Updated 2021-05-17
Run Quantum ESPRESSO on the Cluster¶
Overview¶
- Quantum ESPRESSO is an integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials.
- This guide will cover how to run Quantum ESPRESSO on the Cluster.
- The example used in this guide comes from this link.
Summary¶
- To run Quantum ESPRESSO, you need an input file and a pseudopotential.
- You will run a PWscf (pw.x) calculation on the input file to produce an output file containing the results of the calculation.
Tips¶
- You can view all possible calculations using
ls /usr/local/pacerepov1/espresso/6.2.1/mvapich2-2.1/gcc-4.9.0/bin
. - You can run the calculation with multiple processors using
mpirun -np 2 pw.x <input.in> output.out
substituting 2 with the number of processors you would like to use. Make sure to request the proper number of processors in your PBS script if you do this.
Walkthrough: Run AMPL on the Cluster¶
- This walkthrough will run a PWscf (pw.x) calculation on an input file which contains a reference to a pseudopotential.
- The input file can be found here
- The pseudopotential can be found here. For everything to work properly, a directory should be created called
pseudopotential
and this file should be saved inside of that directory. - PBS script can be found here
- You can transfer the files to your account on the cluster to follow along. The file transfer guide may be helpful.
Part 1: The PBS Script¶
#PBS -N qespressoTest
#PBS -A [Account]
#PBS -l nodes=1:ppn=2
#PBS -l pmem=2gb
#PBS -l walltime=3:00
#PBS -q inferno
#PBS -j oe
#PBS -o qespressoTest.out
cd $PBS_O_WORKDIR
module load gcc/4.9.0
module load mvapich2/2.1
module load mkl/11.2
module load espresso/6.2.1
pw.x <input.in> output.out
- The
#PBS
directives are standard, requesting just 3 minutes of walltime and 1 node with 2 cores. More on#PBS
directives can be found in the PBS guide $PBS_O_WORKDIR
is a variable that represents the directory you submit the PBS script from. Make sure the files you want to use are in the same directory you put the PBS script.- Output Files will also show up in this dir as well
module load espresso/6.2.1
loads the 6.2.1 version of Quantum ESPRESSO. To see what Quantum ESPRESSO versions are available, runmodule avail espresso
, and load the one you want. The other module are dependencies that must be loaded before Quantum ESPRESSO is loaded.pw.x <input.in> output.out
runs a PWscf calculation on theinput.in
file and prints the results to theoutput.out
file.
Part 2: Submit Job and Check Status¶
- Be sure to change to the directory that contains the
PBS
Script. qsub qespressoTest.pbs
- Check job status with
qstat -t <jobid>
, replacing the number with the job id returned after running qsub. - You can delete the job with
qdel <jobid>
, again replacing the number with the jobid returned after running qsub.
Part 3: Collecting Results¶
- In the directory where you submitted the
PBS
script, you should see aqespressoTest.out
file which contains the results of the job, anoutput.out
file which contains the output from Quantum ESPRESSO, a directory calledpwscf.save
, and apwscf.xml
file. - Use
cat qespressoTest.out
or open the file in a text editor to take a look at the ouput messages from running the PBS script.quespressoTest.out
should look like this:
---------------------------------------
Begin PBS Prologue Fri Jun 21 11:51:56 EDT 2019
Job ID: 26115230.shared-sched.pace.gatech.edu
User ID: svemuri8
Job name: qespressoTest
Queue: inferno
End PBS Prologue Fri Jun 21 11:51:56 EDT 2019
---------------------------------------
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL
---------------------------------------
Begin PBS Epilogue Fri Jun 21 11:51:59 EDT 2019
Job ID: 26115230.shared-sched.pace.gatech.edu
User ID: svemuri8
Job name: qespressoTest
Resources: neednodes=1:ppn=2,nodes=1:ppn=2,pmem=2gb,walltime=00:03:00
Rsrc Used: cput=00:00:00,energy_used=0,mem=0kb,vmem=0kb,walltime=00:00:03
Queue: inferno
Nodes:
iw-c42-25.pace.gatech.edu
End PBS Epilogue Fri Jun 21 11:51:59 EDT 2019
---------------------------------------
- Use
cat output.out
or open the file in a text editor to take a look at the results of running Quantum Espresso.ouput.out
should look like this:
Program PWSCF v.6.2 starts on 21Jun2019 at 11:51:57
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 1 processors
MPI processes distributed on 1 nodes
Waiting for input...
Reading input from standard input
Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 3
Subspace diagonalization in iterative solution of the eigenvalue problem:
a serial algorithm will be used
G-vector sticks info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Sum 241 241 85 2445 2445 531
bravais-lattice index = 2
lattice parameter (alat) = 7.6526 a.u.
unit-cell volume = 112.0383 (a.u.)^3
number of atoms/cell = 1
number of atomic types = 1
number of electrons = 3.00
number of Kohn-Sham states= 6
kinetic-energy cutoff = 30.0000 Ry
charge density cutoff = 120.0000 Ry
convergence threshold = 1.0E-06
mixing beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation = LDA ( 1 1 0 0 0 0)
celldm(1)= 7.652597 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
crystal axes: (cart. coord. in units of alat)
a(1) = ( -0.500000 0.000000 0.500000 )
a(2) = ( 0.000000 0.500000 0.500000 )
a(3) = ( -0.500000 0.500000 0.000000 )
reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( -1.000000 -1.000000 1.000000 )
b(2) = ( 1.000000 1.000000 1.000000 )
b(3) = ( -1.000000 1.000000 -1.000000 )
PseudoPot. # 1 for Al read from file:
./pseudopotential/Al.pz-n-rrkjus_psl.0.1.UPF
MD5 check sum: 3b788946f5b2ec323a58a29a5ff2368a
Pseudo is Ultrasoft + core correction, Zval = 3.0
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415
Using radial grid of 1135 points, 4 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
Q(r) pseudized with 0 coefficients
atomic species valence mass pseudopotential
Al 3.00 26.98150 Al( 1.00)
48 Sym. Ops., with inversion, found
Cartesian axes
site n. atom positions (alat units)
1 Al tau( 1) = ( 0.0000000 0.0000000 0.0000000 )
number of k points= 29 Marzari-Vanderbilt smearing, width (Ry)= 0.0050
cart. coord. in units 2pi/alat
k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 0.0039062
k( 2) = ( -0.1250000 0.1250000 -0.1250000), wk = 0.0312500
k( 3) = ( -0.2500000 0.2500000 -0.2500000), wk = 0.0312500
k( 4) = ( -0.3750000 0.3750000 -0.3750000), wk = 0.0312500
k( 5) = ( 0.5000000 -0.5000000 0.5000000), wk = 0.0156250
k( 6) = ( 0.0000000 0.2500000 0.0000000), wk = 0.0234375
k( 7) = ( -0.1250000 0.3750000 -0.1250000), wk = 0.0937500
k( 8) = ( -0.2500000 0.5000000 -0.2500000), wk = 0.0937500
k( 9) = ( 0.6250000 -0.3750000 0.6250000), wk = 0.0937500
k( 10) = ( 0.5000000 -0.2500000 0.5000000), wk = 0.0937500
k( 11) = ( 0.3750000 -0.1250000 0.3750000), wk = 0.0937500
k( 12) = ( 0.2500000 0.0000000 0.2500000), wk = 0.0468750
k( 13) = ( 0.0000000 0.5000000 0.0000000), wk = 0.0234375
k( 14) = ( -0.1250000 0.6250000 -0.1250000), wk = 0.0937500
k( 15) = ( 0.7500000 -0.2500000 0.7500000), wk = 0.0937500
k( 16) = ( 0.6250000 -0.1250000 0.6250000), wk = 0.0937500
k( 17) = ( 0.5000000 0.0000000 0.5000000), wk = 0.0468750
k( 18) = ( 0.0000000 0.7500000 0.0000000), wk = 0.0234375
k( 19) = ( 0.8750000 -0.1250000 0.8750000), wk = 0.0937500
k( 20) = ( 0.7500000 0.0000000 0.7500000), wk = 0.0468750
k( 21) = ( 0.0000000 -1.0000000 0.0000000), wk = 0.0117188
k( 22) = ( -0.2500000 0.5000000 0.0000000), wk = 0.0937500
k( 23) = ( 0.6250000 -0.3750000 0.8750000), wk = 0.1875000
k( 24) = ( 0.5000000 -0.2500000 0.7500000), wk = 0.0937500
k( 25) = ( 0.7500000 -0.2500000 1.0000000), wk = 0.0937500
k( 26) = ( 0.6250000 -0.1250000 0.8750000), wk = 0.1875000
k( 27) = ( 0.5000000 0.0000000 0.7500000), wk = 0.0937500
k( 28) = ( -0.2500000 -1.0000000 0.0000000), wk = 0.0468750
k( 29) = ( -0.5000000 -1.0000000 0.0000000), wk = 0.0234375
Dense grid: 2445 G-vectors FFT dimensions: ( 20, 20, 20)
Estimated max dynamical RAM per process > 4.41 MB
Check: negative/imaginary core charge= -0.000006 0.000000
Initial potential from superposition of free atoms
starting charge 2.99797, renormalised to 3.00000
Starting wfc are 4 randomized atomic wfcs + 2 random wfc
total cpu time spent up to now is 0.9 secs
Self-consistent Calculation
iteration # 1 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap
ethr = 1.00E-02, avg # of iterations = 5.0
Threshold (ethr) on eigenvalues was too large:
Diagonalizing with lowered threshold
Davidson diagonalization with overlap
ethr = 1.89E-04, avg # of iterations = 2.1
total cpu time spent up to now is 1.4 secs
total energy = -5.48853082 Ry
Harris-Foulkes estimate = -5.49029436 Ry
estimated scf accuracy < 0.00542037 Ry
iteration # 2 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap
ethr = 1.81E-04, avg # of iterations = 1.2
total cpu time spent up to now is 1.6 secs
total energy = -5.48850283 Ry
Harris-Foulkes estimate = -5.48862096 Ry
estimated scf accuracy < 0.00036210 Ry
iteration # 3 ecut= 30.00 Ry beta= 0.70
Davidson diagonalization with overlap
ethr = 1.21E-05, avg # of iterations = 1.8
total cpu time spent up to now is 1.7 secs
End of self-consistent calculation
k = 0.0000 0.0000 0.0000 ( 331 PWs) bands (ev):
-3.4383 20.1765 20.1765 21.3995 21.3995 21.3995
k =-0.1250 0.1250-0.1250 ( 316 PWs) bands (ev):
-3.0166 15.8703 19.1643 19.1645 22.1845 22.9741
k =-0.2500 0.2500-0.2500 ( 311 PWs) bands (ev):
-1.7595 11.0367 18.3883 18.3884 21.8811 22.1847
k =-0.3750 0.3750-0.3750 ( 308 PWs) bands (ev):
0.3122 6.7618 18.2898 18.2899 20.2365 20.2369
k = 0.5000-0.5000 0.5000 ( 302 PWs) bands (ev):
3.0988 3.2354 18.7735 18.7735 19.0509 19.0511
k = 0.0000 0.2500 0.0000 ( 307 PWs) bands (ev):
-2.8764 17.4109 17.4109 17.7853 20.2798 22.1618
k =-0.1250 0.3750-0.1250 ( 308 PWs) bands (ev):
-1.8986 12.8876 16.3511 17.9177 19.0814 21.5770
k =-0.2500 0.5000-0.2500 ( 317 PWs) bands (ev):
-0.1001 8.4517 16.0037 16.7601 17.7228 23.6598
k = 0.6250-0.3750 0.6250 ( 312 PWs) bands (ev):
2.4880 4.6417 15.1373 16.3713 18.1653 22.1692
k = 0.5000-0.2500 0.5000 ( 308 PWs) bands (ev):
1.5408 5.8311 14.2599 17.4512 19.3408 21.3434
k = 0.3750-0.1250 0.3750 ( 309 PWs) bands (ev):
-0.7891 9.8460 14.1566 19.2124 21.2104 21.2190
k = 0.2500 0.0000 0.2500 ( 317 PWs) bands (ev):
-2.3169 14.0419 15.2072 21.2662 21.3463 22.8610
k = 0.0000 0.5000 0.0000 ( 311 PWs) bands (ev):
-1.2042 15.0349 15.0349 15.1393 15.8116 18.4238
k =-0.1250 0.6250-0.1250 ( 316 PWs) bands (ev):
0.3108 10.8312 13.1561 14.4409 15.9501 19.8592
k = 0.7500-0.2500 0.7500 ( 311 PWs) bands (ev):
2.6170 6.8753 11.2393 14.5657 16.2829 23.5055
k = 0.6250-0.1250 0.6250 ( 307 PWs) bands (ev):
3.5618 5.6615 10.1189 15.4090 17.2652 25.0687
k = 0.5000 0.0000 0.5000 ( 315 PWs) bands (ev):
0.9957 8.8771 10.3142 16.9684 18.9661 24.9701
k = 0.0000 0.7500 0.0000 ( 322 PWs) bands (ev):
1.5343 10.1874 13.4911 13.6031 13.6031 17.0120
k = 0.8750-0.1250 0.8750 ( 314 PWs) bands (ev):
3.5281 7.9905 9.8166 13.4856 14.8972 18.9319
k = 0.7500 0.0000 0.7500 ( 308 PWs) bands (ev):
5.7739 6.3003 7.1688 14.0869 15.7643 23.0998
k = 0.0000-1.0000 0.0000 ( 302 PWs) bands (ev):
4.7421 6.0085 12.9375 13.1263 13.1263 16.5096
k =-0.2500 0.5000 0.0000 ( 311 PWs) bands (ev):
-0.6511 11.4669 12.7994 16.2992 19.6855 21.3170
k = 0.6250-0.3750 0.8750 ( 313 PWs) bands (ev):
1.4035 7.7617 12.1519 14.1764 20.2645 22.3195
k = 0.5000-0.2500 0.7500 ( 308 PWs) bands (ev):
4.1386 4.3239 12.5935 12.9463 20.7464 21.2422
k = 0.7500-0.2500 1.0000 ( 309 PWs) bands (ev):
2.0767 9.9149 10.6283 11.3951 18.2031 20.0850
k = 0.6250-0.1250 0.8750 ( 308 PWs) bands (ev):
4.5907 6.7073 9.0603 11.1748 19.3464 23.3839
k = 0.5000 0.0000 0.7500 ( 311 PWs) bands (ev):
3.6913 7.3245 8.7317 12.2806 20.5357 23.7927
k =-0.2500-1.0000 0.0000 ( 308 PWs) bands (ev):
5.2578 6.5514 9.3969 10.8138 17.6969 19.6367
k =-0.5000-1.0000 0.0000 ( 308 PWs) bands (ev):
6.8074 6.8074 7.8494 8.5758 23.3237 23.6923
the Fermi energy is 7.7294 ev
! total energy = -5.48852569 Ry
Harris-Foulkes estimate = -5.48852591 Ry
estimated scf accuracy < 0.00000078 Ry
The total energy is the sum of the following terms:
one-electron contribution = 2.92909932 Ry
hartree contribution = 0.00591130 Ry
xc contribution = -3.03130200 Ry
ewald contribution = -5.39212484 Ry
smearing contrib. (-TS) = -0.00010947 Ry
convergence has been achieved in 3 iterations
Writing output data file pwscf.save
init_run : 0.43s CPU 0.44s WALL ( 1 calls)
electrons : 0.82s CPU 0.84s WALL ( 1 calls)
Called by init_run:
wfcinit : 0.06s CPU 0.07s WALL ( 1 calls)
potinit : 0.01s CPU 0.01s WALL ( 1 calls)
Called by electrons:
c_bands : 0.67s CPU 0.69s WALL ( 4 calls)
sum_band : 0.13s CPU 0.13s WALL ( 4 calls)
v_of_rho : 0.01s CPU 0.01s WALL ( 4 calls)
newd : 0.01s CPU 0.01s WALL ( 4 calls)
mix_rho : 0.00s CPU 0.00s WALL ( 4 calls)
Called by c_bands:
init_us_2 : 0.02s CPU 0.03s WALL ( 261 calls)
cegterg : 0.65s CPU 0.66s WALL ( 116 calls)
Called by sum_band:
sum_band:bec : 0.00s CPU 0.00s WALL ( 116 calls)
addusdens : 0.01s CPU 0.01s WALL ( 4 calls)
Called by *egterg:
h_psi : 0.57s CPU 0.58s WALL ( 437 calls)
s_psi : 0.01s CPU 0.01s WALL ( 437 calls)
g_psi : 0.00s CPU 0.00s WALL ( 292 calls)
cdiaghg : 0.06s CPU 0.06s WALL ( 379 calls)
Called by h_psi:
h_psi:pot : 0.56s CPU 0.57s WALL ( 437 calls)
h_psi:calbec : 0.01s CPU 0.01s WALL ( 437 calls)
vloc_psi : 0.53s CPU 0.55s WALL ( 437 calls)
add_vuspsi : 0.02s CPU 0.01s WALL ( 437 calls)
General routines
calbec : 0.01s CPU 0.01s WALL ( 553 calls)
fft : 0.01s CPU 0.01s WALL ( 26 calls)
fftw : 0.56s CPU 0.56s WALL ( 4714 calls)
Parallel routines
PWSCF : 1.68s CPU 2.01s WALL
This run was terminated on: 11:51:59 21Jun2019
=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
- After the result files are produced, you can move the files off the cluster, refer to the file transfer guide for help.
- Congratulations! You successfully ran Quantum ESPRESSO on the cluster.