Dear all
We have successfully installed Quantum Espresso on our cluster and calculations
with 1 to 7 processors are ok... using example submission scripts as follows
and job script as attached: But when increase the processor from 7, then the
calculations stop without any error, although our cluster can run a simulation
with 120 processors (in case of Metlab).
#!/bin/bash
#$ -N qe
#$ -q all.q
#$ -cwd
# Send mail at submission and completion of script
#$ -m be
#$ -M [email protected]
# Parallel Job
#$ -pe openmpi_ib 7
. /etc/profile.d/modules.sh
module load shared espresso
cd /home/ISAD/hu203/Test
mpirun pw.x -inp 96BiVO4-001.in > 96BiVO4-001.out
Searching online found this document:
http://www.quantum-espresso.org/wp-content/uploads/Doc/pw_user_guide.pdf
pw.x can run in principle on any number of processors.
Wondering if the following is pertinent to our current problems (or if there is
a problem with our Espresso installation on the cluster):
Parallelization on PWs:
* yields good to very good scaling, especially if the number of processors in a
pool is a divisor of N3 and Nr3 (the dimensions along the z-axis of the FFT
grids, nr3 and nr3s, which coincide for NCPPs);
* requires heavy communications (suitable for Gigabit ethernet up to 4, 8 CPUs
at most, specialized communication hardware needed for 8 or more processors );
* yields almost linear reduction of memory per processor with the number of
processors in the pool.
We have Mellanox Infiniband cards between servers ... each server has 192GB RAM
and 4x 12 Core 2.4GHz AMD processor
Kind regards,
Habib
&CONTROL
calculation='scf',
outdir='/home/ISAD/hu203/Bismuth/BiVO4_001',
prefix='BiVO4Big-001',
restart_mode='from_scratch' ,
wf_collect=.true. ,
pseudo_dir='/home/ISAD/hu203/habib/espresso-5.0.3/pseudo/',
verbosity='low',
tstress=.false.,
tprnfor=.false.,
/
&SYSTEM
ibrav=6,
celldm(1)=19.4528401063d0, celldm(3)=2.1101224277d0,
nat=96,
ntyp=3,
ecutwfc=50.0d0,
ecutrho=120.0d0,
input_dft='LDA',
occupations='smearing',
smearing='gaussian',
degauss=0.002000d0,
/
&ELECTRONS
diagonalization='david',
conv_thr=1d-06,
mixing_mode='plain',
mixing_beta=0.700d0,
/
&IONS
ion_dynamics='bfgs'
/
&CELL
cell_dynamics='bfgs'
/
ATOMIC_SPECIES
Bi 208.980000d0 Bi.pz-hgh.UPF
O 15.999400d0 O.pz-hgh.UPF
V 50.941500d0 V.pz-hgh.UPF
ATOMIC_POSITIONS {alat}
Bi 0.000000482 0.124999208 0.726181969
Bi 0.000000347 0.625000561 0.726182406
Bi 0.499999751 0.125000867 0.726176320
Bi 0.499999312 0.624999121 0.726176600
Bi -0.000000157 0.375000236 0.412894153
Bi -0.000000104 0.874999880 0.412893424
Bi 0.500000102 0.375000103 0.412897098
Bi 0.500000099 0.875000060 0.412897215
Bi 0.249999771 0.375002468 0.158607143
Bi 0.249999478 0.875002653 0.158609833
Bi 0.750000093 0.374997803 0.158606726
Bi 0.750000096 0.874997511 0.158608719
Bi 0.250000319 0.125001998 0.980705945
Bi 0.250000021 0.625002590 0.980704735
Bi 0.749999463 0.124997729 0.980701397
Bi 0.749999507 0.624997736 0.980699057
V -0.000009793 0.125006963 0.148169381
V 0.000006786 0.624995099 0.148168613
V 0.499992249 0.125005013 0.148172968
V 0.500010495 0.624992938 0.148172466
V 0.000008775 0.374994095 0.989794782
V -0.000000664 0.875000858 0.989796171
V 0.500000607 0.374999187 0.989790998
V 0.499990215 0.875006325 0.989789645
V 0.250003692 0.374998950 0.719861758
V 0.250004728 0.874999128 0.719862291
V 0.749996924 0.374999095 0.719857620
V 0.749995815 0.875001864 0.719858698
V 0.250003473 0.125001624 0.418521034
V 0.250003792 0.624998160 0.418520457
V 0.749996962 0.125000825 0.418519786
V 0.749996320 0.624999555 0.418519730
O 0.082718870 0.257304040 0.241301039
O 0.082718795 0.757304666 0.241302020
O 0.582720111 0.257302080 0.241303756
O 0.582719678 0.757303887 0.241304639
O 0.417269270 0.241719629 0.897973080
O 0.417268669 0.741719009 0.897971570
O 0.917273704 0.241713737 0.897977100
O 0.917272782 0.741715561 0.897977168
O 0.170420620 0.243190442 0.810885779
O 0.170421216 0.743189260 0.810885561
O 0.670423964 0.243191289 0.810884037
O 0.670422666 0.743191243 0.810883732
O 0.329102416 0.257824167 0.328857889
O 0.329103044 0.757824364 0.328857172
O 0.829102789 0.257824635 0.328859220
O 0.829102907 0.757825796 0.328857941
O 0.134734505 0.185728040 0.508795651
O 0.134735110 0.685725493 0.508795736
O 0.634730989 0.185724485 0.508795086
O 0.634729241 0.685724997 0.508794413
O 0.364862321 0.314311352 0.629068091
O 0.364863916 0.814310192 0.629068498
O 0.864858979 0.314309268 0.629064788
O 0.864856709 0.814312661 0.629065474
O 0.109981606 0.308056473 1.079323471
O 0.109983172 0.808055206 1.079327709
O 0.609972110 0.308059841 1.079315953
O 0.609975183 0.808058812 1.079316116
O 0.390284884 0.192351260 0.058533134
O 0.390275960 0.692357435 0.058525860
O 0.890286867 0.192350148 0.058529958
O 0.890279244 0.692354937 0.058523357
O 0.329579336 0.506808859 0.810887395
O 0.329579425 1.006808980 0.810885921
O 0.829577230 0.506808481 0.810884312
O 0.829575469 1.006809933 0.810883101
O 0.170896708 -0.007823960 0.328857971
O 0.170897769 0.492175784 0.328858975
O 0.670896561 -0.007825199 0.328856934
O 0.670897033 0.492175746 0.328857880
O 0.417279829 -0.007303717 0.241304865
O 0.417279783 0.492697924 0.241303516
O 0.917281320 -0.007305149 0.241302250
O 0.917280984 0.492696797 0.241301207
O 0.082729911 0.508282674 0.897976449
O 0.082729796 1.008281272 0.897977425
O 0.582727316 0.508283852 0.897972819
O 0.582727193 1.008284503 0.897972221
O 0.390014466 0.441945647 1.079322959
O 0.390018596 0.941943571 1.079318115
O 0.890025739 0.441940448 1.079322591
O 0.890028410 0.941940793 1.079321787
O 0.109722570 0.057644298 0.058523455
O 0.109714345 0.557648624 0.058528683
O 0.609722138 0.057643349 0.058526819
O 0.609713330 0.557649719 0.058533242
O 0.365269699 0.064276023 0.508796704
O 0.365269919 0.564273691 0.508796038
O 0.865266347 0.064273372 0.508793254
O 0.865265130 0.564274164 0.508794305
O 0.135142723 0.435689541 0.629069897
O 0.135144145 0.935688056 0.629069330
O 0.635138554 0.435687174 0.629062846
O 0.635137038 0.935690115 0.629063308
K_POINTS {automatic}
5 5 1 0 0 0_______________________________________________
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