Installation

System requirements

In principle, BDF supports all Unix-like platforms. However, we strongly advise you to use BDF on a Linux platform together with Intel or GCC compilers because the BDF package was developed and most thoroughly tested on such platforms. System requirements of BDF are summarized as following lines:

 OS: Linux, Mac, FreeBSD, Unix
 Compiler: Fortran 90 compiler such as Intel, gfortran, g95
 Support softwares: Python, make
 Parallel environments: MPI

Configure and compile BDF package

Several steps are needed to install BDF package.

1. Set fortran and C compiler.

If you use bash shell, you can set fortran and C compiler:

$export FC=ifort
$export CC=gcc
$export CXX=g++

Tips: If you ignored this step, the configure script will pick up the gfortran and gcc compiler as default.

2. Set blas and lapack library. The external Blas and Lapack libraries are needed for compiling BDF. In addition, C language Blas and Lapack are required. It is easiest to use Intel MKL. You only need to set "MATHLIB" and "MATHINCLUDE" as

$export MATHLIB="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread"
$export MATHINCLUDE="-I/opt/intel/mkl/include"

However, you may choose to use Blas and Lapack from netlib. You may download lapack library from http://www.netlib.org/lapack/lapack-3.6.0.tgz. Do not forget also compile "lapacke" and "cblas", which is a C interface for lapack and blas library.

Then, you need to set "MATHLIB" and "MATHINCLUDE"

$export MATHLIB="-L/Users/aaa/mathlib/ -llapack -lblas -llapacke -lcblas"
$export MATHINCLUDE="-I/Users/aaa/lapack-3.6.0/lapacke/include -I/Users/aaa/lapack-3.6.0/cblas/include"

And, due to netlib only offer 32-bit cblas and lapacke officially, you need either modify codes from netlib, or specific FORTINT=int:

$export MATHINCLUDE="-I/Users/aaa/lapack-3.6.0/lapacke/include -I/Users/aaa/lapack-3.6.0/cblas/include -DFORTINT='int'"

the latter option can make the package compile, but may meet unexpected errors when the job involves cblas and lapacke. 3.(optional)Set processor specific compiling flags. If you need to speed up the program, you can turn on specific compiling flag in config/simd.mh for example, you can turn on core-avx2 with intel compiler on intel CPU with Haswell microarchitecture or later on.

SIMDFLAGS := -march=core-avx2

CFLAGS :=$(SIMDFLAGS) $(CFLAGS)
CXXFLAGS :=$(SIMDFLAGS) $(CXXFLAGS)
F77FLAGS :=$(SIMDFLAGS) $(F77FLAGS)
F90FLAGS :=$(SIMDFLAGS) $(F90FLAGS)

4. Configure BDF package.

After setting compiler and mathematic library. You can configure BDF by command configure in BDF root directory.

$./configure

Configure supports several parameters.

 --enable-debug=yes[no]     Compile BDF in debug mode.
 --enable-i8=yes[no]            Compile BDF with 64 bit integers.
 --enable-openmp=yes[no]  Compile BDF with OpenMP support.
 --enable-mpi=yes[no]         Compile BDF with MPI support.
 --enable-parallel=yes[no]   Compiler BDF with MPI and OpenMP support.
 --enable-mkl=yes[no]   Compiler BDF withIntel MKL support.

5. Compile BDF package.

 $make

Compile parallel bdf

Some of BDF modules support parallel calculation. You can compiler BDF as parallel mode. At present, we support MPI and OpenMP.

1. MPI and OpenMP hybrid.

 $./configure  --enable-parallel=yes

2. Only MPI.

 $./configure  --enable-mpi=yes

3. Only OpenMP.

 $./configure  --enable-openmp=yes

Examples of some typical installations

1. A 64bit machine with intel compiler and MKL library.

  export FC=ifort
  export CC=gcc
  export CXX=g++
  export MATHLIB="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread"
  export MATHINLCUDE="-I/opt/intel/mkl/include"
  ./configure --enable-i8=yes --enable-openmp=yes --enable-mkl=yes
  make

2. A Mac laptop with gfortran, gcc and user compiled lapack and blas library

  $export FC=gfortran
  $export CC=gcc
  $export CXX=g++
  $export MATHILIB="-L/Users/mike/mathlib -lblas -llapack"
  $export MATHINCLUDE="-I/Users/mike/lapack-3.6.0/lapacke/include -I/Users/mike/lapack-3.6.0/cblas/include"
  $./configure --enable-i8=yes --enable-openmp=yes
  $make

3. A Linux cluster with fort, icc, openmpi and intel MKL library.

Check MPI flags by using command

  $mpif90 --shownme

You may get such output.

  ifort -I/opt/openmpi/include -I/opt/openmpi/lib -L/opt/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -ldl -lm -Wl,--export-dynamic -lrt -lnsl -lutil

You can compile bdf package as

  $export FC=ifort
  $export CC=icc
  $export CXX=icpc
  $export MATHLIB="-lmkl_intel_ilp64 -lmkl_sequential -lmkl_core -lpthread"
  $export MATHINCLUDE="I/opt/intel/mkl/include"
  $export MPILIB="-I/opt/openmpi/include -I/opt/openmpi/lib -L/opt/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi -ldl -lm -Wl,--export-dynamic -lrt -lnsl -lutil"
  $./configure --enable-i8=yes --enable-parallel=yes --enable-mkl=yes
  $make

If you only want to evoke MPI, just use

  $./configure --enable-i8=yes --enable-mpi=yes --enable-mkl=yes

Enable PCM solver

PCM solver is interfaced with BDF to include solvent effect. By default PCM solver is disabled, since we have found this package to be less portable than other parts of the program so that compilation may fail on many machines. To enable PCM solver, you should use --enable-pcmsolver=yes in configuration.