Using the Linux Servers

Getting Started

Contrary to Windows, running programs on the Linux servers requires opening a command line window, called a terminal, and typing a command in the terminal window to open your program. Generally, using the Linux servers requires these steps.

  • Connect to the Linux server using this guide
  • If you have not connected using SSH or X2go using a terminal window, and instead have connected with XRDP, or X2Go with GNOME, you must open a terminal window.
  • (If Required) set your environment variables with the source, setenv, or module command
  • Run your program by typing the command needed. See below for some common programs

Most programs are installed in /usr/local/. Please check our Software List to see if you are licensed to use the specific software.

 

Running Common Programs

  • Matlab

    • Open a terminal window and type matlab for the default install.
    • Otherwise you can type the command module avail to see what versions we have available. Use the command module load matlab-xxxxx with the proper version. Then run normally.
  • Ansys.

    • Fluent.
      • Open a terminal window and type fluent to run latest version available.
      • Otherwise navigate to /usr/local and pick from one of the versions labeled ANSYS-XX.X to pick your version of Ansys.
      • Fluent can be found under /usr/local/ANSYS-XX.X/ansys_inc/vXXX/fluent/bin/fluent
    • For All Other Ansys Products.
      • Navigate to /usr/local/ANSYS-XX.X to pick your version of Ansys.
      • Programs will be found under /usr/local/ANSYS-XX.X/ansys_inc/vXXX/ProductName/bin/ExecutableName for most products.
      • e.g. /usr/local/bin/ANSYS-16.1/ansys_inc/v161/CFX/bin/cfx5
  • Cadence/Virtuoso

    • Open a terminal window
    • Setup (You only need to do this once)
      • Copy the setup files to a new directory in your home directory. We call it “cadence” in this example. This includes a file on library locations (cds.lib), a color file (display.drf), and a hidden virtuoso environment file (.cdsenv)
        • cp -rT /usr/local/Cadence-2018/setup ~/cadence
    • To Run (Do this everytime you start the program)
      • Change to the directory you created during setup
        • cd ~/cadence
      • Load the virtuoso module to set up the needed environement variables
        • module load virtuoso
      • Run the program.
        • virtuoso
  • FDS

    • Open a terminal window and enter bash to switch to bash shell
    • Set the environment variables needed by entering source /usr/local/FDS/FDS6/bashrc_fds
    • Enter fds to run FDS
  • Synopsys (Hspice, Synthesis, VCS, etc.)

    • For the latest version, set your environment variables needed by entering source /usr/local/synopsys/synopsys.cshrc from a terminal
    • From your home directory run the program you require. e.g. hspice
    • To find the software available browse to /usr/local/synopsis/ for the latest version available.
    • For older versions of Synopys programs navigate to /usr/local/ and look for synopsys-XXXX
  • Gromacs

    • Load the proper environment variables. Open a terminal window and execute source /usr/local/gromacs/bin/GMXRC
    • Command line options can be found with gmx -h or more help is available at Gromacs.org
  • MPI development and services

    • OpenMPI
      • Load the proper environment variables. Open a terminal window and execute module load mpi/openmpi-x86_64
      • Executables include mpirun, mpicc, mpifort, and others. Navigate to /usr/lib64/openmpi/bin for all available.
    • MPICH
      • Load the proper environment variables. Open a terminal window and execute module load mpi/mpich-x86_64
      • Executables include mpirun, mpicc, mpif90, and others. Navigate to /usr/lib64/mpich/bin for all available.
  • Lammps

    • Serial/OpenMP version
      • Open a terminal window and execute with lmp_g++ < input_file
      • Command line options can be found with lmp_g++ -h
    • Lammps + OpenMPI
      • Load the proper environment variables. Open a terminal window and execute module load openmpi-x86_64
      • Execute with lmp_g++ < input_file
      • Execute lmp_g++ -h for command line options
    • Lammps + MPICH
      • Load the proper environment variables. Open a terminal window and execute module load mpich-x86_64
      • Execute with lmp_g++ < input_file
      • Execute lmp_g++ -h for command line options
  • NWChem

    • NWChem + OpenMPI
      • Load the proper environment variables. Open a terminal window and execute module load openmpi-x86_64
      • Execute with nwchem_openmpi input_file
      • Find more information here
    • NWChem + MPICH
      • Load the proper environment variables. Open a terminal window and execute module load mpich-x86_64
      • Execute with nwchem_mpich input_file
      • Find more information here

Quick Help

Command Description Example
cd path Change directories. cd .. goes up a level. cd ~ goes to your home directory. cd /usr/local/
ls -al optional_path Show items and their permissions in the current folder or location specified. ls -al /usr/local/
pwd Show where you are in the file hierarchy. pwd
setenv variable value Set an environment variable. Use a colon for multiple values. setenv PATH /usr/local/:${PATH}
source filename Used to set environment variables and execute commands in the current shell. source my_environment_variables.csh

If you want more information on how to use a certain UNIX command, type man command at any UNIX prompt. The command “man” is the help page tool for UNIX and command should be replaced with the UNIX command for which you need more information. For example: man cd  or for a general overview of a certain command you can use explain shell.