Magento – Magento 2 – bin/magento Commands not working in Cpanel Terminal

In my case, it worked using sudo

sudo bin/magento setup:upgrade

EDIT 19/02/16

Actually, the "sudo" solution is more a workaround for bad permissions/ownership of Magento files.

If you don't already have a Magento file system owner, create one and add it to the apache group.

adduser magento
passwd magento
    //CentOS
    usermod -g apache magento

    //Ubuntu
    usermod -g www-data magento

//restart apache
    //CentOS
    service httpd restart

    //Ubuntu
    service apache2 restart

Now that you have your user, you can set the ownership and permissions (with root or an user with sudo)

cd /var/www/html/magento2beta/magento2
find . -type d -exec chmod 770 {} \; && sudo find . -type f -exec chmod 660 {} \; && sudo chmod +x bin/magento
//CentOS
chown -R magento:apache .
//Ubuntu
chown -R magento:www-data .

Switch to the magento user

su magento

Now you should be able to run php bin/magento setup:upgrade or any other command with your magento user

I don't know what have you done after adding some new code but i guess this is the issue cause your new code is not compiled. I am writing some command you should run after adding new code.

Go to the root folder of your Magento project and run the following commands :

sudo rm -rf var/cache var/generation var/di

sudo php bin/magento setup:upgrade

sudo php bin/magento setup:di:compile

sudo php bin/magento cache:clean

sudo chmod 777 -R var/

Hope it will solve your problem.