Quick start: Cheyenne

Logging in | Environment | Compiling | Debugging | Cheyenne queues | Submitting jobs

Once you have an account and the necessary software, you can log in and run jobs on the Cheyenne supercomputer.

Logging in also gives users access to these resources, depending on their allocations:

To run data analysis and visualization jobs on the Casper system's nodes, log in to Cheyenne and follow the procedures described here. There is no need to transfer output files from Cheyenne for this since Cheyenne and Casper mount the same GLADE file systems.


Logging in

To log in to the Cheyenne system, start your terminal or Secure Shell client and run an ssh command as shown here:

ssh -X -l username cheyenne.ucar.edu

You can use this shorter command if your Cheyenne username is the same as your username on your local computer:

ssh -X cheyenne.ucar.edu

After running the ssh command, you will be asked to authenticate to finish logging in.

 


Environment

The Cheyenne HPC system uses a Linux operating system and supports widely used shells on its login and compute nodes. Users also have several compiler choices. See Compiling below.

Operating system

SUSE Linux.

Scheduler

Altair PBS Pro. See Submitting jobs below for some basic information or this detailed documentation about using PBS Pro and running jobs.

Shells

The default login shell for new Cheyenne users is bash.To change the default, log in to the CISL Systems Accounting Manager (SAM). It may take several hours for a change to take effect. You can confirm which shell is set as your default by entering echo $SHELL on your Cheyenne command line. 

Environment modules

The Cheyenne module utility enables users to easily load and unload compilers and compatible software packages as needed, and to create multiple customized environments for various tasks.

Here are some of the most commonly used commands. (See the Environment modules page for more details.)

module av - Show which modules are available for use with the current compiler.

module help - List switches, subcommands, and arguments for the module utility. Specify a modulefile by name for help with an individual module.

module help netcdf

module list - List the modules that are loaded.

module load - Load the default version of a software package, or load a specified version.

module load modulefile_name
module load modulefile_name/n.n.n

module spider - List all modules that exist on the system.

module swap - Unload one module and load a different one. Example:

module swap netcdf pnetcdf

module unload - Unload the specified software package.

module unload modulefile_name

Compiling

Cheyenne users have access to Intel, PGI, and GNU compilers. The Intel compiler module is loaded by default.

After loading the compiler module that you want to use, identify and run the appropriate compilation wrapper command from the table below. (If your script already includes one of the following generic MPI commands, there is no need to change it: mpif90, mpif77, ftn; mpicc, cc; mpiCC and CC.)

Also consider using the compiler's diagnostic flags to identify potential problems.

Compiler Language Commands for serial programs Commands for programs
using MPI
Flags to enable OpenMP
(for serial and MPI)
Intel (default) Fortran ifort foo.f90 mpif90 foo.f90 -qopenmp
  C icc foo.c mpicc foo.c -qopenmp
  C++ icpc foo.C mpicxx foo.C -qopenmp

Include these flags for best performance when you use the Intel compiler:
-march=corei7 -axCORE-AVX2

PGI Fortran pgfortran (or pgf90 or pgf95) foo.f90 mpif90 foo.f90 -mp
  C pgcc foo.c mpicc foo.c -mp
  C++ pgcpp (or pgCC) foo.C mpicxx foo.C -mp
GNU Fortran gfortran foo.f90 mpif90 foo.f90 -fopenmp
  C gcc foo.c mpicc foo.c -fopenmp
  C++ g++ foo.C mpicxx foo.C -fopenmp

Debugging

CISL provides the ARM Forge tools, DDT and MAP, for debugging, profiling, and optimizing code in the Cheyenne environment.

Performance Reports is another ARM tool for Cheyenne users. It summarizes the performance of HPC application runs.

See Running DT, MAP and PR jobs.


Cheyenne queues

Most of the Cheyenne batch queues are for exclusive use, and jobs are charged for all 36 cores on each node that is used. Jobs in the shared use "share" queue are charged only for the cores used.

The "regular" queue, which has a 12-hour wall-clock limit, meets most users' needs for running batch jobs.

See the table on this page for information about other queues.


Submitting jobs

Schedule your jobs to run on Cheyenne by submitting them through the PBS Pro workload management system.

To submit a batch job, use the qsub command followed by the name of your batch script file.

qsub script_name

See this page for job script examples.

To start an interactive job, use the qsub command with the necessary options but no script file.

qsub -I -l select=1:ncpus=36:mpiprocs=36 -l walltime=01:00:00 -q regular -A project_code

To run jobs on the Casper cluster, see this documentation.


More detailed PBS Pro documentation

Submitting jobs with PBS

Scripts that you can adapt for your own jobs

 

Related training courses