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Basic rules

always check the location where you read/write files and space availability. See df command.
AVOID using nfs file systems/mounts for your simulations, especially when running on multiple nodes.
This will double sometimes your execution time since for every read/write operation an extra IOwait time is needed to transfer information over the network.
Use a location mounted on a local disk, usually /export/work, /export-b/work/ or /scratch (on HPC nodes) and move your data after finishing in a desired location.

To learn

Commands

basic commands !!!
environment variables in Linux !!!
df (Check Disk Space) especially usefull options:
show mounts including Type: df -T
show mount location and type of current working directory: df -T .
du (disk usage) and especially useful option:
show total size, in human readable format, of current working forlder: du -hs
ncdu if it's installed, the simplest way to find out what and much space it occupies. RECOMMENDED instead of du
ssh command

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.

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Alternatively, you can use text-based web browsers such as "links" or "lynx".

Example:

Anaconda

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

Code Block

[username@computername ~]$ ml anaconda3

#################################################################################
#### Please remember to run "init-conda" to fully setup the environment
#### 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
fermi                    /cluster/apps/software/anaconda3/2022.05/envs/fermi
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
(astrosource) [username@computername ~]$

heasoft: A Unified Release of the FTOOLS and XANADU Software Packages (https://heasarc.gsfc.nasa.gov/docs/software/heasoft/)
- Description:
- To load it: ml ASTRO heasoft
  which also loads CALDB automatically
- Version installed: 6.31 (6.30)
- Acknowledgement:

caldb: HEASARC's calibration database (CALDB) system (https://heasarc.gsfc.nasa.gov/docs/heasarc/caldb/caldb_intro.html)
- Description:
- To load it: ml ASTRO CALDB
- Version installed: LAST UPDATE: 20220331
- 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: ml anaconda3 then init-conda then conda activate ciao
  or from own module with: ml conda+/ciao
- Version installed:
- Acknowledgement:

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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 astro-software you should have these lines in your .bashrc

Code Block

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

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Software

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Description: The Starlink Software Collection provides access to a large number of Astronomical data reduction, analysis, and visualisation tools.
To load it: ml starlink
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: ml

ASTRO

trm

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: ml ds9
- Version installed: 8.3
- 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: ml anaconda3 then init-conda then conda activate astroconda
- Version installed:
- Acknowledgement: STScI

astrosource: Analysis script for sources with variability in their brightness (https://pypi.org/project/astrosource/).
- Description:
- To load it: ml anaconda3 then init-conda then conda activate astrosource
- Version installed:
- Acknowledgement: Fitzgerald et al. (2021)

iraf: Image Reduction and Analysis Facility (https://iraf-community.github.io/)
- Description:
- To load it: ml ASTRO iraf; init-iraf
- To set it up (first time only): setup-iraf
- Version installed: 2.17
- 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/start it use NE2001 and ymw16 commands
- 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

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Software

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Basic rules

To learn

Commands