Tag: software

Bash

Bash

Description

GNU Bash or simply Bash is a Unix shell and command language written by Brian Fox for the GNU Project as a free software replacement for the Bourne shell. First released in 1989, it has been used widely as the default login shell for most Linux distributions and Apple’s macOS Mojave and earlier versions. Bash is the default environment and scripting language for the cluster.

Bash keeps two hidden files in your home directory which are executed when you log in.  The first is your .bash_profile which is executed when you initially ssh onto the cluster. The second is your .bashrc which is executed each time you start a shell.  Updating these files is how you customize your environment on the cluster. In general you want to keep these clean and as close to the defaults as possible, as the more you put in there the more your login will slow down. See our guide for editing your .bashrc for more details.

For more on Bash see the following guides:

Examples

FASRC User Codes

Gaussian

Gaussian

Access

Please contact us if you require Gaussian access. It is controlled on a case-by-case basis and requires membership in a security group.

When you are not a member of this security group, you can still load the module, but you will not only be able to run Gaussian.

FASRC provides the module and basic instructions on how to launch Gaussian, but we do not provide support specifics on how to run Gaussian. For how to run Gaussian, refer to Gaussian documentation or your department.

Running Gaussian

Example batch file runscript.sh:

#!/bin/bash
#SBATCH -J my_gaussian # job name
#SBATCH -c 1 # number of cores
#SBATCH -t 01:00:00 # time in HH:MM:SS
#SBATCH -p serial_requeue # partition
#SBATCH --mem-per-cpu=800 # memory per core
#SBATCH -o rchelp.out # standard output file
#SBATCH -e rchelp.err # standard error file

module load gaussian/16-fasrc04

g16 CH4_s.gjf

To submit the job:

sbatch runscript.sh

Versions

You can search for gaussian modules with the command module spider gaussian:

[jharvard@boslogin02 ~]$ module spider gaussian

-----------------------------------------------------------------------------------------------------------------------------------------
gaussian:
-----------------------------------------------------------------------------------------------------------------------------------------
Description:
Gaussian, a computational chemistry software program

Versions:
gaussian/16-fasrc01
gaussian/16-fasrc02
gaussian/16-fasrc03
gaussian/16-fasrc04

And to see the details about a particular module, use commands module spider or module display:

[jharvard@boslogin02 ~]$ module spider gaussian/16-fasrc04

-----------------------------------------------------------------------------------------------------------------------------------------
gaussian: gaussian/16-fasrc04
-----------------------------------------------------------------------------------------------------------------------------------------
Description:
Gaussian, a computational chemistry software program

This module can be loaded directly: module load gaussian/16-fasrc04

Help:
gaussian-16-fasrc04
Gaussian, a computational chemistry software program

[jharvard@boslogin02 ~]$ module display gaussian/16-fasrc04
-----------------------------------------------------------------------------------------------------------------------------------------
/n/sw/helmod-rocky8/modulefiles/Core/gaussian/16-fasrc04.lua:
-----------------------------------------------------------------------------------------------------------------------------------------
help([[gaussian-16-fasrc04
Gaussian, a computational chemistry software program
]], [[
]])
whatis("Name: gaussian")
whatis("Version: 16-fasrc04")
whatis("Description: Gaussian, a computational chemistry software program")
setenv("groot","/n/sw/g16_sandybridge")
setenv("GAUSS_ARCHDIR","/n/sw/g16_sandybridge/g16/arch")
setenv("G09BASIS","/n/sw/g16_sandybridge/g16/basis")
setenv("GAUSS_SCRDIR","/scratch")
setenv("GAUSS_EXEDIR","/n/sw/g16_sandybridge/g16/bsd:/n/sw/g16_sandybridge/g16/local:/n/sw/g16_sandybridge/g16/extras:/n/sw/g16_sandybridge/g16")
setenv("GAUSS_LEXEDIR","/n/sw/g16_sandybridge/g16/linda-exe")
prepend_path("PATH","/n/sw/g16_sandybridge/g16/bsd:/n/sw/g16_sandybridge/g16/local:/n/sw/g16_sandybridge/g16/extras:/n/sw/g16_sandybridge/g16")
prepend_path("PATH","/n/sw/g16_sandybridge/nbo6_x64_64/nbo6/bin")

GaussView

RC users can download these clients from our Downloads page. You must be connected to the FASRC VPN to access this page. Your FASRC username and password are required to log in.

On MacOS: Move the downloaded file to the ‘Applications’ folder, unarchive it, and double click on the gview icon located in gaussview16_A03_macOS_64bit.

On Windows: Unarchive the file in the Downloads folder itself.

A pop up will appear saying “Gaussian is not installed”.

Click on OK. This would now open the gview interface.

In the case Gaussview doesn’t open on MacOS, do the following:

Go to the Applications folder > gaussview16 folder > Right click on gview and choose “Show Package Contents”

Go to the Contents folder of gview > MacOS folder > Right click on the gview executable and choose “Open”

A pop up will appear saying “Gaussian is not installed”. Click on OK. This would now open the gview interface.

 

Note: We do not have a license for Gaussview on the cluster. It needs to be run locally.  

Perl

Perl

Introduction & Setup

Perl is a high-level, general-purpose, interpreted, dynamic programming language. Perl packages are provided by CPAN. For newer versions of Perl, we recommend installing via Spack.

cpan

The CPAN module and it’s command line tool (cpan) can be used to install modules by name from the CPAN repository. Additionally, it recursively installs any modules that it depends on. If you’re using the cpan command for the first time, you’ll need to run through a series of configuration prompts. Running the cpan command will initiate a configuration session.

You may be prompted at the end to manually set the download URL list. Use the o conf init urllist command to initiate the configuration.
Setting the download URL preferences from the cpan prompt

Setting the download URL preferences from the cpan prompt.

You may also want cpan to automatically install dependencies. This can either be set in the interactive configuration, or later at the cpan prompt using the command:

cpan> o conf prerequisites_policy follow

Once cpan is setup, either simple one line command at the terminal prompt can be used to install CPAN modules:

perl -MCPAN -e 'install DBD::SQLite'   OR   cpan DBD::SQLite

Of course, your module will be something other than ‘DBD::SQLite’

Alternatively, cpan can be run interactively.
CPAN module install from the interactive shell

CPAN module install from the interactive shell

Examples

FASRC User Codes

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