HPC user guide

System Overview

Joker Linux cluster is supporting research at NMSU. Joker is running CentOS 7.x with a common file system for storing data.

Joker is implemented with Lenovo NextScale M5 servers and QDR Infiniband for the interconnect.chassis.

Joker

OSCENTOS 7
CPUs (cores)328
RAM4GB/core
GPUs2 NVidia Tesla K40
InterconnectInfiniband FDR (56Gbps)
SchedulerSlurm 16.05
HardwareLenovo NextScale M5

Joker has 7 compute nodes. Each node has 64GB of RAM, two Intel E5-2640 v3 CPUs with 8 cores each. One of the compute nodes doubles as GPU node, it has 2 Nvidia Tesla K40 GPUs installed as well.

 

Getting Started

To request access to Joker, visit our account request page. Most requests are honored within 2 business days.

Once your account has been created, you can login to Joker via SSH from on campus. If you need to access either cluster from off campus, you must use the NMSU VPN.

Login Nodes

  • joker.nmsu.edu

Remember the login nodes are not to be used for computationally intensive tasks.

Using Slurm to submit jobs on Joker

The module system

We use a tool called environment modules to manage what software is loaded into your environment. This allows you to select different MPI libraries, or Java versions for example.

Module Tutorial

Available modules/software packages

All of the software listed below is available on Joker. ICT’s Systems Group works to expand and update the software listed below on a regular basis. If you need an additional software package, or something needs to be updated please fill out the software request form.

Software Module nameSource
CUDA SDK version 7cuda7
DIYABC 2.1.0diyabc/210http://www1.montpellier.inra.fr/CBGP/diyabc/
GNU Compiler Collection 5.2gcc/520gcc.gnu.org
Gromacs 5.1gromacs/51www.gromacs.org
JAVA JDK version 7java/jdk7
JAVA JDK version 8java/jdk8
Julia 0.3.11julia/311julialang.org
LAMMPSlammps/aug15-mpilammps.sandia.gov/
Mathlab Version R2015Amatlab/r2015ahttps://www.mathworks.com/products/matlab/
METIS 5.1.0metis/510http://glaros.dtc.umn.edu/gkhome/views/metis
MPICH version 3mpi/mpich-x86_64CentOS stock RPM
OpenMPI version 1.6mpi/openmpi-x86_64CentOS stock RPM
NCL version 6.21ncl-621
GNU Octave version 4octave/400
Parmetis 4.0.3parmetis/403http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
PGI Compilers & Tools 16.4pgi/16.4http://www.pgroup.com/
Python 2.7.11python/2711http://www.continuum.io
Python 3.5.1python/3511http://www.continuum.io
R version 312R/312
R version 322R/322
R version 322 compiled with OpenBLASR/322-openblas
suitesparse version 4.4.5suitesparse-445

Using Python

GCC Compiler