Java HotSpot(TM) 64-Bit Server VM warning: You have loaded library /home/sandaruwan/altera/12.1sp1/nios2eds/bin/eclipse_nios2/plugins/org.eclipse.equinox.launcher.gtk.linux.x86_1.1.100.v20110505/eclipse_1407.so which might have disabled stack guard. The VM will try to fix the stack guard now. It's highly recommended that you fix the library with 'execstack -c ', or link it with '-z noexecstack'.

 

and exit.

This is cauesed by the java version you are using as the jvm for Nios II.
It requires Java 7 32 bit version.

To install java 7 32 bit, use following

sudo add-apt-repository ppa:webupd8team/java sudo apt-get install openjdk-7-jre:i386

Then afterwards you don’t need to switch into java versions using update alternatives. You can -vm option to provide the java version.

./eclipse -vm /usr/lib/jvm/java-7-openjdk-i386/jre/bin/java

This is the niosIIeclipse.desktop file I created for icon.

[Desktop Entry]
Name=Nios II Eclipse
GenericName=Development
Comment=Altera Nios II
Exec=env /home/sandaruwan/altera/12.1sp1/nios2eds/bin/eclipse_nios2/eclipse -vm /usr/lib/jvm/java-7-openjdk-i386/jre/bin/java
Terminal=false
Type=Application
StartupNotify=true
Icon=/home/sandaruwan/altera/12.1sp1/nios2eds/bin/eclipse_nios2/icon.xpm
Categories=IDE;
Actions=Window;Document;
Keywords=IDE;Editor;Plaintext;Write;

It will show a nice icon as well. Change the path as you want.