VLC and other common video players  in Raspberry pi not support GPU.

You can use Omxplayer a text based video player for running 720p and 1080p mkv and almost all other video formats.

for installing omxplayer

sudo apt-get install omxplayer

omxplayer is a textbased player , so it is very difficult to use.

you can provide a graphical front end by using tboplayer

https://github.com/KenT2/tboplayer

Download the zip file from above site

run the following commands
sudo su
unzip tboplayer-master.zip
cd tboplayer-master
./setup.sh

This will take some time to complete

now run the following
python /opt/tboplayer/tboplayer.py

if any python module missing issue

pip install

Example:

raceback (most recent call last):
  File "/opt/tboplayer/tboplayer.py", line 65, in
    import pexpect
ImportError: No module named pexpect

Solution :  pip install pexpect