Getting Started
Connect to the Linux server and 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. Software on the Linux compute servers are installed as requested. If you require a certain program or a particular version, please have your advisor or faculty member contact us to get it installed.
Running Common Programs
Matlab
- Open a terminal window and type
matlabfor the default install. - Otherwise you can type the command
module availto see what versions we have available. Use the commandmodule load matlab-xxxxxwith the proper version. Then run normally.
- Open a terminal window and type
Ansys.
- Fluent.
- Open a terminal window and type
fluentto run latest version available. - Otherwise navigate to
/usr/localand pick from one of the versions labeledANSYS-XX.Xto pick your version of Ansys. - Fluent can be found under
/usr/local/ANSYS-XX.X/ansys_inc/vXXX/fluent/bin/fluent
- Open a terminal window and type
- For All Other Ansys Products.
- Navigate to
/usr/local/ANSYS-XX.Xto pick your version of Ansys. - Programs will be found under
/usr/local/ANSYS-XX.X/ansys_inc/vXXX/ProductName/bin/ExecutableNamefor most products. - e.g.
/usr/local/bin/ANSYS-16.1/ansys_inc/v161/CFX/bin/cfx5
- Navigate to
- Fluent.
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
- 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)
- 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
- Change to the directory you created during setup.
FDS
- Open a terminal window and enter
bashto switch to bash shell - Set the environment variables needed by entering
source /usr/local/FDS/FDS6/bashrc_fds - Enter
fdsto run FDS
- Open a terminal window and enter
Synopsys (Hspice, Synthesis, VCS, etc.)
- For the latest version, set your environment variables needed by entering
source /usr/local/synopsys/synopsys.cshrcfrom 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
- For the latest version, set your environment variables needed by entering
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 -hor more help is available at Gromacs.org
- Load the proper environment variables. Open a terminal window and execute
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/binfor all available.
- Load the proper environment variables. Open a terminal window and execute
- 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/binfor all available.
- Load the proper environment variables. Open a terminal window and execute
- OpenMPI
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
- Open a terminal window and execute with
- 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++ -hfor command line options
- Load the proper environment variables. Open a terminal window and execute
- 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++ -hfor command line options
- Load the proper environment variables. Open a terminal window and execute
- Serial/OpenMP version
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
- Load the proper environment variables. Open a terminal window and execute
- 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
- Load the proper environment variables. Open a terminal window and execute
- NWChem + OpenMPI
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.
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