#! /bin/bash

#### Mandatory requirements: intel parallel_studio_xe_2015 or above and ifftw3 have been installed
#### 1. libz-dev is installed. Else install it using 
# apt-get install libz-dev

###### automatically sourcing intel parallel studio ##########################
# Assiming intel parallel studio has been installed, the following script extracts automatically intel path automatically in a machine. Tested for intel parallel studio XE 2017
# this package should be included in any installation of package that would make use of intel compilers
# Mandatory for this script to work: libfftw3xf_intel.a is found in $MKLROOT/lib/intel64/


#### 2.
source $(locate compilervars.sh | awk 'NR==1') intel64
source $(locate mpivars.sh | awk 'NR==1') intel64
source $(locate mklvars.sh | awk 'NR==1') intel64
echo '$MKLROOT=' $MKLROOT
mklroot=$(echo $MKLROOT)
echo 'mklroot=' $mklroot
####

wifort=$(which ifort)
echo $wifort
ifortpath=$(echo $wifort | awk -F  "/ifort" '{print $1}')
echo $ifortpath
intelbinpath=$(echo $wifort | awk -F  "/intel64/ifort" '{print $1}')
echo $intelbinpath

source $intelbinpath/compilervars.sh intel64
source $intelbinpath/compilervars_global.sh intel64
mklroot=$(echo $MKLROOT)
echo $MKLROOT

wmpiifort=$(which mpiifort)
echo $wmpiifort
mpibinpath=$(echo $wmpiifort | awk -F  "/mpiifort" '{print $1}')
echo $mpibinpath
mpipath=$(echo $wmpiifort | awk -F  "/bin/mpiifort" '{print $1}')
echo $mpipath
mpilibpath=$(echo $wmpiifort | awk -F  "/bin/mpiifort" '{print $1}')/lib
echo $mpilibpath
mpiincpath=$(echo $wmpiifort | awk -F  "/bin/mpiifort" '{print $1}')/include
echo $mpiincpath
source $mpibinpath/mpivars.sh intel64
###### end of automatically sourcing intel parallel studio ##########################


#3. install lammps in ~/share/apps

mkdir ~/share
mkdir ~/share/apps
mkdir ~/share/apps/configrepo

#4. 
cd ~/share/apps/configrepo
mkdir lammps-16Mar18
cd lammps-16Mar18
filesize=$(ls -la stable.zip | awk '{print $5}')
if [ "$filesize" -eq 98837930 ]; then
	echo 'found stable.zip with the right size =' $filesize'. Not to wget it from the cloud'
else
	echo 'found stable.zip with the wrong size =' $filesize'. To wget it from the cloud'
	echo "$filesize"
	rm -rf stable.zip
	wget https://www.dropbox.com/s/5vpk14vj7qg0ie8/stable.zip?dl=0 -O stable.zip
fi

### wget http://comsics.usm.my/tlyoon/configrepo/howto/customise_centos/lammps/lammps-16Mar18/stable.zip
### Note that the date for stable version is to be updated from time to time

#5. 
cd ~/share/apps; unzip configrepo/lammps-16Mar18/stable.zip
mv lammps-stable lammps-16Mar18; cd lammps-16Mar18/

#6. 
cd lib/atc
rm -f *.a *.o
## !!!!!!!!!!!!!!!!!!!! to modify Makefile.icc
	filetomod=Makefile.icc
	keyword=fPIC
	# backup orig $filetomod copy
	cp $filetomod $filetomod'.orig'
	### target line number to be replaced
	#lineno=$(cat $filetomod | awk -v keyword=$keyword '/keyword/ {print NR}')
	lineno=$(cat $filetomod | awk -v keyword=$keyword '$0 ~ keyword {print NR}')
	#echo $lineno
	### end of target line number to be replaced
	#### original target string 
	os=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print}')
	#echo $os 
	#### end of original target string 
	#### modified string 
	##	s2a='-I/opt/intel/impi_latest/include64'
	s2a='-I'$mpiincpath
	
	ns=$os' '$s2a
	#### end of modified string 
	echo To replace 
	echo $os 
	echo 'in line' "$lineno" 'in' $filetomod
	echo by 
	echo $ns 
	cat $filetomod | awk -v lineno=$lineno -v ns="$ns" 'NR==lineno {$0=ns} {print}' > output.txt
	mv output.txt $filetomod
## end of !!!!!!!!!!!!!!!!!!!! to modify Makefile.icc


## To modify Makefile.lammps.installed so that it is pointing to mkl library
cp Makefile.lammps.installed Makefile.lammps.installed.orig


######################
#cat <<EOF >outfile.txt 
#user-atc_SYSINC = -I/opt/intel/mkl/include
#user-atc_SYSLIB = -L/opt/intel/mkl/lib/intel64 #-lblas -llapack
#user-atc_SYSPATH = -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core ## -lmkl_lapack95_lp64
#EOF
################
line1='user-atc_SYSINC = -I/opt/intel/mkl/include'
line2='user-atc_SYSLIB = -L/opt/intel/mkl/lib/intel64 #-lblas -llapack'
line3='user-atc_SYSPATH = -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core ## -lmkl_lapack95_lp64'
cat <<EOF >outfile.txt
$line1
$line2
$line3
EOF
#################
mv outfile.txt Makefile.lammps.installed
echo 'Makefile.lammps.installed in' $PWD modified to point to mkl library
## end of To modify Makefile.lammps.installed so that it is pointing to mkl library
	make -f $filetomod


#7. 
cd ../awpmd
rm -f *.a *.o
## To modify Makefile.lammps.installed so that it is pointing to mkl library
cp Makefile.lammps.installed Makefile.lammps.installed.orig

#################
line1='user-awpmd_SYSINC = -I$(MKLROOT)/include'
line2='user-awpmd_SYSPATH = -L$(MKLROOT)/lib/intel64'
line3='user-awpmd_SYSLIB = -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core ## -lmkl_lapack95_lp64'
cat <<EOF >outfile.txt
$line1
$line2
$line3
EOF
#################
#cat <<EOF >outfile.txt
#user-awpmd_SYSINC = -I$(MKLROOT)/include
#user-awpmd_SYSPATH = -L$(MKLROOT)/lib/intel64
#user-awpmd_SYSLIB = -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core ## -lmkl_lapack95_lp64
#EOF

mv outfile.txt Makefile.lammps.installed
echo 'Makefile.lammps.installed in' $PWD modified to point to mkl library
## end of To modify Makefile.lammps.installed so that it is pointing to mkl library
make -f Makefile.mpicc


#8. linalg #
cd ../linalg
rm -f *.a *.o
## To modify Makefile.mpi so that it is using mpiifort
	filetomod=Makefile.mpi
	keyword=mpifort
## backup orig $filetomod copy
	cp $filetomod $filetomod'.orig'

### target line number to be replaced
	lineno=$(cat $filetomod | awk -v keyword=$keyword '$0 ~ keyword {print NR}')

#### original target string 
	os=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print}')
#echo $os 
#### end of original target string 

#### modified string 
	s2a='FC = mpiifort'
	ns=$s2a
#### end of modified string 
	echo To replace 
	echo $os 
	echo 'in line' "$lineno" 'in' $filetomod
	echo by 
	echo $ns 
	cat $filetomod | awk -v lineno=$lineno -v ns="$ns" 'NR==lineno {$0=ns} {print}' > output.txt
	mv output.txt $filetomod
## end of To modify Makefile.mpi so that it is using mpiifort 
make -f Makefile.mpi


#9. meam #
cd ../meam
rm -f *.a *.o
## To modify Makefile.lammps.ifort so that it is pointing to the right mkl library
targetf=Makefile.lammps.ifort
cp $targetf $targetf'.orig'

#cat <<EOF >outfile.txt
#meam_SYSINC = -I$(MKLROOT)/include
#meam_SYSLIB = -lifcore -lsvml -liompstubs5 -limf -lintlc #-lompstub
#meam_SYSPATH = -L$(MKLROOT)/lib/intel64 -L/opt/intel/lib/intel64 #-L/opt/intel/fce/10.0.023/lib
#EOF

#################
line1='meam_SYSINC = -I$(MKLROOT)/include'
line2='meam_SYSLIB = -lifcore -lsvml -liompstubs5 -limf -lintlc #-lompstub'
line3='meam_SYSPATH = -L$(MKLROOT)/lib/intel64 -L/opt/intel/lib/intel64 #-L/opt/intel/fce/10.0.023/lib'
cat <<EOF >outfile.txt
$line1
$line2
$line3
EOF
#################
mv outfile.txt $targetf
echo $targetf 'in' $PWD is modified to point to mkl library
## end of To modify Makefile.lammps.ifort so that it is pointing to the right mkl library
make -f Makefile.ifort


#10. poems #
cd ../poems
rm -f *.a *.o
make -f Makefile.icc


#11. reax #
cd ../reax
rm -f *.a *.o
make -f Makefile.ifort

# 12. qmmm  #### has to be linked against QE. Modify Makefile.ifort so that $QETOPDIR is properly linked
cd ../qmmm
rm -f *.a *.o
make -f Makefile.ifort


#13. colvars #
cd ../colvars
rm -f *.a *.o
make -f Makefile.mpi

#14. src #
cd ../../src

make yes-all
make no-kokkos
make no-user-netcdf
make no-user-quip
make no-voronoi
make no-user-h5md
make no-kim
make no-latte
make no-mscg
make no-user-smd
make no-user-vtk
make no-gpu

#15. make gpu #
### check if nvidia-smi is working. If yes, make yes-gpu; else make no-gpu
command=nvidia-smi
$command > /dev/null 2>&1
if [ $? -eq 0 ]; then
    echo command $command OK
    echo To install gpu
    cd ../lib/gpu
    make -f Makefile.linux clean
    make -f Makefile.linux 
    cd ../../src
    make yes-gpu
else
    echo command $command FAIL
    echo Not to install gpu
    make no-gpu
fi
### end of check if nvidia-smi is working. If yes, make yes-gpu; else make no-gpu


#16. To modify Makefile.xx in MAKE/OPTIONS and copy it to MAKE

	filetomod=Makefile.intel_cpu_intelmpi
	cd MAKE
	cp OPTIONS/$filetomod .

## 1
	keyword='-DMPICH_SKIP_MPICXX'
## backup orig $filetomod copy
	cp $filetomod $filetomod'.orig'

### target line number to be replaced
	lineno=$(cat $filetomod | awk -v keyword=$keyword '$0 ~ keyword {print NR}')
#	echo $lineno
#### original target string 
	os=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print}')
	#echo $os 
#### end of original target string 

#### modified string 
	s2a='MPI_INC = -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1 -I'$mpiincpath
#	/opt/intel/impi_latest/include64'
	ns=$s2a
#### end of modified string 
	echo To replace 
	echo $os 
	echo 'in line' "$lineno" 'in' $filetomod
	echo by 
	echo $ns 
	cat $filetomod | awk -v lineno=$lineno -v ns="$ns" 'NR==lineno {$0=ns} {print}' > output.txt
	mv output.txt $filetomod
	echo '1 is done'
	echo ' ' 

### 2 
### target line number to be replaced
	keyword='MPI_PATH ='
	lineno=$(cat $filetomod | awk -v keyword='MPI_PATH =' '$0 ~ keyword {print NR}')
	echo $lineno
#### original target string 
	os=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print}')
	echo $os 
#### end of original target string 

#### modified string 
	s2a='MPI_PATH = -L$mpilibpath
#	/opt/intel/impi_latest/lib64'
	ns=$s2a
#### end of modified string 
	echo To replace 
	echo $os 
	echo 'in line' "$lineno" 'in' $filetomod
	echo by 
	echo $ns 
	cat $filetomod | awk -v lineno=$lineno -v ns="$ns" 'NR==lineno {$0=ns} {print}' > output.txt
	mv output.txt $filetomod
	echo '2 is done'
	echo ' ' 

### 3
### target line number to be replaced
	keyword='MPI_LIB ='
	lineno=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print NR}')
	echo $lineno
#### original target string 
	os=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print}')
	echo $os 
#### end of original target string 

#### modified string 
	s2a='MPI_LIB = -lmpi'
	ns=$s2a
#### end of modified string 
	echo To replace 
	echo $os 
	echo 'in line' "$lineno" 'in' $filetomod
	echo by 
	echo $ns 
	cat $filetomod | awk -v lineno=$lineno -v ns="$ns" 'NR==lineno {$0=ns} {print}' > output.txt
	mv output.txt $filetomod
	echo '3 is done'
	echo ' ' 

### 4
### target line number to be replaced
	keyword='FFT_PATH = '
	lineno=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print NR}')
	echo $lineno
#### original target string 
	os=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print}')
	echo $os 
#### end of original target string 

#### modified string 
	s2a='FFT_PATH = -L$(MKLROOT)/lib/intel64'
	ns=$s2a
#### end of modified string 
	echo To replace 
	echo $os 
	echo 'in line' "$lineno" 'in' $filetomod
	echo by 
	echo $ns 
	cat $filetomod | awk -v lineno=$lineno -v ns="$ns" 'NR==lineno {$0=ns} {print}' > output.txt
	mv output.txt $filetomod
	echo '4 is done'
	echo ' ' 

### 5
### target line number to be replaced
	keyword='FFT_LIB ='
	lineno=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print NR}')
	echo $lineno
#### original target string 
	os=$(cat $filetomod | awk -v keyword="$keyword" '$0 ~ keyword {print}')
	echo $os 
#### end of original target string 

#### modified string 
	s2a='FFT_LIB = -lfftw3xf_intel #-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core	'
	ns=$s2a
#### end of modified string 
	echo To replace 
	echo $os 
	echo 'in line' "$lineno" 'in' $filetomod
	echo by 
	echo $ns 
	cat $filetomod | awk -v lineno=$lineno -v ns="$ns" 'NR==lineno {$0=ns} {print}' > output.txt
	mv output.txt $filetomod
	echo '5 is done'
	echo ' ' 

### 6
### to delete the specific line 
	ERR=$(( $lineno + 1 ))
	line2del=$(cat $filetomod | awk -v ERR=$ERR 'NR==ERR {print}')
	echo $line2del 'in line' "$ERR" 'in' $filetomod 'is deleted'
	awk -v no="$ERR" 'NR!=no' $filetomod > output.txt
	mv output.txt $filetomod
	echo '6 is done'
	echo ' '
## end To modify Makefile.xx in MAKE/OPTIONS and copy it to MAKE

cd ../
fn=$(echo $filetomod | awk -F  "." '{print $2}')
make $fn