copy of the script smart and start the script.

For more information consult the SMART website.

STARLINK

Rainer Wichmann

 

Starlink is/was (projekt officially ended in July 2005, maintained by Joint Astronomy Centre) 'yet another kitchen sink', similar to IRAF and MIDAS.

To use starlink:

source /usr/local/hssoft/star/etc/profile

oder (csh)

source /usr/local/hssoft/star/etc/login
source /usr/local/hssoft/star/etc/cshrc

TOPCAT abd STILTS

Jochen Liske

 

TOPCAT is a great table manipulation and plotting tool. STILTS offers essentially the same functionality as TOPCAT, but as a command-line tool.

tab_calc

Alexey Mints

 

Simple statistics tool. For documentation see /hslocal/local/hssoft/tab_calc/doc/manual.html

VisIt

Bastian Koertgen

 

VisIt is a tool for  visualising large data, similar to Paraview. Its advantage is that the complete simulation grid is read in.

export PATH="/usr/local/hssoft/visit/bin:${PATH}"
visit

XPA

Jan Robrade

 

The XPA messaging system (Homepage) provides seamless communication between many kinds of Unix programs, including X programs and Tcl/Tk programs. It also provides an easy way for users to communicate with XPA-enabled programs by executing XPA client commands in the shell or by utilizing such commands in scripts.

Required by the SAS software.