Siesta v4.1.b3 openmpi compilation with slurm example

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

tar zxvf siesta-4.1-b3.tar.gz
cd siesta-4.1-b3/Obj/
bash ../Src/
vim arch.make

arch.make file contents with intel compiler and openmpi

ml load compiler/intel/15 openmpi/1.10 intel-mkl/15
# Copyright (C) 1996-2016       The SIESTA group
#  This file is distributed under the terms of the
#  GNU General Public License: see COPYING in the top directory
#  or
# See Docs/Contributors.txt for a list of contributors.
# arch.make file for gfortran compiler.
# To use this arch.make file you should rename it to
#   arch.make
# or make a sym-link.
# For an explanation of the flags see DOCUMENTED-TEMPLATE.make

.SUFFIXES: .f .F .o .c .a .f90 .F90

SIESTA_ARCH = unknown

CC = mpicc
FPP = $(FC) -E -P -x c
FC = mpif90

FFLAGS = -O2 -fPIC -ftree-vectorize

AR = ar
RANLIB = ranlib

SYS = nag

LDFLAGS = -L/util/opt/openmpi/1.10/intel/15/lib -lmpi

COMP_LIBS = libsiestaLAPACK.a libsiestaBLAS.a


MKL              = /util/comp/intel/15/mkl
INTEL_LIBS       = $(MKL)/lib/intel64/libmkl_intel_lp64.a \
                   $(MKL)/lib/intel64/libmkl_sequential.a \
                   $(MKL)/lib/intel64/libmkl_core.a \
                   $(MKL)/lib/intel64/libmkl_blacs_openmpi_lp64.a \
MKL_LIBS         = -Wl,--start-group $(INTEL_LIBS) \
                   -Wl,--end-group -lpthread -lm
MKL_INCLUDE      = -I$(MKL)/include

MPI_INTERFACE = libmpi_f90.a
MPI_INCLUDE = /util/opt/openmpi/1.10/intel/15/include
MPI_LIBS = -L/util/opt/openmpi/1.10/intel/15/lib -lmpi

DUMMY_FOX= --enable-dummy


# Dependency rules ---------

FFLAGS_DEBUG = -g -O1   # your appropriate flags here...

# The atom.f code is very vulnerable. Particularly the Intel compiler
# will make an erroneous compilation of atom.f with high optimization
# levels.
atom.o: atom.F
        $(FC) -c $(FFLAGS_DEBUG) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<

        $(CC) -c $(CFLAGS) $(INCFLAGS) $(CPPFLAGS) $<
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F)  $<
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f)  $<
        $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90)  $<

Slurm file

#SBATCH -n 4
#SBATCH -t 01:00:00
#SBATCH --mem-per-cpu=1G
#SBATCH --error=job.%J.err
#SBATCH --output=job.%J.out

ml load compiler/intel/15 openmpi/1.10 intel-mkl/15
mpirun -np 4 siesta ch4.fdf


  1. siesta often cannot take command line re-direction. So “mpirun -np 4 siesta < ch4.fdf” is not suggested.
  2. The number of cores for parallel siesta cannot be larger than the number of atoms in the system. So example like Fe.fdf cannot run in paralle, since the system only has 1 atom. (Ref:,