6.1

Pre requirements

  • Intel Parell Studio XE Cluster Edition 2017 - Update 1
  • Intel Compilers Fortran and C
  • Intel MPI (Fortran and C)
  • Intel MKL

Installation

  1. Download the latest version of the software (Repository) (https://github.com/QEF/q-e):
cd /home/mgomezzul/apps/qe/src/intel
wget https://github.com/QEF/q-e/archive/qe-6.1.0.tar.gz
tar xf qe-6.1.tar.gz
cd qe-6.1
  1. To proceed with the configuration and compilation we must continue with the following steps:
module load intel/2017_update-1 impi/2017_update-1 mkl/2017_update-1
unset LD
export CPP="$CC -E"
export LD=$MPIF90

./configure --prefix=/share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1 --build=x86_64-redhat-linux --enable-openmp --enable-parallel --with-scalapack=yes FC=ifort F90=ifort F77=ifort CC=icc CXX=icpc CPP="icc -E" LD=mpiifort BLAS_LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" LAPACK_LIBS="" SCALAPACK_LIBS="-lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64" FFT_LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl" 2>&1 | tee conf.log
sudo mkdir -p /share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1
sudo chown -R mgomezzul.apolo /share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1
emacs make.inc
...
DFLAGS         =  -D__INTEL -D__SCALAPACK -D__OPENMP -D__DFTI -D__MPI
...
make all -j 8 2>&1 | tee qe-make.log
make install 2>&1 | tee qe-make-install.log
sudo chown -R root.root /share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1
  1. Add the potential pseudos
sudo mkdir -p /share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1/pseudos
cd /share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1/pseudos
# Verificar la última versión de los pseudos - http://www.quantum-espresso.org/pseudopotentials/
wget http://www.quantum-espresso.org/wp-content/uploads/upf_files/upf_files.tar
tar xf upf_files.tar
rm upf_files.tar

Module

#%Module1.0#####################################################################
##
## modules qe/6.1_intel-17.0.1 Written by Mateo Gómez Zuluaga
##

proc ModulesHelp { } {
        puts stderr "\tSets the environment for Quantum Espresso 6.1 in the \
                    \n\tfollowing shared directory \
            \n\t/share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1\n"
}

module-whatis "\n\n\tQuatum Espresso-6.1 is  an integrated suite of \
        \n\tOpen-Source computer codes for electronic-structure \
        \n\tcalculations and materials modeling at the nanoscale \
            \n\tbuilded with Intel Parallel Studio XE Cluster Edition \
        \n\t2017 Update 1 (Intel MPI and Intel MKL)\n"


# for Tcl script use only
set           topdir        /share/apps/qe/6.1/intel_17.0.1_impi_17.0.1_mkl_17.0.1
set   version       6.1
set       sys               x86_64-redhat-linux
set       user              [exec bash -c "echo \$USER"]

conflict qe

module load intel/2017_update-1
module load impi/2017_update-1
module load mkl/2017_update-1

prepend-path PATH           $topdir/bin
setenv           BIN_DIR            $topdir/bin

setenv       OMP_NUM_THREADS    1
setenv           ESPRESSO_PSEUDO    $topdir/pseudo
setenv           PSEUDO_DIR         $topdir/pseudo
setenv           ESPRESSO_TMPDIR    /scratch-local/$user/qe
setenv       TMP_DIR                /scratch-local/$user/qe
setenv           NETWORK_PSEUDO     http://www.quantum-espresso.org/wp-content/uploads/upf_files/

Mode of use

Load the necessary environment through the module:

..code-block:: bash

module load qe/6.1_intel-17.0.1

Slurm template

#!/bin/sh
#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=32
#SBATCH --time=1-00
#SBATCH --job-name=qe_test
#SBATCH -o result_%N_%j.out
#SBATCH -e result_%N_%j.err
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jrendon8@eafit.edu.co


# Don't share environment variables
export SBATCH_EXPORT=NONE
export OMP_NUM_THREADS=1

module load qe/6.1_intel-17.0.1

srun pw.x < test_1.in

Input file

&CONTROL
calculation = "scf", ! single point calculation (default, could be omitted)
prefix = "CO", ! all auxiliary files will have filename beginning by prefix
tprnfor = .true.
/
&SYSTEM
ibrav = 0, ! Bravais lattice defined by user in CELL_PARAMETERS card
celldm(1)= 1.88972687, ! define length unit as 1 AA= 1/0.529177 bohr
ntyp = 2, ! number of atomic species (see later ATOMIC_SPECIES)
nat = 2, ! number of atoms in the unit cell (see later ATOMIC_POSITIONS)
ecutwfc = 24.D0,
ecutrho = 144.D0,
/
&ELECTRONS
conv_thr = 1.D-7, ! convergence threshold on total energy , in Rydberg
/
CELL_PARAMETERS cubic
10.0  0.0  0.0
0.0 10.0  0.0
0.0  0.0 10.0
ATOMIC_SPECIES
O 1.00 O.pbe-rrkjus.UPF
C 1.00 C.pbe-rrkjus.UPF
ATOMIC_POSITIONS angstrom
C 1.152 0.0 0.0
O 0.000 0.0 0.0
K_POINTS gamma

Author

  • Mateo Gómez Zuluaga