#!/bin/bash

export ROOT_DIR=$HOME/NAMD_BUILD
export LIBRARY_PATH=$LIBRARY_PATH
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH
export C_INCLUDE_PATH=$C_INCLUDE_PATH
export C_COMP=icc
export F_COMP=ifort
export CXX_COMP=icpc
export MPIC_COMP=mpiicc
export MPICXX_COMP=mpiicpc
export MPIF_COMP=mpiifort
export MPIF77_COMP=mpiifort

export LIBRARY_PATH=$ROOT_DIR/common_dependencies/lib:$LIBRARY_PATH
export LD_LIBRARY_PATH=$ROOT_DIR/common_dependencies/lib:$LD_LIBRARY_PATH
export PATH=$ROOT_DIR/common_dependencies/bin:$PATH
export C_INCLUDE_PATH=$ROOT_DIR/common_dependencies/include:$C_INCLUDE_PATH

if [ ! -d $ROOT_DIR ]; then
	mkdir -p $ROOT_DIR/common_dependencies
	mkdir -p $ROOT_DIR/logs
fi

cd $ROOT_DIR


if [ ! -f tcl8.5.18-src.tar.gz ]; then
	wget http://downloads.sourceforge.net/project/tcl/Tcl/8.5.18/tcl8.5.18-src.tar.gz?r=&ts=1437718859&use_mirror=liquidtelecom 
fi
if [ ! -f tk8.5.18-src.tar.gz ]; then
	wget http://downloads.sourceforge.net/project/tcl/Tcl/8.5.18/tk8.5.18-src.tar.gz?r=&ts=1437718913&use_mirror=liquidtelecom
fi

if [ ! -f fftw-2.1.5.tar.gz ]; then
	wget http://www.fftw.org/fftw-2.1.5.tar.gz
fi

if [ ! -f fftw-3.3.4.tar.gz ]; then

	wget http://www.fftw.org/fftw-3.3.4.tar.gz
fi
if [ ! -f NAMD_2.10_Source.tar.gz ]; then
	wget http://www.ks.uiuc.edu/Research/namd/2.10/download/578621/NAMD_2.10_Source.tar.gz
fi
if [ ! -f apoa1.tar.gz ]; then
	wget http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
fi

	tar -xzvf tk8.5.18-src.tar.gz
	tar -xzvf tcl8.5.18-src.tar.gz
	tar -xzvf fftw-2.1.5.tar.gz
	tar -xzvf fftw-3.3.4.tar.gz
	tar -xzvf NAMD_2.10_Source.tar.gz


echo "#################| TCL 8.5  |##########################"
if [ ! -f $ROOT_DIR/common_dependencies/lib/libtcl8.5.so ]; then

	cd $ROOT_DIR/tcl8.5.18/unix
	CC=$MPIC_COMP CFLAGS="-fPIC" ./configure --prefix="$ROOT_DIR/common_dependencies" --enable-threads --enable-64bit |tee $ROOT_DIR/logs/tcl_8.5_config.log 
	make| tee $ROOT_DIR/logs/tcl_8.5_make.log 
	make install
fi


echo "#################| TK 8.5  |#########################"
if [ ! -f $ROOT_DIR/common_dependencies/lib/libtk8.5.so ]; then

	cd $ROOT_DIR/tk8.5.18/unix
	CC=$MPIC_COMP CFLAGS="-fPIC" LDFLAGS="-L$ROOT_DIR/common_dependencies/lib" ./configure --prefix="$ROOT_DIR/common_dependencies" --enable-threads --enable-64bit|tee $ROOT_DIR/logs/tk_8.5_config.log
	make|tee $ROOT_DIR/logs/tk_8.5_make.log
	make install
fi

echo "################| FFTW 2 installation |####################"
if [ ! -f $ROOT_DIR/common_dependencies/lib/libfftw.a ]; then
	cd $ROOT_DIR/fftw-2.1.5
	MPICC=$MPIC_COMP CC=$C_COMP CFLAGS="-fPIC" F77=$F_COMP FFLAGS="-fPIC" ./configure --prefix="$ROOT_DIR/common_dependencies" --enable-type-prefix --enable-float --with-openmp  --enable-mpi
	make
	make install
	make clean
	./configure --prefix="$ROOT_DIR/common_dependencies" 
	make
	make install	
fi
<<comment
echo "#################| FFTW3 installation |####################"
if [ ! -f $ROOT_DIR/common_dependencies/lib/libfftw3f.a ]; then
        cd $ROOT_DIR/fftw-3.3.4
        sed  -i '13042s/mpicc/mpiicc/' configure
        CC=$MPIC_COMP CXX=$MPICXX_COMP F77=$MPIF77_COMP CFLAGS="-fPIC" FFLAGS="-fPIC" LDFLAGS="-L$ROOT_DIR/common_dependencies/lib" LIBS="-lifcore -lifport" ./configure --prefix=$ROOT_DIR/common_dependencies --enable-openmp --enable-mpi --enable-single|tee $ROOT_DIR/logs/fftw3.3.4_config.log
        make |tee $ROOT_DIR/logs/fftw3.3.4_make.log
        make install
	make clean
        CC=$MPIC_COMP CXX=$MPICXX_COMP F77=$MPIF77_COMP CFLAGS="-fPIC" FFLAGS="-fPIC" LDFLAGS="-L$ROOT_DIR/common_dependencies/lib" LIBS="-lifcore -lifport" ./configure --prefix=$ROOT_DIR/common_dependencies --enable-openmp --enable-mpi |tee $ROOT_DIR/logs/fftw3.3.4_config.log
        make |tee $ROOT_DIR/logs/fftw3.3.4_make.log
        make install
fi
comment

#read namd

echo "################| Charm 6.6 installation |##################"

export MY_CHARM_ARCH=mpi-linux-x86_64

if [ ! -f $ROOT_DIR/NAMD_2.10_Source/charm-6.6.1/$MY_CHARM_ARCH-ifort-smp-mpicxx/bin/charmrun ]; then
	cd $ROOT_DIR/NAMD_2.10_Source
	tar -xvf charm-6.6.1.tar
	cd charm-6.6.1/

	sed -i "s/mpicxx/mpiicpc/g" $ROOT_DIR/NAMD_2.10_Source/charm-6.6.1/smart-build.pl
	export CHARM_CONFIG_FILES=$ROOT_DIR/NAMD_2.10_Source/charm-6.6.1/src/arch/$MY_CHARM_ARCH


	sed -i "/^g++/a mpiicc\) CMK_AMD64=\"-O3 -fPIC\" ;;" $CHARM_CONFIG_FILES/conv-mach.sh
	sed -i "/^CMK_NATIVE_[CC|LD]/ s/gcc/$C_COMP/g" $CHARM_CONFIG_FILES/conv-mach.sh
	sed -i "/^CMK_NATIVE_[CXX|LDXX]/ s/g++/$CXX_COMP/g" $CHARM_CONFIG_FILES/conv-mach.sh
	sed -i "/^CMK_CF90/ s/f95/$F_COMP/g" $CHARM_CONFIG_FILES/conv-mach.sh
	sed -i "s/conv-mach-gfortran.sh/conv-mach-ifort.sh/g" $CHARM_CONFIG_FILES/conv-mach.sh


	sed -i "/^CMK_CF77/a CMK_CF77=\"$MPIF_COMP -auto -fPIC \"" $CHARM_CONFIG_FILES/cc-mpicxx.sh
	sed -i "/^CMK_CF90/a CMK_CF90=\"$MPIF_COMP -auto -fPIC \"" $CHARM_CONFIG_FILES/cc-mpicxx.sh
	sed -i "s/^MPICXX_DEF/MPICXX_DEF=$MPICXX_COMP/g" $CHARM_CONFIG_FILES/cc-mpicxx.sh
	sed -i "s/^MPICC_DEF/MPICC_DEF=$MPIC_COMP/g" $CHARM_CONFIG_FILES/cc-mpicxx.sh


#why mpicxx needed hete?
	MPICXX=$MPICXX_COMP CXX=$CXX_COMP ./build charm++  $MY_CHARM_ARCH mpicxx $F_COMP smp --with-production --no-shared -O3 -DCMK_OPTIMIZE=1 -j8 | tee $ROOT_DIR/logs/charmm6.6_build.log
	##./build charm++ mpi-linux-x86_64 smp mpicxx --with-production -DCMK_OPTIMIZE -DMPICH_IGNORE_CXX_SEEK
	#cd $MY_CHARM_ARCH-ifort-mpicxx/tests/charm++/megatest
	cd $MY_CHARM_ARCH-ifort-smp-mpicxx/tests/charm++/megatest
	make pgm|tee $ROOT_DIR/logs/charmm6.6_testmake.log
	mpirun -n 4 ./pgm
	if [ $(echo $?) == "0" ]; then
		echo "CHARM++ installed properly"
	else
		echo "CHARM++:some error occured "
		read namd_err
	fi
fi

read charm 

echo "#############| NAMD |###############"
export MY_NAMD_ARCH=Linux-x86_64-icc

if [ ! -f $ROOT_DIR/NAMD_2.10_Source/$MY_NAMD_ARCH/namd2 ]; then

	cd $ROOT_DIR/NAMD_2.10_Source
	sed -i  "/^CHARMBASE/c CHARMBASE=$ROOT_DIR/NAMD_2.10_Source/charm-6.6.1" Make.charm
	sed -i  "/^CHARMARCH/c CHARMARCH=mpi-linux-x86_64-ifort-smp-mpicxx" arch/$MY_NAMD_ARCH.arch
#	sed -i  "/^FLOATOPTS/c FLOATOPTS=-ip -fno-rtti -no-vec" arch/$MY_NAMD_ARCH.arch
	sed -i  "/^FLOATOPTS/c FLOATOPTS= -fomit-frame-pointer -fp-model fast=2 -xHost -qopenmp " arch/$MY_NAMD_ARCH.arch
	sed -i  "/^CXXOPTS/c CXXOPTS= -static-intel -Ofast \$\(FLOATOPTS\)" arch/$MY_NAMD_ARCH.arch
	sed -i  "/^COPTS/c COPTS= -static-intel -Ofast \$\(FLOATOPTS\)" arch/$MY_NAMD_ARCH.arch

	sed -i  "/^FFTDIR/c FFTDIR=$ROOT_DIR/common_dependencies" arch/Linux-x86_64.fftw3
	sed -i  "/^FFTINCL/c FFTINCL=-I\$\(FFTDIR\)/include" arch/Linux-x86_64.fftw3
	sed -i  "/^FFTLIB/c FFTLIB=-L\$\(FFTDIR\)/lib -lsrfftw -lsfftw " arch/Linux-x86_64.fftw3
	sed -i  "/^FFTFLAGS/c FFTFLAGS=-DNAMD_FFTW" arch/Linux-x86_64.fftw3


	sed -i  "/^TCLDIR/c TCLDIR=$ROOT_DIR/common_dependencies" arch/Linux-x86_64.tcl
	sed -i  "/^TCLLIB/c TCLLIB=-L\$\(TCLDIR\)/lib64 -ltcl8.5 -ldl " arch/Linux-x86_64.tcl
	sed -i  "/^TCLFLAGS/c  TCLFLAGS=-DNAMD_TCL" arch/Linux-x86_64.tcl
#	if [ $# == "1" -a $1 == "mic-enable" ] ; then
#		sed -i "/^CXXMICOPTS/c CXXMICOPTS= -offload-option,mic,compiler,-vec -offload-option,mic,compiler,-restrict -qopenmp" arch/Linux-x86_64.mic
#	fi
# mpi-linux-x86_64-ifort-mpicxx ?
	./config $MY_NAMD_ARCH --charm-base ./charm-6.6.1 --charm-arch $MY_CHARM_ARCH-ifort-smp-mpicxx --with-fftw --fftw-prefix $ROOT_DIR/common_dependencies  --cxx "$MPICXX_COMP "  --cxx-opts " -Ofast -fomit-frame-pointer -fp-model fast=2 -xHost -qopenmp " --with-mic  --cc "$MPIC_COMP " --cc-opts " -Ofast -fomit-frame-pointer -fp-model fast=2 -xHost -qopenmp "  --with-tcl  --tcl-prefix $ROOT_DIR/common_dependencies | tee $ROOT_DIR/logs/NAMD_config.log
	cd $MY_NAMD_ARCH
	make -j8 VERBOSE=1 all | tee $ROOT_DIR/logs/NAMD_make.log
	echo "status:$?"
fi
	cd $ROOT_DIR/NAMD_2.10_Source/$MY_NAMD_ARCH/
	cp $ROOT_DIR/apoa1.tar.gz .
	tar -xzvf apoa1.tar.gz
	
	sed -i "/^timestep/c timestep             0.001" ./apoa1/apoa1.namd
        sed -i "/^numsteps/c numsteps             500" ./apoa1/apoa1.namd
	
	( time mpirun -np 1 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/01namd_with1_procs_1ppn.log
	( time mpirun -np 1 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/02namd_with1_procs_2ppn.log
	( time mpirun -np 1 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/03namd_with1_procs_4ppn.log
	( time mpirun -np 1 ./namd2 +ppn 8 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/04namd_with1_procs_8ppn.log
	( time mpirun -np 1 ./namd2 +ppn 10 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/05namd_with1_procs_10ppn.log
	( time mpirun -np 1 ./namd2 +ppn 12 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/06namd_with1_procs_12ppn.log
	( time mpirun -np 1 ./namd2 +ppn 16 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/07namd_with1_procs_16ppn.log
	( time mpirun -np 1 ./namd2 +ppn 19 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/08namd_with1_procs_19ppn.log
	( time mpirun -np 1 ./namd2 +ppn 23 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/09namd_with1_procs_23ppn.log
	( time mpirun -np 1 ./namd2 +ppn 24 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/10namd_with1_procs_24ppn.log
	( time mpirun -np 1 ./namd2 +ppn 28 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/11namd_with1_procs_28ppn.log
	( time mpirun -np 1 ./namd2 +ppn 32 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/12namd_with1_procs_32ppn.log
	( time mpirun -np 1 ./namd2 +ppn 38 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/13namd_with1_procs_38ppn.log
	( time mpirun -np 1 ./namd2 +ppn 39 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/14namd_with1_procs_39ppn.log
	( time mpirun -np 1 ./namd2 +ppn 40 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/15namd_with1_procs_40ppn.log
	( time mpirun -np 1 ./namd2 +ppn 46 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/16namd_with1_procs_46ppn.log
	( time mpirun -np 1 ./namd2 +ppn 47 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/17namd_with1_procs_47ppn.log
	( time mpirun -np 1 ./namd2 +ppn 48 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/18namd_with1_procs_48ppn.log
	( time mpirun -np 1 ./namd2 +ppn 56 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/19namd_with1_procs_56ppn.log
	( time mpirun -np 1  ./namd2 +ppn 57 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/20namd_with1_procs_57ppn.log
	( time mpirun -np 1  ./namd2 +ppn 64 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/21namd_with1_procs_64ppn.log
	( time mpirun -np 1  ./namd2 +ppn 114 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/22namd_with1_procs_114ppn.log
	( time mpirun -np 1  ./namd2 +ppn 228 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/23namd_with1_procs_228ppn.log

#chosen for 16 core config
	#8cores (underutilizing 16 core s!!)
	
	#16 cores

	#32 cores (overutilizing 16 cores!!-more procs)
	#32 cores (overutilizing 16 cores!!-more threads)
	
#chosen for 20 core config
	#10 cores(underutilizing 20 core machine!)
	
	#20 cores (utilizing all cores!)
	#40 cores (doubling load on 20 cores)

#chosen for 24 core config	
	#12 cores (underutilizing 24 core machine)
<<comment
	( time mpirun -np 2 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/24namd_with2_procs_2ppn.log
	( time mpirun -np 2 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/25namd_with2_procs_4ppn.log
	( time mpirun -np 2 ./namd2 +ppn 5 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/26namd_with2_procs_5ppn.log
	( time mpirun -np 2 ./namd2 +ppn 6 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/27namd_with2_procs_6ppn.log
	( time mpirun -np 2 ./namd2 +ppn 8 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/28namd_with2_procs_8ppn.log
	( time mpirun -np 2 ./namd2 +ppn 10 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/29namd_with2_procs_10ppn.log
	( time mpirun -np 2 ./namd2 +ppn 12 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/30namd_with2_procs_12ppn.log
	( time mpirun -np 2 ./namd2 +ppn 14 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/31namd_with2_procs_14ppn.log
	( time mpirun -np 2 ./namd2 +ppn 16 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/32namd_with2_procs_16ppn.log
	( time mpirun -np 2 ./namd2 +ppn 20 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/33namd_with2_procs_20ppn.log
	( time mpirun -np 2 ./namd2 +ppn 24 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/34namd_with2_procs_24ppn.log
	( time mpirun -np 2 ./namd2 +ppn 28 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/35namd_with2_procs_28ppn.log
	( time mpirun -np 2 ./namd2 +ppn 57 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/36namd_with2_procs_57ppn.log
	( time mpirun -np 2 ./namd2 +ppn 114 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/37namd_with2_procs_114ppn.log

	( time mpirun -np 3 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/38namd_with3_procs_4ppn.log
	( time mpirun -np 3 ./namd2 +ppn 8 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/39namd_with3_procs_8ppn.log
	( time mpirun -np 3 ./namd2 +ppn 16 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/40namd_with3_procs_16ppn.log
	( time mpirun -np 3 ./namd2 +ppn 38 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/41namd_with3_procs_38ppn.log
	( time mpirun -np 3 ./namd2 +ppn 76 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/42namd_with3_procs_76ppn.log

	( time mpirun -np 4 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/43namd_with4_procs_2ppn.log
	( time mpirun -np 4 ./namd2 +ppn 3 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/44namd_with4_procs_3ppn.log
	( time mpirun -np 4 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/45namd_with4_procs_4ppn.log
	( time mpirun -np 4 ./namd2 +ppn 5 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/46namd_with4_procs_5ppn.log
	( time mpirun -np 4 ./namd2 +ppn 6 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/47namd_with4_procs_6ppn.log
	( time mpirun -np 4 ./namd2 +ppn 7 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/48namd_with4_procs_7ppn.log
	( time mpirun -np 4 ./namd2 +ppn 8 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/49namd_with4_procs_8ppn.log
	( time mpirun -np 4 ./namd2 +ppn 10 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/50namd_with4_procs_10ppn.log
	( time mpirun -np 4 ./namd2 +ppn 12 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/51namd_with4_procs_12ppn.log
	( time mpirun -np 4 ./namd2 +ppn 14 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/52namd_with4_procs_14ppn.log
	( time mpirun -np 4 ./namd2 +ppn 57 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/53namd_with4_procs_57ppn.log

	( time mpirun -np 5 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/54namd_with5_procs_2ppn.log
	
	( time mpirun -np 6 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/55namd_with6_procs_2ppn.log
	( time mpirun -np 6 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/56namd_with6_procs_4ppn.log
	( time mpirun -np 6 ./namd2 +ppn 19 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/57namd_with6_procs_19ppn.log
	( time mpirun -np 6 ./namd2 +ppn 38 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/58namd_with6_procs_38ppn.log
	
	( time mpirun -np 7 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/59namd_with7_procs_4ppn.log
	( time mpirun -np 7 ./namd2 +ppn 7 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/60namd_with7_procs_7ppn.log
	( time mpirun -np 7 ./namd2 +ppn 8 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/61namd_with7_procs_8ppn.log
	
	( time mpirun -np 8 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/62namd_with8_procs_1ppn.log
	( time mpirun -np 8 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/63namd_with8_procs_2ppn.log
	( time mpirun -np 8 ./namd2 +ppn 3 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/64namd_with8_procs_3ppn.log
	( time mpirun -np 8 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/65namd_with8_procs_4ppn.log
	( time mpirun -np 8 ./namd2 +ppn 5 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/66namd_with8_procs_5ppn.log
	( time mpirun -np 8 ./namd2 +ppn 6 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/67namd_with8_procs_6ppn.log
	( time mpirun -np 8 ./namd2 +ppn 7 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/68namd_with8_procs_7ppn.log

	( time mpirun -np 10 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/69namd_with10_procs_1ppn.log
	( time mpirun -np 10 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/70namd_with10_procs_2ppn.log
	( time mpirun -np 10 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/71namd_with10_procs_4ppn.log

	( time mpirun -np 12 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/72namd_with12_procs_1ppn.log
	( time mpirun -np 12 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/73namd_with12_procs_4ppn.log
	( time mpirun -np 12 ./namd2 +ppn 19 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/74namd_with12_procs_19ppn.log

	( time mpirun -np 14 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/75namd_with14_procs_2ppn.log
	( time mpirun -np 14 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/76namd_with14_procs_4ppn.log

	( time mpirun -np 16 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/77namd_with16_procs_2ppn.log
	( time mpirun -np 16 ./namd2 +ppn 3 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/78namd_with16_procs_3ppn.log

	( time mpirun -np 19 ./namd2 +ppn 6 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/79namd_with19_procs_6ppn.log
	( time mpirun -np 19 ./namd2 +ppn 12 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/80namd_with19_procs_12ppn.log

	( time mpirun -np 20 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/81namd_with20_procs_2ppn.log

	( time mpirun -np 24 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/82namd_with24_procs_1ppn.log
	( time mpirun -np 24 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/83namd_with24_procs_2ppn.log

	( time mpirun -np 26 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/84namd_with26_procs_2ppn.log

	( time mpirun -np 28 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/85namd_with28_procs_1ppn.log

	( time mpirun -np 38 ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/86namd_with38_procs_4ppn.log
	( time mpirun -np 38 ./namd2 +ppn 6 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/87namd_with38_procs_6ppn.log

	( time mpirun -np 40 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/88namd_with40_procs_1ppn.log

	( time mpirun -np 48 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/89namd_with48_procs_1ppn.log

	( time mpirun -np 56 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/90namd_with56_procs_1ppn.log

	( time mpirun -np 57 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/91namd_with57_procs_2ppn.log
	( time mpirun -np 57  ./namd2 +ppn 4 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/92namd_with57_procs_4ppn.log

	( time mpirun -np 76 ./namd2 +ppn 3 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/93namd_with76_procs_3ppn.log

	( time mpirun -np 114 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/94namd_with114_procs_1ppn.log
	( time mpirun -np 114 ./namd2 +ppn 2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/95namd_with114_procs_2ppn.log

	( time mpirun -np 228 ./namd2 +ppn 1 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/96namd_with228_procs_1ppn.log

	touch $ROOT_DIR/output.data && cp /dev/null $ROOT_DIR/output.data
	for logfile in `ls $ROOT_DIR/*ppn.log`
	do
		tail -6 $logfile |head -1| awk  '{print $6 " " $2}' >> $ROOT_DIR/output.data
	done
comment
	#24 core full
	
	#48 

#chosen for mic 57 cores!
	
	#unserutilisinglmic	(28)
	#full utilization mic
	#doubling load mic (114)	
	#quadrupling load miv (228)
	
#chosen for mic 
#	time mpiexec.hydra -perhost 1 -n 1 ./namd2 +ppn 4 ./apoa1/apoa1.namd |tee $ROOT_DIR/namd_with1_procs_hydra.log
	#( time mpirun -np 2 ./namd2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/namd_with2_procs.log
	#( time mpirun -np 4 ./namd2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/namd_with4_procs.log
	#( time mpirun -np 8 ./namd2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/namd_with8_procs.log
#	( time mpirun -np 16 ./namd2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/namd_with16_procs.log
#	( time mpirun -np 23 ./namd2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/namd_with23_procs.log
	
#	( time mpirun -np 32 ./namd2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/namd_with32_procs.log
#	( time mpirun -np 64 ./namd2 ./apoa1/apoa1.namd ) 2>&1 | tee $ROOT_DIR/namd_with64_procs.log
# GCC VERSION:
# ./build charm++ net-linux-x86_64
# net-linux-x86_64/
#./build charm++ mpi-linux-x86_64   $MPIC_COMP tcp
# mpi-linux-x86_64