#! /bin/bash

#What I will do after a fresh copy of CENTOS 7 system is up
==========================================================

#Preliminary
#==========

# specify user here. Modify as deemed neccesary for your case

	user=tlyoon

#! /bin/bash

#	Alert sound effect off (done manually, optional)
	su - 
	cd /
	mkdir share
	mkdir state
	chmod -R 777 share
	chmod -R 777 state
	
	useradd $user
	usermod -g users $user
	passwd $user
	su - $user
	mkdir ~/share
	mkdir ~/share/apps
	mkdir ~/share/apps/configrepo
	mkdir ~/share/apps/local
	mkdir ~/share/apps/local/bin
	mkdir ~/share/apps/local/lib
	mkdir ~/state
	mkdir ~/state/partition1
	cd /share
	ln -s /home/$user/share/apps/ .
	cd /share/apps/local/bin/
	cd /state 
	ln -s /home/$user/state/partition1/ .

	su -
	echo 'export PATH=/share/apps/local/bin:$PATH'>> ~/.bashrc
	echo 'export LD_LIBRARY_PATH=/share/apps/local/lib:$LD_LIBRARY_PATH' >> ~/.bashrc

	cd /share/apps/local/bin/
	scp comsics.usm.my:/share/apps/local/bin/check_pbs .
	chmod +x check_pbs
	
	yum install -y epel-release
	yum install -y python-devel.x86_64 ##needed by lammps	
 	yum install -y seamonkey	
	yum install -y libjpeg-turbo-devel.x86_64
	yum groups mark convert
	yum groupinstall "Development Tools"
	yum install -y glib.x86_64
	yum install -y vim
	yum install -y zlib-devel.x86_64
	yum install -y openmpi.x86_64 openmpi-devel.x86_64 
	echo 'export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
	echo 'export PATH=/usr/lib64/openmpi/bin:$PATH' >> ~/.bashrc

#1
### Install Intel Paralell studio
##	1. Obtain the file (huge, ~ 4 GB) parallel_studio_xe_2017_update2.tgz
	cd /share/apps/configrepo; wget https://staffusm-my.sharepoint.com/personal/tlyoon_usm_my/_layouts/15/guestaccess.aspx?docid=15eb9f5ebb18e4cbba413143f88e799a9&authkey=AZ6iimEVoqEgLFnpm7b6oa8 ## this links to parallel_studio_xe_2017_update2.tgz;
	tar -xzvf parallel_studio_xe_2017_update2.tgz; cd parallel_studio_xe_2017_update2;
	./install_GUI.sh

###     Need to obtain the license and activation manually. The license is MAC address dependent. You can check your MAC address of current hardware by issuing ifconfig 

# After finish installation,
	echo '# sourcing INTEL compilers' >> ~/.bashrc  
	echo 'source $PROD_DIR/bin/compilervars.sh intel64' >> ~/.bashrc  

#2
### Install google chrome ###
	cd /share/apps/configrepo; wget https://dl.google.com/linux/direct/google-chrome-stable_current_x86_64.rpm;
	yum -y install redhat-lsb libXScrnSaver;
	rpm -Uvh google-chrome-stable_current_x86_64.rpm

#3
### Tunned ATLAS library
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/BLAS_and_LAPACK/inst_atlas; sh inst_atlas

#4
### yummed lapack and blas lib
	yum install -y lapack.x86_64 lapack-devel.x86_64 lapack-static.x86_64 lapack64.x86_64 lapack64-devel.x86_64 lapack64-static.x86_64 

#5
## Install ptmbhga
cd /share/apps/configrepo; wget https://staffusm-my.sharepoint.com/personal/tlyoon_usm_my/Documents/Downloads/ptmbhga_v2.1.tar ; mv ptmbhga_v2.1.tar ../ ; mkdir ptmbhga ; cd ptmbhga; mv ../ptmbhga_v2.1.tar . ; tar -zxvf ptmbhga_v2.1.tgz ; cd template; ./config.make; cd ../VER2.1/; make

#6	
## Install pev6.0 ## Note that pev6.0 is equivalent to p0 ###
	cd /share/apps; scp root@comsics.usm.my:/share/apps/pe/VER6.0.tar.gz . ; mkdir pe; cd pe; mv ../VER6.0.tar.gz . ; tar -zxvf VER6.0.tar.gz; cd VER6.0/ ; make -f Makefile.centos7 ; ln -s /share/apps/pe/VER6.0/pev6.0 /share/apps/local/bin ; ./config.make

#7
## Install gaussian 09
	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/gaussian/inst_g09 ; ./inst_g09

## Add an exsiting user as gaussian 09 user
	cd /share/apps/configrepo ; wget http://comsics.usm.my/tlyoon/configrepo/howto/gaussian/add_g09_user.sh ; ./add_g09_user.sh ; 

## Install pg9v6.0.2

	mkdir /share/apps/pe ; cd /share/apps/pe ; scp -r comsics.usm.my:/share/apps/pe/pg9v6.0.2.SN_CENTOS.tar.gz . ; 	tar -zxvf pg9v6.0.2.SN_CENTOS.tar.gz ; 

#8
## Install fftw3 gnu version
	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/fftw/inst_fftw334_sa_openmpi ; sh inst_fftw334_sa_openmpi

#9
## Install Quantum Expresso version 6.1
	cd /share/apps/; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_qe_6.1 ; sh inst_qe_6.1

#10
## Install lammps gnu version
	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_lammps_31Mar17_gnu.txt ; sh inst_lammps_31Mar17_gnu.txt

#11
## Install plmpv6.0.1
## First, create the directory /share/apps/mylammps/potentials, in which all potential files from lammps are copied there. 

	mkdir /share/apps/mylammps/; ln -s /share/apps/lammps-31Mar17/potentials /share/apps/mylammps/ ; cd /share/apps/pe ; scp comsics.usm.my:/share/apps/pe/plmpv6.0.1.tar.gz . ; tar -xzvf plmpv6.0.1.tar.gz

#12
## Install dftb+ (version 1.3.0)
	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_dftb+; sh inst_dftb+ 

#13
## Install template_pd+v6.0.1
	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_template_pd+v6.0.1; sh inst_template_pd+v6.0.1 

#14
## Install p0 (original ptmbhga without USM cut & splice, equivalent to pev6.0)
	cd /share/apps; scp root@comsics.usm.my:/share/apps/configrepo/p0.tar.gz . ; tar -zxvf p0.tar.gz; cd p0/ ; make -f Makefile ; ln -s /share/apps/p0/p0 /share/apps/local/bin ; ./config.make

#15
## Install p1 (ptmbhga USM cut & splice)
	cd /share/apps; scp root@comsics.usm.my:/share/apps/configrepo/p1.tar.gz . ; tar -zxvf p1.tar.gz; cd p1/ ; make -f Makefile ; ln -s /share/apps/p1/p1 /share/apps/local/bin; ./config.make

#16 Install template_p1d+

	cd /share/apps; scp -r root@comsics.usm.my:/share/apps/template_p1d+ . 

#17 Install p2 (ptmbhga USM cut & splice, by default it is to be used by Gaussian 09 to implement EMBH. p2 is equivalent to EMBH); Based on /home/mhlian/embh_amended_from_tw_mbh/EMBH/EMBH@comsics

	cd /share/apps; scp -r root@comsics.usm.my:/share/apps/p2 . ; cd p2/ ; make clean; make -f Makefile ; ln -s /share/apps/p2/p2 /share/apps/local/bin; ./config.make


#18 Install template_p2g (it uses p2 as global optimizer.)

	cd /share/apps; scp -r root@comsics.usm.my:/share/apps/template_p2g . 


#19. Install netcdf version 4.3.2

	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_netcdf_4.3.2; sh inst_netcdf_4.3.2
#	yum -y install netcdf.x86_64

#20. Install abinit 7.6.4

	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_abinit_7.6.4; sh inst_abinit_7.6.4

#21. Install wien2k 14.2

	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_wien2k_14.2_intel; sh inst_wien2k_14.2_intel




##### the following may be obsolete ########################
#########################################################################################

#20. Install etsf gnu version 1.0.4 ### not working. to fix
 	cd /share/apps/configrepo; wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/inst_etsf_104_gnu; sh inst_etsf_104_gnu

#27. Install scalapack gnu version 2.0.2

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/BLAS_and_LAPACK/inst_scalapack
	sh inst_scalapack

#28. Install libxc-2.1.2 gnu 

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_libxc212
	sh inst_libxc212

29. Install bigdft gnu 1.7.1

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/abinit/inst_bigdft
	sh inst_bigdft

#29. Install abinit gnu ver 7.10.5

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/abinit/inst_abinit_7105_gnu
	sh inst_abinit_7105_gnu



2. Install nux repo

	yum localinstall --nogpgcheck http://li.nux.ro/download/nux/dextop/el7/x86_64/nux-dextop-release-0-1.el7.nux.noarch.rpm

3. Install EL repo, refer to http://www.certdepot.net/rhel7-install-elrepo-repository/
	yum install -y "http://www.elrepo.org/elrepo-release-7.0-2.el7.elrepo.noarch.rpm"

4. Install rpmforge repo, refer to http://www.tecmint.com/enable-rpmforge-repository/

	cd /share/apps/configrepo
	wget http://packages.sw.be/rpmforge-release/rpmforge-release-0.5.2-2.el6.rf.i686.rpm
	rpm -Uvh rpmforge-release-0.5.2-2.el6.rf.i686.rpm

6. Prioritized installation: 
	yum install perl-devel.i686 perl-core.x86_64 ## needed by openmpi

Software installation (Must proceed in order, or else you dependence issue may occur)
=====================================================================================

1. 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

2. Install intel ifort into /share/apps
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/intel/inst_ifort_111072_sa

3. Install intel ifftw into /share/apps
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/intel/inst_ifftw_111072_sa

9. Install impi into /share/apps
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/intel/inst_impi_410024_sa

10. Install ATLAS library:
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/BLAS_and_LAPACK/inst_atlas

11. Install openmpi based on gnu 
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/openmpi/inst_openmp185_gcc

12. Install mpich2 based on gnu 
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/mpich2/inst_mpich2_314_gcc_sa

13. Install openmpi based on intel 
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/openmpi/inst_openmp185_intel

14. 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

15. Install fftw3 based on gnu
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/fftw/inst_fftw334_gnu

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

17. yum install mpich.x86_64 mpich-devel.x86_64

	Since somehow /usr/lib64 (where mpich2 is sitting) is not in the PATH and LD_LIBRARY_PATH, these path have to be added manually into ~/.bashrc 

	export PATH=/share/apps/local/bin:/usr/lib64/mpich/bin:$PATH
	export LD_LIBRARY_PATH=/share/apps/local/lib:/usr/lib64/mpich/lib:$LD_LIBRARY_PATH

18. cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/BLAS_and_LAPACK/inst_atlas; sh inst_atlas

19. Lammps gnu 
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_lammps_gnu_sa

20. Lammps intel 
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_lammps_intel_sa

21. Install pev6.0
 
	cd /share/apps/configrepo; mkdir pe; cd pe; scp $user@comsics.usm.my:/share/apps/pe/VER6.0.tar.gz . ;
	tar -zxvf VER6.0.tar.gz; cd /share/apps/configrepo/pe/VER6.0/
	makefile -f Makefile.ptmbhga	
	ln -s /share/apps/pe/VER6.0/pev6.0 /share/apps/local/bin
	./config.make

22. Install gaussian 09
	cd /share/apps/
	scp root@comsics.usm.my:/share/apps/configrepo/g09.tar.gz .
	tar -zxvf g09.tar.gz
	mv g09.tar.gz configrepo

a. As su, create a new group "g09group". Do it only once. 

	groupadd g09group
	

b. Configure permission for /share/apps/g09
	
	chown -R root:g09group /share/apps/g09
	chmod -R 750 /share/apps/g09

c. Add an user with suffix "c", e.g., $userc, who will use gaussian 09.

	adduser $userc
	passwd $userc

d. Add the user $userc to existing group g09group

	usermod -a -G g09group $userc

e. Change the user $userc ssh environment. Replace the last string from bash to csh in file /etc/passwd as example below. The ? shows the sequence number of user or group creation in operating system.

From
	$userc:x:5??:1??::/home/$userc:/bin/bash
To
	$userc:x:5??:1??::/home/$userc:/bin/csh

f. Copy cshrc_sample from http://www2.fizik.usm.my/configrepo/howto/customise_centos/cshrc_sample to replace all user's ~/.cshrc

	cd ~/home/$userc
	wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/cshrc_sample
	cp ~/.cshrc ~/.cshrc.orig
	mv cshrc_sample ~/.cshrc

You should find the following lines in /home/$userc/.cshrc:

 	if (! -e /state/partition1/$user) mkdir /state/partition1/$user
	setenv GAUSS_SCRDIR /state/partition1/$user
	setenv g09root /share/apps
	source $g09root/g09/bsd/g09.login

	setenv PATH ${PATH}:/share/apps/local/bin:/usr/lib64/mpich/bin:
	setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/share/apps/local/lib:/usr/lib64/mpich/lib:/share/apps/atlas-3-10-2/gnu/lib:

If not, then, add it yourself manually, as user $userc. Try re-loging in as $userc. You should not see any 'permission denied' warning from /share/apps/g09/bsd/g09.login. Type in 

	which g09

You should see 

	/share/apps/g09/g09

23. Install pg9v6.0.1

	mkdir /share/apps/pe
	cd /share/apps/pe
	scp -r comsics.usm.my:/share/apps/pe/pg9v6.0.1.tar.gz .
	tar -zxvf pg9v6.0.1.tar.gz

24. Install plmpv6.0.1

Assure that the directory

	/share/apps/mylammps/potentials 

exists, where all potential files from lammps have been copied there. If not, creat the directory and copy all forcefields from the latest lammps package into it. 
	
	cd /share/apps/pe
	scp comsics.usm.my:/share/apps/pe/plmpv6.0.1.tar.gz .
	tar -xzvf plmpv6.0.1.tar.gz

25. Install netcdf gnu version 4.3.3.1

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/netcdf/inst_netcdf_4331_gnu
	sh inst_netcdf_4331_gnu

26. Install netcdf_fortran gnu version 4.3.3.1

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/netcdf/inst_netcdf_4331_gnu_fortran
	sh inst_netcdf_4331_gnu_fortran

27. Install netcdf_parallel gnu version 4.3.3.1

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/netcdf/inst_netcdf_4331_gnu_parallel
	sh inst_netcdf_4331_gnu_parallel


26. Install etsf gnu version 1.0.4

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/etsf/inst_etsf_104_gnu
	sh inst_etsf_104_gnu

27. Install scalapack gnu version 2.0.2

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/BLAS_and_LAPACK/inst_scalapack
	sh inst_scalapack

28. Install libxc-2.1.2 gnu 

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_libxc212
	sh inst_libxc212

29. Install bigdft gnu 1.7.1

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/abinit/inst_bigdft
	sh inst_bigdft

29. Install abinit gnu ver 7.10.5

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/abinit/inst_abinit_7105_gnu
	sh inst_abinit_7105_gnu

30. Install ptmbhga_abinit (pab version 6.0.1)

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_pab_v6.0.1
	sh inst_pab_v6.0.1


30. Install ptmbhga_dftb+ (pd+ version 6.0.1)

	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/pd+/inst_pd+_v6.0.1
	sh inst_pd+_v6.0.1

### failed. 30. dftb+
	cd /share/apps/configrepo; wget http://www2.fizik.usm.my/configrepo/howto/customise_centos/inst_dftb+
	


Software installation (less troublesome ones)
============================================

1. Install Mathematica

2. install vlc (after nux repo is installed)
	yum install vlc
3. gftp
	cd /share/apps/configrepo
	 wget http://pkgs.repoforge.org/gftp/gftp-2.0.19-4.el6.rf.x86_64.rpm
	rpm -ivh gftp-2.0.19-4.el6.rf.x86_64.rpm

4. Install chrome. Refer to http://www.tecmint.com/install-google-chrome-on-redhat-centos-fedora-linux/

cat << EOF > /etc/yum.repos.d/google-chrome.repo
[google-chrome]
name=google-chrome
baseurl=http://dl.google.com/linux/chrome/rpm/stable/$basearch
enabled=1
gpgcheck=1
gpgkey=https://dl-ssl.google.com/linux/linux_signing_key.pub
EOF

	yum install google-chrome-stable

5. Install virtual box. Refer to http://www.itzgeek.com/how-tos/linux/centos-how-tos/install-virtualbox-4-3-on-centos-7-rhel-7.html

	yum list VirtualBox* 

or 	yum install VirtualBox-5.0.x86_64

	service vboxdrv setup
	usermod -a -G vboxusers $user

5. Move w7_32.vdi from www2 into ~/

6. yum install lapack64-devel.x86_64

7. Install dropbox for centos 7. Refer to http://computechtips.com/790/install-dropbox-centos-7
	yum install libgnome.x86_64
	cd /share/apps/configrepo

Download from https://www.dropbox.com/install?os=lnx rpm for Fedora 64 bit for Dropbox installation, or use the version from www2

	wget http://www2.fizik.usm.my/$user/Downloads/nautilus-dropbox-2015.10.28-1.fedora.x86_64.rpm
	
	yum install nautilus-dropbox-2015.10.28-1.fedora.x86_64.rpm
	yum-config-manager --disable Dropbox

8. Install flash plugin player for adobe in firefox. Refer to http://grokbase.com/t/centos/centos/1498emabyc/flash-plugin-for-centos-7

	rpm -ivh http://linuxdownload.adobe.com/adobe-release/adobe-release-x86_64-1.0-1.noarch.rpm
	yum install flash-plugin
	yum-config-manager --disable Adobe

Some useful command:
====================
1. To verify the repo installed: 
	yum repolist

2. To clean up repo
#	yum clean all

3. Assuming you have a dual-boot hardisk with windows installed prior to the centos. To detect windows right after installation of fresh centos, refer: 
http://unix.stackexchange.com/questions/169787/windows-boot-option-is-missing-after-installing-centos-7-how-can-i-get-it-back

	yum install ntfs-3g
	grub2-mkconfig > /dev/null #check if see windows loader. If yes, proceed: 
	cp /boot/grub2/grub.cfg /boot/grub2/grub.cfg.old
	grub2-mkconfig -o /boot/grub2/grub.cfg  

This will allow the windows and other OS installed to appear in the grub when rebooting.

4. Change host name: Refer to http://www.cyberciti.biz/faq/rhel-redhat-centos-7-change-hostname-command/

	hostnamectl   #to check host name
	hostnamectl set-hostname $user
	hostnamectl status

5. To compare running kernel with installed source: 
	uname -r
against 
	rpm -q kernel-devel 

if not, update the kernel via
#	yum upgrade kernel kernel-devel ##not recommended unless ulmost necessary