Local Linux Cluster
- info about the cluster status using ganglia (works only internally). If you choose then "cluster linux" , you see in "choose a node" the available computers.
- from outside, you have first to connect via ssh to login.stud.ntnu.no (or login.ansatt.ntnu.no). From there you can connect in the next step to a local computer.
- use nice/renice to lower the priority of your processes
- you can ran processes in parallel using MPI. Multithread libraries in C++, such as pthread, are also available.
Ganglia
Ganglia provides a web-based user interface that can be used to view activity and available processes on the Linux cluster. It can only be accessed internally. To do this, use ssh to access one of the computers in the cluster.
If one wants to use a graphical web browser, such as FireFox, one needs to use the optional argument -X (enables X11 forwarding). The arguments -Y (enables trusted X11 forwarding) and C (Requests compression of all data) can speed up the web browser.
Alternatively, you can use text-based web browsers such as "links" or "lynx".
Example:
ssh -XYC username@login.stud.ntnu.no
ssh -XYC computername.phys.ntnu.no
# Open browser
firefox -no-remote -no-xshm http://bird/ganglia/
# links http://bird/ganglia/
# lynx http://bird/ganglia/
Software
All centralized astro-software (binaries and source) is placed under /cluster/apps/software/, which should be exported as the environmental variable $SOFTWARE.
To use it, run first "ml ASTRO" to load the ASTRO workspace. This will set environmental variables required for some tools/programs to run.
Note: currently only bash shell is supported (SHELL=/bin/bash).
Some python packages are installed via anaconda (https://anaconda.cloud/package-categories/scientific). To load it type:
$ ml anaconda3
Then run:
$ init-conda
or
$ eval "$(conda shell.bash hook)"
Then to see the available environments type:
$ 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
#fermi /cluster/apps/software/anaconda3/2022.05/envs/fermi
#iraf /cluster/apps/software/anaconda3/2022.05/envs/iraf
#python-2.7 /cluster/apps/software/anaconda3/2022.05/envs/python-2.7
More details on all the available astro-software:
- heasoft: A Unified Release of the FTOOLS and XANADU Software Packages (https://heasarc.gsfc.nasa.gov/docs/software/heasoft/)
- Description:
- To load it:
- Version installed:
- Acknowledgement:
- caldb: HEASARC's calibration database (CALDB) system (https://heasarc.gsfc.nasa.gov/docs/heasarc/caldb/caldb_intro.html)
- Description:
- To load it:
- Version installed:
- Acknowledgement:
- 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:
- Version installed:
- Acknowledgement:
- fermitools: Fermi-LAT Data Analysis Tools (https://fermi.gsfc.nasa.gov/ssc/data/analysis/software/)
- Description:
- To load it:
- Version installed:
- Acknowledgement:
- 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:
- Version installed: 2021A ?
- Acknowledgement:
- TRM: Tom Marsh's ultracam and molly (and related) software packages (https://cygnus.astro.warwick.ac.uk/phsaap/software/)
- Description: molly: 1D spectrum analysis program. ultracam: aperture photometry pipeline.
- To load it:
- Version installed:
- Acknowledgement: T. Marsh, V. Dhillon, ...
- 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:
- Version installed:
- Acknowledgement: SAO
- 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:
- Version installed:
- Acknowledgement: STScI
- astrosource: Analysis script for sources with variability in their brightness (https://pypi.org/project/astrosource/).
- Description:
- To load it:
- Version installed:
- Acknowledgement: Fitzgerald et al. (2021)
- iraf: Image Reduction and Analysis Facility (https://iraf-community.github.io/)
- Description:
- To load it:
- Version installed:
- Acknowledgement:
- psrcat: ATNF pulsar catalog (https://www.atnf.csiro.au/research/pulsar/psrcat/)
- Description:
- To load it:
- Version installed: $ psrcat -v. Software version: 1.50. Catalogue version number = 1.69
- Acknowledgement: Manchester, R. N., Hobbs, G. B., Teoh, A. & Hobbs, M., Astron. J., 129, 1993-2006 (2005) (astro-ph/0412641)
- ne2001 and ymw16: Dispersion measure (pulsar) distance models.
- Description:
- To load it:
- Version installed:
- Acknowledgement:
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