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.outsubstituting 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
pseudopotentialand 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
#PBSdirectives are standard, requesting just 3 minutes of walltime and 1 node with 2 cores. More on#PBSdirectives can be found in the PBS guide $PBS_O_WORKDIRis 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/6.2.1loads 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.outruns a PWscf calculation on theinput.infile and prints the results to theoutput.outfile.
Part 2: Submit Job and Check Status¶
- Be sure to change to the directory that contains the
PBSScript. 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
PBSscript, you should see aqespressoTest.outfile which contains the results of the job, anoutput.outfile which contains the output from Quantum ESPRESSO, a directory calledpwscf.save, and apwscf.xmlfile. - Use
cat qespressoTest.outor open the file in a text editor to take a look at the ouput messages from running the PBS script.quespressoTest.outshould 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.outor open the file in a text editor to take a look at the results of running Quantum Espresso.ouput.outshould 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.