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Redwood User Guide

Redwood is an HPC cluster of the New CHPC Protected Environment, designed and built for researchers whose data contains Protected Health Information (PHI) and other sensitive data. This cluster is considered HIPAA Compliant.

Contents

Redwood general cluster hardware overview

  • 4 Intel XeonSP (Skylake) nodes each with 32 cores and 192GB RAM (128 total cores)
  • 11  Intel Broadwell nodes each with  28 cores and 128GB RAM (308 total cores)
  • 2 GPU nodes 
    • 32 cores each (Intel XeonSP), 192GB RAM
    • 4 x GTX1080Ti GPUs
  • Mellanox EDR Infiniband interconnect (with the pre-skylake generation nodes connected at FDR)
  • Gigabit Ethernet interconnect for management
  • 160TB General Scratch server (/scratch/mammoth/serial)
  • 2 interactive nodes

In addition to the general resources, there are owner nodes.  Owner nodes can be accessed by all users of redwood in a premptable guest manner using the partition redwood-guest and account owner-guest.

Important Differences between Redwood and Other CHPC Clusters - NEW!

The design of the protected environment is fundamentally different than other CHPC clusters. The general clusters (ember, kingspeak, lonepeak etc.) were designed to be open (within reason, taking a balanced approach on security). Redwood was designed primarily to mitigate risk and protect data.  If you have used the general clusters, the first thing you will notice when you login is that the home directory is on a completely different file system, where your other CHPC home directory is mounted on all the various general and more open clusters.  

FAQ section - NEW!

Please refer to the Protected Environment Frequently Asked Questions (FAQ).

 Redwood Cluster Usage

CHPC resources are available to qualified faculty, students (under faculty supervision), and researchers from any Utah institution of higher education. Users can request accounts for CHPC computer systems by filling out an account request form. This can be found by following this link: account request form.

As Redwood is part of the CHPC Protected Environment, users must also have permission to access that. See the Protected Environment Frequently Asked Questions (FAQ) for how to apply and qualify for access.

Redwood will be using allocation - see the Alloction section on our Protected Environment page for details.

Redwood Cluster Access and Environment

 As part of the CHPC protected environment, redwood requires that you undergo authentication more rigorous than is needed for the other CHPC clusters. See the Protected Environment Frequently Asked Questions (FAQ).

 Once you are able to connect to the Protected Environment, the redwoodcluster can be accessed via ssh (secure shell) at the following addresses:

  • redwood.chpc.utah.edu (general PE users; round robins between redwood1.chpc.utah.edu and redwood2.chpc.utah.edu)
  • poet.chpc.utah.edu (owned by Dr. Hurdle; others may be granted access on request)

Redwood does not mount the same account directory as the unprotected clusters do. If you have files on your regular CHPC account that you wish to use on redwood, you must copy them using a secure protocol such as scp.

You will have access to a project directory on the mammoth file system. This is the location for storage of  data common to a project.  All PE users who are vetted by the Institutional Review Board or other relevant authority as having rights to access it will be able to work with the data in this directory. Project members may create files there or modify them, as well.

At the present time, the CHPC supports two types of shells: tcsh and bash. Tcsh shell users need to select the .tcshrc login script. Users whose shell is bash need the .bashrc file to log in.

Your environment is setup through the use of modules. Please see the User Environment section of the General Cluster Information page for details in setting up your environment for batch and other applications.

Using the Batch System on Redwood

The batch implementation on all CHPC systems is Slurm. 

The creation of a batch script on the redwood cluster

A shell script is a bundle of shell commands which are fed one after another to a shell (bashtcsh,..). As soon as the first command has successfully finished, the second command is executed. This process continues until either an error occurs or the complete array of individual shell commands has been executed. A batch script is a shell script which defines the tasks a particular job has to execute on a cluster.

Below this paragraph a batch script example for running in Slurm on the Ember cluster is shown. The lines at top of the file all begin with #SBATCH which are interpreted by the shell as comments, but give options to Slurm.

Example Slurm Script for Redwood:

#!/bin/csh

#SBATCH --time=1:00:00 # walltime, abbreviated by -t
#SBATCH --nodes=2 # number of cluster nodes, abbreviated by -N
#SBATCH -o slurm-%j.out-%N # name of the stdout, using the job number (%j) and the first node (%N)
#SBATCH --ntasks=16 # number of MPI tasks, abbreviated by -n # additional information for allocated clusters
#SBATCH --account=baggins # account - abbreviated by -A
#SBATCH --partition=redwood # partition, abbreviated by -p # # set data and working directories

setenv WORKDIR <projectspace>

setenv SCRDIR /scratch/<path>/UNID/myscratch
mkdir -p $SCRDIR
cp -r $WORKDIR/* $SCRDIR
cd $SCRDIR

# load appropriate modules, in this case Intel compilers, MPICH2
module load intel mpich2
# for MPICH2 over Ethernet, set communication method to TCP - for general lonepeak nodes
# see above for network interface selection options for other MPI distributions
setenv MPICH_NEMESIS_NETMOD tcp
# run the program
# see above for other MPI distributions
mpirun -np $SLURM_NTASKS my_mpi_program > my_program.out

For more details and example scripts please see our Slurm documentation. Also, to help with specifying your job and instructions in your slurm script, please review CHPC Policy 2.3.1 Redwood Job Scheduling Policy.

Job Submission on Redwood

In order to submit a job on redwood one has to login first into an interactive node (see above). 

To submit a script named slurmjob, just type:

sbatch slurmjob

Checking the status of your job in slurm

To check the status of your job, use the "sinfo" command

sinfo

For information on compiling on the clusters at CHPC, please see  our Programming Guide

Last Updated: 10/26/18