6.1¶
Table of contents
- Installation date: 16/03/2017
- URL: http://www.quantum-espresso.org
- Apolo version: Apolo II
- License: GNU GENERAL PUBLIC LICENSE Version 2
Pre requirements¶
- Intel Parell Studio XE Cluster Edition 2017 - Update 1
- Intel Compilers Fortran and C
- Intel MPI (Fortran and C)
- Intel MKL
Installation¶
- 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
- 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
- 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
References¶
- http://www.archer.ac.uk/documentation/software/espresso/compiling_5.0.3_mkl-phase1.php
- https://glennklockwood.blogspot.com.co/2014/02/quantum-espresso-compiling-and-choice.html
- https://proteusmaster.urcf.drexel.edu/urcfwiki/index.php/Compiling_Quantum_Espresso
- https://www.hpc.ntnu.no/ntnu-hpc-group/vilje/user-guide/software/quantum-espresso
- https://nishaagrawal.wordpress.com/2013/03/21/quantum-espresso-5-0-2qe-64-bit-installation-with-intel-compser-xe-2013-and-intel-mpi/
- https://software.intel.com/en-us/articles/quantum-espresso-for-intel-xeon-phi-coprocessor
- http://www.quantum-espresso.org/pseudopotentials/