Linux-rt Patch for Petalinux 

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Copy Pentalinux kernel sources: <pentalinux-root>/components/linux-lernel/xlnx-* where 'pentalinux-root' is the folder with settings.sh, and '*' is the kernel revision number

Rename the copy to xlnx-*_rt

Get the linux-rt patch version for the kernel at this site

Be certain to download the version which matches your kernel, and it was suggested to use *.patch.gz

Copy the *-patch.gz file to <petalinux-root>/components/linux-kernel/

Open a terminal and to the kernel directory cd xlnx-*/

Patch the kernel sources by executing zcat ../*.patch.gz | patch -p1

Go back to the petalinux and run petalinux-config  

Go to linux Components Selection/kernel

Select your patched linux kernel and exit configuration program

Run petalinux-config -c kernel

Go to General setup / Timers sub system / and select 'High Resolution timer Support'

Go back to main menu and go to Kernel Features / Preemption Model

Select 'Fully Premptive Kernel (RT)' to activate the linux-rt features

Go to Kernel Features, and select Timer Frequency.  Set it to 1000Hz

Go back to the main menu again and select CPU Power Management, disable CPU Frequency Scaling

Exit the configuration and wait for system generation to finish

Run petalinux-build, copy the generated image.ub to your sd-card

Reboot the FPGA, check  the kernel version using uname -a 

 PREEMPT_RT Patch
Xilinx Forum