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Month: September 2013
Compiling VASP 5.3.3 with OpenMPI 1.6.5 and Intel 12.1.5
Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles.
To compile VASP, I will be using the following
- Intel Compiler XE 12.1.5
- OpenMPI 1.6.5
- Maths Kernel Library (MKL)
- CentOS 6.3 / RH 6.3
A. Prerequisites
Step 1: Install and Compile Intel XE Compilers 12.1.5 and OpenMPI 1.6.5
Step 2: Intel MKL FFTW wrappers
B. Compiling VASP Libraries
Assuming you have unpacked the VASP files. Here is may make file
.SUFFIXES: .inc .f .F #----------------------------------------------------------------------- # Makefile for LINUX NAG f90 #----------------------------------------------------------------------- # fortran compiler FC=ifort # C-preprocessor #CPP = /usr/lib/gcc-lib/i486-linux/2.7.2/cpp -P -C $*.F >$*.f CPP = gcc -E -P -C -DLONGCHAR $*.F >$*.f CFLAGS = -O FFLAGS = -Os -FI FREE = -FR DOBJ = preclib.o timing_.o derrf_.o dclock_.o diolib.o dlexlib.o drdatab.o #----------------------------------------------------------------------- # general rules #----------------------------------------------------------------------- libdmy.a: $(DOBJ) linpack_double.o -rm libdmy.a ar vq libdmy.a $(DOBJ) linpack_double.o: linpack_double.f $(FC) $(FFLAGS) $(NOFREE) -c linpack_double.f # files which do not require autodouble lapack_double.o: lapack_double.f $(FC) $(FFLAGS) $(NOFREE) -c lapack_double.f lapack_single.o: lapack_single.f $(FC) $(FFLAGS) $(NOFREE) -c lapack_single.f #lapack_cray.o: lapack_cray.f # $(FC) $(FFLAGS) $(NOFREE) -c lapack_cray.f .c.o: $(CC) $(CFLAGS) -c $*.c .F.o: $(CPP) $(FC) $(FFLAGS) $(FREE) $(INCS) -c $*.f .F.f: $(CPP) .f.o: $(FC) $(FFLAGS) $(FREE) $(INCS) -c $*.f
C. Compiling VASP
1. Copy the Makefile from makefile.linux_ifc_P4 in the vasp software.
# cp makefile.linux_ifc_P4 Makefile
2. Edit the Makefile
FC (~ line 62)
#----------------------------------------------------------------------- # fortran compiler and linker #----------------------------------------------------------------------- FC=mpif90 # fortran linker FCL=$(FC) -mkl
FFLAGS (~line 108)
#----------------------------------------------------------------------- # general fortran flags (there must a trailing blank on this line) # byterecl is strictly required for ifc, since otherwise # the WAVECAR file becomes huge #----------------------------------------------------------------------- FFLAGS = -FR -names lowercase -assume byterecl
BLAS (~ line 149)
# BLAS # setting -DRPROMU_DGEMV -DRACCMU_DGEMV in the CPP lines usually speeds up program execution # BLAS= -Wl,--start-group $(MKL_PATH)/libmkl_intel_lp64.a $(MKL_PATH)/libmkl_intel_thread.a $(MKL_PATH)/libmkl_core.a -Wl,--end-group -lguide # faster linking and available from at least version 11 BLAS= -mkl=sequential
LAPACK (~ line 158)
# LAPACK from mkl, usually faster and contains scaLAPACK as well #LAPACK= $(MKL_PATH)/libmkl_intel_lp64.a LAPACK =
CPP ( ~ line 223)
#----------------------------------------------------------------------- CPP = $(CPP_) -DMPI -DHOST=\"LinuxIFC\" -DIFC \ -DCACHE_SIZE=4000 -DPGF90 -Davoidalloc -DNGZhalf \ -DMPI_BLOCK=8000 -Duse_collective -DscaLAPACK \ -DRPROMU_DGEMV -DRACCMU_DGEMV
SCALAPACK (~ line 233)
#----------------------------------------------------------------------- # location of SCALAPACK # if you do not use SCALAPACK simply leave this section commented out #----------------------------------------------------------------------- # usually simplest link in mkl scaLAPACK BLACS= -lmkl_blacs_openmpi_lp64 SCA= $(MKL_PATH)/libmkl_scalapack_lp64.a $(BLACS)
LIBRARIES (~line 238)
#----------------------------------------------------------------------- # libraries #----------------------------------------------------------------------- LIB = -L../vasp.5.lib -ldmy \ ../vasp.5.lib/linpack_double.o \ $(SCA) $(LAPACK) $(BLAS)
Parallel FFT (~ line 246)
#----------------------------------------------------------------------- # parallel FFT #----------------------------------------------------------------------- # FFT: fftmpi.o with fft3dlib of Juergen Furthmueller FFT3D = fftmpi.o fftmpi_map.o fft3dfurth.o fft3dlib.o
References:
Compiling GCC 4.7.2 on CentOS 5
Step 1: Download the following prerequistics applications libraries from ftp://gcc.gnu.org/pub/gcc/infrastructure/
- gmp-4.3.2.tar.bz2
- mpfr-2.4.2.tar.bz2
- mpc-0.8.1.tar.gz
1. Install gmp-4.3.2
# bunzip2 gmp-4.3.2.tar.bz2 # tar -zxvf gmp-4.3.2.tar # cd gmp-4.3.2 # ./configure --prefix=/usr/local/gmp-4.3.2 # make # make install
2. Install mpfr-2.4.2 (requires gmp-4.3.2 as prerequisites)
# bunzip2 mpfr-2.4.2.tar.bz2 # tar -zxvf mpfr-2.4.2.tar # cd mpfr-2.4.2 # ./configure --prefix=/usr/local/mpfr-2.4.2 --with-gmp=/usr/local/gmp-4.3.2/ # make # make install
3. Install mpc-0.8.1 (requires gmp-4.3.2 and mpfr-2.4.2 as prerequisites )
# tar -zxvf mpc-0.8.1.tar.gz # cd mpc-0.8.1 #./configure --prefix=/usr/local/mpc-0.8.1/ --with-gmp=/usr/local/gmp-4.3.2/ --with-mpfr=/usr/local/mpfr-2.4.2 # make # make install
4. Update your LD_LIBRARY_PATH at your ~/.bashrc
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1:/usr/local/mpfr-2.4.2/lib:/usr/local/gmp-4.3.2/lib
5. Install the glibc-devel.i686. For more information, do look at Error when compiling GCC 4.8.1 (linuxtoolkit.blogspot.com)
6. Finally install GNU CC 4.7.2
# tar -zxvf gcc-4.7.2.tar.gz # cd gcc-4.7.2 # mkdir build-gcc # cd build-gcc # ../configure --prefix=/usr/local/gcc-4.7.2 \ --with-mpfr=/usr/local/mpfr-2.4.2 \ --with-mpc=/usr/local/mpc-0.8.1 \ --with-gmp=/usr/local/gmp-4.3.2 \ --with-mpfr-include=/usr/local/mpfr-2.4.2/include \ --with-mpc-include=/usr/local/mpc-0.8.1/include # make all-gcc # make install-gcc
Compiling OpenMPI 1.6.5 with Intel 12.1.5 on CentOS 6
Step 1: Download the OpenMPI Software from http://www.open-mpi.org/ . The current stable version at point of writing is OpenMPI 1.6.5
Step 2: Download and Install the Intel Compilers from Intel Website. More information can be taken from Free Non-Commercial Intel Compiler Download
Step 3: Add the Intel Directory Binary Path to the Bash Startup
At my ~/.bash_profile directory, I've added source /usr/local/intel/composerxe/bin/compilervars.sh intel64 export PATH=$PATH:/usr/local/intel/composerxe/bin export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/RH6_apps/intel/composerxe/lib/intel64:/usr/local/intel/composerxe/mkl/lib/intel64
At command prompt
# source .bashrc
Step 4: Configuration Information
# gunzip -c openmpi-1.6.5.tar.gz tar xf - # cd openmpi-1.6.5 # /configure --prefix=/usr/local/openmpi-1.6.5-intel-v12.1.5 CC=icc CXX=icpc F77=ifort FC=ifort --with-devel-headers --enable-binaries # make all install
You will need to include –devel-headers –enable-binaries” or you will face the error Cannot open OpenMPI Configuration mpif90-wrapper-data.txt
Step 5: Test the configuration
$ mpicc -v cc version 12.1.5 (gcc version 4.4.6 compatibility)
Compile and Build FFTW3 wrapper routines on MKL implementation of FFT
Software like VASP uses calling statements of the FFTW3 which differ to the implementation of FFT in MKL. You will need to compile the wrapper routines for MKL
# cd $MKLROOT/interfaces/fftw3xf
# make
After a successful compilation libfftw3xf_intel.a was created in this directory