Starting from ParallelCluster 2.5.0 you can disable hyperthreading by configuring the disable_hyperthreading configuration parameter in the cluster section.

If you're using an instance type that doesn't support disabling hyperthreading specifying CpuOptions (see CPU Cores and Threads Per CPU Core Per Instance Type) or if you are using ParallelCluster 2.4.1 or older versions you can disable hyperthreading (on Amazon Linux) by following the two steps below.

You have to pass an additional setting at cluster creation time, by using the extra_json parameter, which enable you to set the number of slots per instances to vpcus, cores, or a number.

To set the number of slots per instance to be only the number of cores, you have to set the following in your config:

[cluster yourcluster]
...
extra_json = { "cluster" : { "cfn_scheduler_slots" : "cores" } }

If you are using Amazon Linux, you have to create a script with the following content:

#!/bin/bash

for cpunum in $(cat /sys/devices/system/cpu/cpu*/topology/thread_siblings_list | cut -s -d, -f2- | tr ',' '\n' | sort -un)
do
    echo 0 > /sys/devices/system/cpu/cpu$cpunum/online
done

Upload the script with the correct permissions to S3 and use as Post Install script by configuring the post_install configuration parameter.

[cluster yourcluster]
...
post_install = s3://<bucket-name>/yourscript.sh

See Disabling Intel Hyper-Threading Technology on Amazon Linux for more details.