Useful Makefiles

This page is a place to stick Makefiles or other config files for common codes that you've got working on the local compute servers

Tardis

cp2k with intel compilers

You need the mkl, mpi/mvapich/intel, blacs/mvapich/intel64, and scalapack/intel modules loaded

# The following settings worked for:
# - AMD64 Opteron cluster
# - SUSE Linux 10.0 (x86_64)
# - Intel(R) Fortran Compiler for Intel(R) EM64T-based applications, Version 9.1.037
# - Intel(R) Cluster Math Kernel Library v7.2 for Linux
# - MVAPICH
# - BLACS and ScaLAPACK compiled for Intel
#
PERL     = perl
CC       = cc
CPP      = cpp
FC       = mpif90 -FR
LD       = mpif90
AR       = ar -r
DFLAGS   = -D__INTEL -D__FFTSG\
          -D__parallel -D__BLACS -D__SCALAPACK\
          -Dfftwnd_f77=fftwnd_f77_\
          -Dfftwnd_f77_one=fftwnd_f77_one_\
          -Dfftw3d_f77_create_plan=fftw3d_f77_create_plan_\
          -Dfftw2d_f77_create_plan=fftw2d_f77_create_plan_\
          -Dfftwnd_f77_destroy_plan=fftwnd_f77_destroy_plan_\
          -Dfftw_f77_create_plan=fftw_f77_create_plan_\
          -Dfftw_f77=fftw_f77_\
          -Dfftw_f77_destroy_plan=fftw_f77_destroy_plan_
CPPFLAGS = -traditional -C $(DFLAGS) -P
FCFLAGS  = $(DFLAGS) -O2
MKLPATH  = /usr/local/Cluster-Apps/intel/mkl/8.0/lib/em64t
LDFLAGS  = $(FCFLAGS) -i-static
LIBS     = \
          -L/usr/local/Cluster-Apps/scalapack/intel/lib64 -lscalapack \
          $(MKLPATH)/libmkl_lapack.a \
          -L/usr/local/Cluster-Apps/blacs/mvapich/intel/lib64 -lblacsF77init -lblacs \
          $(MKLPATH)/libmkl_em64t.a \
          $(MKLPATH)/libguide.a\
          -lpthread

OBJECTS_ARCHITECTURE = machine_intel.o

#           -D__FFTW\

Jochen's CPMD with Portland compilers and MVAPICH

You need the mpi/mvapich/pgi module but ACML comes in automatically with PGI.

#----------------------------------------------------------------------------
# Makefile for cpmd.x (plane wave electronic calculation)
# Configuration: PGI-AMD64-MPI
# Creation of Makefile: Dec  5 2006
# on Linux tardis 2.6.15.1-clustervision-128_cvos #1 SMP Mon Sep 25 12:05:46 CEST 2006   x86_64 x86_64 x86_64 GNU/Linux
# Author: jb376
#----------------------------------------------------------------------------
#
SHELL = /bin/sh
#
#--------------- Default Configuration for PGI-AMD64-MPI ---------------
SRC  = .
DEST = .
BIN  = .
#QMMM_FLAGS = -D__QMECHCOUPL
#QMMM_LIBS  = -L. -lmm
FFLAGS = -r8 -pc=64 -Msignextend  
#LFLAGS = -Bstatic -L. -latlas_x86-64 $(QMMM_LIBS)
#LFLAGS = -Bstatic -L. -latlas_x86_64 $(QMMM_LIBS)
LFLAGS = -lacml $(QMMM_LIBS)
CFLAGS = 
CPP = /lib/cpp -P -C -traditional
#CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPOINTER8 -D__pgf90 \
#               -DPARALLEL -DMP_LIBRARY=__MPI -DMYRINET  
CPPFLAGS = -D__Linux -D__PGI -DLAPACK -DFFT_DEFAULT -DPOINTER8 -D__pgf90 \
              -DPARALLEL -DMP_LIBRARY=__MPI 
NOOPT_FLAG = 
CC = mpicc -O2 -Wall -m64
FC = mpif77 -c -fastsse -tp k8-64
LD = mpif77 -fastsse -tp k8-64
AR = 
#----------------------------------------------------------------------------

NAMD2 with Intel compilers

This one requires the openmpi/intel64 module

Step 1: charm++

./build charm++ mpi-linux-amd64 icc

my src/arch/mpi-linux-amd64/conv-mach.sh

CMK_REAL_COMPILER=`mpiCC -show 2>/dev/null | cut -d' ' -f1 `
case "$CMK_REAL_COMPILER" in
 g++) CMK_AMD64="-m64 -fPIC" ;;
esac

CMK_CPP_CHARM="/lib/cpp -P"
CMK_CPP_C="mpicc -E"
CMK_CC="mpicc $CMK_AMD64 "
CMK_CXX="mpiCC $CMK_AMD64 "
CMK_CXXPP="mpiCC -E $CMK_AMD64 "

CMK_SYSLIBS=" "
CMK_LIBS="-lckqt $CMK_SYSLIBS "
CMK_LD_LIBRARY_PATH="-Wl,-rpath,$CHARMLIBSO/"

CMK_NATIVE_CC="gcc $CMK_AMD64 "
CMK_NATIVE_LD="gcc $CMK_AMD64 "
CMK_NATIVE_CXX="g++ $CMK_AMD64 "
CMK_NATIVE_LDXX="g++ $CMK_AMD64 "
CMK_NATIVE_LIBS=""

# fortran compiler 
CMK_CF77="f77"
CMK_CF90="f90"
CMK_F90LIBS=" "
CMK_F77LIBS=" "
CMK_MOD_NAME_ALLCAPS=1
CMK_MOD_EXT="mod"
CMK_F90_USE_MODDIR=1
CMK_F90_MODINC="-p"

CMK_QT='generic64'
CMK_RANLIB="ranlib"

and src/arch/common/cc-icc.sh

CMK_CPP_C='mpicc -E '
CMK_CC="mpicc -fpic "
CMK_CXX="mpiCC -fpic "
CMK_CXXPP='mpiCC -E '
CMK_LD='mpicc -i_dynamic '
CMK_LDXX='mpiCC -i_dynamic '
CMK_LD_LIBRARY_PATH="-Wl,-rpath,$CHARMLIBSO/"
CMK_CF90='ifc -auto '
CMK_CF90_FIXED="$CMK_CF90 -132 -FI "
CMK_NATIVE_F90="$CMK_CF90"
CMK_NATIVE_CC="$CMK_CC"
CMK_NATIVE_CXX="$CMK_CXX"
CMK_NATIVE_LD="$CMK_LD"
CMK_NATIVE_LDXX="$CMK_LDXX"
CMK_F90LIBS='-L/usr/local/intel/compiler70/ia32/lib -L/opt/intel/compiler70/ia32/lib -lintrins -lIEPCF90 -lPEPCF90 -lF90 -lintrins -limf  '
CMK_MOD_NAME_ALLCAPS=1
CMK_MOD_EXT="mod"
CMK_F90_USE_MODDIR=""

Step 2: NAMD

./config tcl fftw Linux-amd64-MPI-icc

my arch/Linux-amd64.tcl:

TCLDIR=/usr
TCLINCL=-I$(TCLDIR)/include 
TCLLIB=-L$(TCLDIR)/lib -ltcl8.4 -ldl
TCLFLAGS=-DNAMD_TCL -DUSE_NON_CONST 
TCL=$(TCLINCL) $(TCLFLAGS)

my arch/Linux-amd64.fftw:

FFTDIR=/usr/local/fftw2/intel/64/2.1.5
FFTINCL=-I$(FFTDIR)/include -I$(HOME)/fftw/include
FFTLIB=-L$(FFTDIR)/lib -L$(HOME)/fftw/lib -lsrfftw -lsfftw
FFTFLAGS=-DNAMD_FFTW
FFT=$(FFTINCL) $(FFTFLAGS)

Jochen's Linux-amd64-MPI-icc.arch (Vastly improves performance over the default):

NAMD_ARCH = Linux-amd64
CHARMARCH = mpi-linux-amd64-icc
FLOATOPTS = -fno-rtti
CXX = /usr/local/Cluster-Apps/ofed/1.0/mpi/intel/mvapich-0.9.7-mlx2.1.0/bin/mpicxx
CXXOPTS = -tpp6 -pc64 -i-static -static-libcxa -O2 -unroll $(FLOATOPTS)
CXXNOALIASOPTS = -O2 -unroll -fno-alias $(FLOATOPTS)
CC = /usr/local/Cluster-Apps/ofed/1.0/mpi/intel/mvapich-0.9.7-mlx2.1.0/bin/mpicc
COPTS = -i-static -static-libcxa -O2 $(FLOATOPTS)