#! /bin/bash

#Customising Ubuntu 15.10
========================

sudo -i 

# 0 
mkdir /share
mkdir /share/apps
mkdir /share/apps/configrepo
mkdir /share/apps/local
mkdir /share/apps/local/bin
mkdir /share/apps/local/lib
mkdir /state
mkdir /state/partition1
cd /share/apps/local/bin/
scp comsics.usm.my:/share/apps/local/bin/check_pbs .
chmod +x check_pbs

#1 update using software updater (so that grub can see windows when booted up). Reboot only then proceed.


#2. Install essential packages
	apt-get install vim
	dpkg --add-architecture i386
	apt-get update
	apt-get install libstdc++5:i386
	apt-get install libstdc++5
	apt-get install g++-multilib libc6-dev-i386 libc6:i386 ##needed for icc installtion
	apt-get install ia32-libs  ## not working, but it does not matter
	apt-get install openjdk-7-jre-headless #needed by icc installation

	apt-get install python-dev ##needed by lammps
	apt-get install libjpeg-dev ##needed by lammps
	apt-get install gfortran ##needed by lammps



	apt-get upgrade
	Install flash plugin via ubuntu software center
	Follow http://tecadmin.net/install-google-chrome-in-ubuntu/# to install google chrome


#3 installating icc  (using built-in gcc)
	
	mkdir /usr/lib32
	ln -s /usr/lib/i386-linux-gnu/libstdc++.so.5 /usr/lib32/libstdc++.so.5
	ln -s /home/tlyoon/share/apps/configrepo/l_cprof_p_11.1.072/pset/32/gcc-3.2/libstdc++.so.5 /share/apps/local/lib/
#	ln -s /usr/lib/i386-linux-gnu/libstdc++.so.5 /share/apps/local/lib/

Install intel icc into /share/apps
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/intel/inst_icc_11.0.081_sa
	inst_icc_11.0.081_sa

#4. Install intel ifort into /share/apps  (using built-in gcc)
	cd /share/apps/configrepo
wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/intel/inst_ifort_111072_sa
	sh inst_ifort_111072_sa

#5. Install impi into /share/apps  (using built-in gcc)
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/intel/inst_impi_410024_sa
	sh inst_impi_410024_sa

6. Install intel ifftw into /share/apps  (using built-in gcc)
#	ln -s /usr/lib/i386-linux-gnu/libstdc++.so.5 /share/apps/local/lib #avoid doing if not needed
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/intel/inst_ifftw_111072_sa
	sh inst_ifftw_111072_sa
	#if it does not work, just cp the ifftw2 and ifftw3 lib from elsewhere and paste them in the right place 

# 7. Install gcc version 4.9.0 for enabling cuda in lammps. Cuda in lammps cannot support gcc higher than ver 4.9.0 
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/gcc/inst_gcc_4.9.0
	sh inst_gcc_4.9.0

Creat links to use gcc-4.9.0 in root and users by adding the lines in ~/.bashr:
	##sourcing gcc 4.9.2
	export LD_LIBRARY_PATH=/share/apps/gcc/4.9.0/lib:/share/apps/gcc/4.9.0/lib64:$LD_LIBRARY_PATH
	export PATH=/share/apps/gcc-4.9.0/bin:$PATH

### note: gfortran from gcc-4.9.0 may not work, so for gfortran, has to use the one installed from apt-get install gfortran  ubuntu.

##########################################
## for the following cuda installation, use built-in gcc

#8 Installing CUDA Toolkit 7.5 on Ubuntu 15.10 Linux. To be done manually
# The following explains how to install CUDA Toolkit 7.5 on 64-bit Ubuntu 15.10 Linux.
# Retrieve the CUDA repository package for Ubuntu 15 from the CUDA download site and install it in a terminal.
# From https://developer.nvidia.com/cuda-downloads, 
# Download Target Installer for Linux Ubuntu 15.10 x86_64. As of 10 Nov 2015, the version is
# cuda-repo-ubuntu1404-7-5-local_7.5-18_amd64.deb (md5sum: 5cf65b8139d70270d9234d5ff4d697c7)
# Installation Instructions:


    dpkg -i cuda-repo-ubuntu1504-7-5-local_7.5-18_amd64.deb
    mv /share/apps/gcc-4.9.0/lib64/libstdc++.so.6 /share/apps/gcc-4.9.0/lib64/libstdc++.so.6.orig
    ln -s /usr/lib/x86_64-linux-gnu/libstdc++.so.6 /share/apps/gcc-4.9.0/lib64/libstdc++.so.6

    apt-get update
    apt-get install cuda 

# You should reboot the system afterwards and verify the driver installation with the nvidia-settings utility.

# Environment Variables
# As part of the CUDA environment, you should add the following in the .bashrc file of your home folder.

export CUDA_HOME=/usr/local/cuda-7.5 
export LD_LIBRARY_PATH=${CUDA_HOME}/lib64:LD_LIBRARY_PATH
PATH=${CUDA_HOME}/bin:${PATH} 
export PATH

# CUDA SDK Samples
# Now you can copy the SDK samples into your home directory, and build a test sample.
# $ cuda-install-samples-7.5.sh  ~ 
# $ cd ~/NVIDIA_CUDA-7.5_Samples 
# $ cd 1_Utilities/deviceQuery 
# $ make 

# If everything goes well, you should be able to verify your CUDA installation by running the deviceQuery sample.

##################################

#9. Install openmpi based on intel (built-in-gcc)
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/openmpi/inst_openmp185_intel
	sh inst_openmp185_intel

#11. 
	apt-get install gfortran ## needed by openmpi gnu installation and also by lammps

#12. Install openmpi based on gnu using gcc-4.9.0
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/openmpi/inst_openmp185_gcc_4.9.0
	sh inst_openmp185_gcc_4.9.0  

#13. Install openmpi based on built-in gnu 
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/openmpi/inst_openmp185_gcc
	sh inst_openmp185_gcc


#14. Install fftw3 based on built-in gnu 
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/fftw/inst_fftw334_gnu
	sh inst_fftw334_gnu

#15. Install tuned atlast libr based on built-in gnu 
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/BLAS_and_LAPACK/inst_atlas
	sh inst_atlas
# or alternatively, just copy the existing folders of these libs into the right place, /share/apps/atlas-3-10-2/gnu.


#14. Install LAMMPS based on gnu, cuda enabled. 
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_lammps_gnu_cuda
	sh inst_lammps_gnu_cuda

Note**: The lib/cuda must be made (by issuing 'make') by changing gcc to version 4.9.0, or it won't work.
Note**: the whole lammps that uses cuda must be compiled using gcc-4.9.0, openmpi-1.8.5_gcc, if possible. Presumable to use it also need to be use gcc-4.9.0.


#####################################
## IGNOR THE REST
#####################################

#13. Install LAMMPS based on intel, cuda enabled. 
	apt-get install python-dev
	apt-get install libjpeg-dev
	apt-get install gfortran
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_lammps_intel_cuda
	sh inst_lammps_intel_cuda

Note**: The lib/cuda must be made (by issuing 'make') by changing gcc to version 4.9.0, or it won't work.
Note**: the whole lammps that uses cuda must be compiled using gcc-4.9.0, openmpi-1.8.5_intel and all intel compilers, if possible. 
for consistency. Presumable to use it also need to be use gcc-4.9.0,.


#10. Install fftw3 based on intel
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/fftw/inst_fftw334_intel
	sh inst_fftw334_intel


#2 
apt-get install libatlas-base-dev
apt-get install liblapack-dev liblapack3
apt-get install cpufrequtils sysfsutils
apt-get install rcconf
apt-get install gksu
apt-get install aptitude

################# not confirmed to work
# for atlas installation use
sudo rcconf
# A list will appear in the terminal window, use the arrow keys to navigate and space bar to select, de-select options.
# For cpu scaling, look for "ONDEMAND"
# Once at the entry, with the space bar un-check the box.
# To save the configuration hit the tab key so that "OK" is highlighted then enter to save and reboot.

# Alternatively,
gksu gedit /sys/devices/system/cpu/cpu0/cpufreq/scaling_governor
# replace ondemand with performance. Repeat for every core (increase cpu0: cpu1, cpu2).
# add the following lines
#devices/system/cpu/cpu0/cpufreq/scaling_governor = performance
#devices/system/cpu/cpu1/cpufreq/scaling_governor = performance
#devices/system/cpu/cpu2/cpufreq/scaling_governor = performance
#devices/system/cpu/cpu3/cpufreq/scaling_governor = performance
################# end of not confirmed to work



#8. Install mpich2 based on intel 
	cd /share/apps/configrepo
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/mpich2/inst_mpich2_314_intel_sa
	sh inst_mpich2_314_intel_sa