Software Available on the Linux Network

Red Hat Enterprise Linux Workstations

From 2020 all Linux desktop workstations have been decommissioned and have been replaced with
AWS hosted virtual machines running RHEL7.

Additional computational facilities are provide by the School's High Performance Computing (HPC) and Physics Cluster resources. Much of the software listed is also available on these resources.

Additional software packages have been either installed on the workstation or placed in a shared file system which is mounted on each workstation under /usr/physics.

Normally /usr/physics/bin will appear first in each user's executable path. Consequently the command foo, for example, will invoke /usr/physics/bin/foo even when /bin/foo exists.

Software package	Command to run
RHEL 7 (64bit) distribution	Package List, run command: `rpm -qa`
Atom editor	The last version to run under RHEL7 was 1.50 this version is still available if required.
COMSOL 5.3a update 4	run: `comsol53` run: `comsol53a`
DS9 7.5	run: `ds9`
fftw^† nfft^† (OMP/threaded) cfitsio hdf5	Package is installed on each workstation
Geant4	see: `/usr/physics/geant4/README`
Gurobi-optimizer	run: `gurobi.sh` run: `gurobi_cl` See gurobi.com/documentation—local copy
IDL 9.0^1,2,3	run: `idl` or `idlde` Note¹ idl86 licensing problem Note² Off campus access Note³ Idl9.0 requires glibc vers ≥ 2.17 Mac version http://macsoft.physics.usyd.edu.au/idl/,choose installer based on chipset. Copy lic_server.dat to /Applications/INSTALL_DIR/license/lic_server.dat.
NEW Intel OneAPI HPC Toolkit	All the Intel Developer Tools now freely available run: `module avail` to see the components Example: `module add icc` enables `icc` and `ifort` See Getting Started Note: the 32 bit components are omitted but are installed
Intel C++ & Fortran Compiler Suite 16 update 4	See /usr/physics/intel/2016.4/documentation_2016/ Kept for the applications built with this toolset. For newer toolset see OneAPI above.
IRAF	see: `/usr/physics/iraf/readme`
julia^†(lts 2021-11-19)	run: `julia`
Karma Tools	see: `/usr/physics/karma/readme`
^♦Kile	run: `kile`
Latex Physics Customisations	see: `/usr/physics/tex/readme`
^♦LyX	run: `lyx`
Magma	run: `magma` Only licensed to run on Stan, Kyle and Cartman.
Mathematica 12.0 Mathematica 11.3	run: `math` or `mathematica` run: `math11` or `mathematica11`
Matlab - various versions are available. Matlab R2022a R2020b ..	run: `matlab2022a` run: `matlab2020a` run: `matlab2019b` etc
MESA Modules for Experiments in Stellar Astrophysics	Consult web site and source `/usr/physics/mesa/etc/mesa-environment.csh` before using. The latest versions of— MesaSDK can be found under /usr/physics/MesaSDK/ mesasdk-21.4.1 MESA can be found under /usr/physics/Mesa/ mesa-r15140 `setenv MESA_DIR /usr/physics/Mesa/mesa-r15140 setenv MESASDK_ROOT /usr/physics/MesaSDK/mesasdk-21.4.1 source $MESASDK_ROOT/bin/mesasdk_init.csh` Gyre can be found under /usr/physics/Gyre/ gyre-6.0.1
MIRIAD	see: `/usr/physics/miriad/readme`
OpenMPI	see: `/usr/physics/openmpi` see: `/usr/physics/openmpi-gnu`
Paraview	run: `paraview` run: `paraview52` run: `paraview55` run: `paraview581`
Period 04	run: `period04`
PGPlot^†	Development files and runtime installed on all workstations run: `pgdemo1, pgdemo2 ...`
Python	2.7.5 is the RHEL7 system version Python3 is available under /usr/physics/python see: `/usr/physics/python/README-*`
R^♣	R version 4.2.1 run: `R`
Rclone	see: rclone.org Access cloud storage (OneDrive, DropBox etc) from Linux.
SExtractor^†	run: `sex`
SolarSoft	see: `/usr/physics/ssw/readme`
Supermongo	run `sm`
^♦Thunderbird	run: `thunderbird` See configure Thunderbird for Office365 (Modern Authentication)
VMD 1.9.3	run `vmd`
^♦gftp ^♦filezilla	run `gftp` run `filezilla`
ansys lumerical	see: `/usr/physics/lumerical/README`

Software package

Command to run

       RHEL 7 (64bit) distribution
       Package List, run command: rpm -qa

Atom editor

The last version to run under RHEL7 was 1.50
this version is still available if required.

COMSOL 5.3a update 4

run: comsol53
run: comsol53a

DS9 7.5

run: ds9

fftw^†
nfft^† (OMP/threaded)
cfitsio
hdf5

Package is installed on each workstation

Geant4

see: /usr/physics/geant4/README

Gurobi-optimizer

run: gurobi.sh
run: gurobi_cl
See gurobi.com/documentation—local copy

IDL 9.0^1,2,3

run: idl or idlde
Note¹ idl86 licensing problem
Note² Off campus access
Note³ Idl9.0 requires glibc vers ≥ 2.17
Mac version http://macsoft.physics.usyd.edu.au/idl/,choose installer based on chipset.
Copy lic_server.dat to /Applications/INSTALL_DIR/license/lic_server.dat.

NEW Intel OneAPI HPC Toolkit

All the Intel Developer Tools now freely available
run: module avail to see the components
Example: module add icc enables icc and ifort
See Getting Started
Note: the 32 bit components are omitted but are installed

Intel
C++ & Fortran Compiler Suite 16 update 4

See /usr/physics/intel/2016.4/documentation_2016/
Kept for the applications built with this toolset.
For newer toolset see OneAPI above.

IRAF

see: /usr/physics/iraf/readme

julia^†(lts 2021-11-19)

run: julia

Karma Tools

see: /usr/physics/karma/readme

^♦Kile

run: kile

Latex Physics Customisations

see: /usr/physics/tex/readme

^♦LyX

run: lyx

Magma

run: magma
Only licensed to run on Stan, Kyle and Cartman.

Mathematica 12.0
Mathematica 11.3

run: math or mathematica
run: math11 or mathematica11

Matlab - various versions are available.
Matlab R2022a R2020b ..

run: matlab2022a
run: matlab2020a
run: matlab2019b
etc

MESA Modules for Experiments in Stellar Astrophysics

Consult web site and source


			/usr/physics/mesa/etc/mesa-environment.csh

before using.

The latest versions of—
MesaSDK can be found under /usr/physics/MesaSDK/
mesasdk-21.4.1
MESA can be found under /usr/physics/Mesa/
mesa-r15140


		setenv	MESA_DIR /usr/physics/Mesa/mesa-r15140

		setenv	MESASDK_ROOT /usr/physics/MesaSDK/mesasdk-21.4.1

		source	$MESASDK_ROOT/bin/mesasdk_init.csh

Gyre can be found under /usr/physics/Gyre/
gyre-6.0.1

MIRIAD

see: /usr/physics/miriad/readme

OpenMPI

see: /usr/physics/openmpi
see: /usr/physics/openmpi-gnu

Paraview

run: paraview
run: paraview52
run: paraview55
run: paraview581

Period 04

run: period04

PGPlot^†

Development files and runtime installed on all workstations
run: pgdemo1, pgdemo2 ...

Python

2.7.5 is the RHEL7 system version
Python3 is available under /usr/physics/python
see: /usr/physics/python/README-*

R^♣

R version 4.2.1
run: R

Rclone

see: rclone.org
Access cloud storage (OneDrive, DropBox etc) from Linux.

SExtractor^†

run: sex

SolarSoft

see: /usr/physics/ssw/readme

Supermongo

run sm

^♦Thunderbird

run: thunderbird
See configure Thunderbird for Office365
(Modern Authentication)

VMD 1.9.3

run vmd

^♦gftp
^♦filezilla

run gftp
run filezilla

ansys lumerical

see: /usr/physics/lumerical/README

♦ —package installed from standard repository
♣ —package installed from Springdale Linux 7 computational core repository
† —locally built RPM in local yum repository