Thankyou so much smlewis, I compiled it in release mode and its done… 
thanks again….
Install file: “build/src/release/linux/2.6/32/x86/gcc/super_aln.default.linuxgccrelease” as “bin/super_aln.default.linuxgccrelease”
g++ -o build/src/release/linux/2.6/32/x86/gcc/super_aln.linuxgccrelease -Wl,-rpath=/home/jamil/rosetta/rosetta_source/build/src/release/linux/2.6/32/x86/gcc/ build/src/release/linux/2.6/32/x86/gcc/apps/public/comparative_modeling/super_aln.o -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -L/usr/local/lib -L/usr/lib -ldevel -lprotocols -lcore -lnumeric -lutility -lObjexxFCL -lz
Install file: “build/src/release/linux/2.6/32/x86/gcc/super_aln.linuxgccrelease” as “bin/super_aln.linuxgccrelease”
scons: done building targets.