HPC/Benchmarks/Generation 1 vs 2

Introduction

Earlier this year, we received 200 additional nodes with E5540 processors. The processors have 8 cores, and support Hyperthreading, a feature which allows 2 threads per core. This benchmark investigates the benefit of hyperthreading (HT), and suggests optimal values for the nodes and processors per node (ppn) parameters in PBS.

Test description

The test runs /opt/soft/vasp-4.6.35-mkl-8/bin/vasp with the following workload (Credit: D. Shin, Northwestern Univ.).

INCAR

SYSTEM = Al12Mg17
ISTART = 0
ISMEAR = 1
SIGMA  = 0.1
ISIF   = 3
PREC   = HIGH
IBRION = 2
LWAVE  = .FALSE.
LCHARG = .FALSE.
LREAL  = .TRUE.
ENCUT  = 346

KPOINTS

KPOINTS file
0
Monkhorst-Pack
10 10 10
0 0 0

POSCAR

Al12Mg17
1.0000000000
-5.2719000000 5.2719000000 5.2719000000
5.2719000000 -5.2719000000 5.2719000000
5.2719000000 5.2719000000 -5.2719000000
12 17
Direct
0.3679000000 0.3679000000 0.1908000000    Al
0.1771000000 0.1771000000 0.8092000000    Al
0.6321000000 0.8229000000 0.0000000000    Al
0.8229000000 0.6321000000 0.0000000000    Al
0.1908000000 0.3679000000 0.3679000000    Al
0.3679000000 0.1908000000 0.3679000000    Al
0.0000000000 0.8229000000 0.6321000000    Al
0.1771000000 0.8092000000 0.1771000000    Al
0.8092000000 0.1771000000 0.1771000000    Al
0.8229000000 0.0000000000 0.6321000000    Al
0.0000000000 0.6321000000 0.8229000000    Al
0.6321000000 0.0000000000 0.8229000000    Al
0.3975000000 0.3975000000 0.7164000000    Mg
0.6811000000 0.6811000000 0.2836000000    Mg
0.6025000000 0.3189000000 0.0000000000    Mg
0.3189000000 0.6025000000 0.0000000000    Mg
0.7164000000 0.3975000000 0.3975000000    Mg
0.3975000000 0.7164000000 0.3975000000    Mg
0.0000000000 0.3189000000 0.6025000000    Mg
0.6811000000 0.2836000000 0.6811000000    Mg
0.2836000000 0.6811000000 0.6811000000    Mg
0.3189000000 0.0000000000 0.6025000000    Mg
0.0000000000 0.6025000000 0.3189000000    Mg
0.6025000000 0.0000000000 0.3189000000    Mg
0.6480000000 0.6480000000 0.6480000000    Mg
0.0000000000 0.0000000000 0.3520000000    Mg
0.3520000000 0.0000000000 0.0000000000    Mg
0.0000000000 0.3520000000 0.0000000000    Mg
0.0000000000 0.0000000000 0.0000000000    Mg

POTCAR

PAW_GGA Al 05Jan2001
3.00000000000000000
parameters from PSCTR are:
VRHFIN =Al: s2p1
LEXCH  = 91
EATOM  =    53.6910 eV,    3.9462 Ry
...

PAW_GGA Mg 05Jan2001
2.00000000000000000
parameters from PSCTR are:
VRHFIN =Mg: s2p0
LEXCH  = 91
EATOM  =    23.0823 eV,    1.6965 Ry
...

(appbreviated)

Data

• HPC/Generation-2 nodes/vasp/vasp.lst, grep-able
• media:Vasp.txt, tab-separated CSV
• media:Vasp.pdf, PDF

Observations

• 4-core runs give a high numerical throughput in each node type (run=01 to 04)
• gen2 nodes are fine for VASP with nodes=1:ppn=8; gen1 nodes are not (run=22 vs. 21)
• Adding more nodes allows for the fastest run (run=54) or 40% slower and a better charge rate (run=52)
• Running two apps in a single job is mostly not worth the effort of managing them (run=04 vs. 22)
• HT allows for slightly better charge rates, but usually only with non-MPI jobs (or unsynced MPI jobs) (run=15, 25, 40, 55), and runtimes are nearly proportionately longer, making HT largely unattractive. This also holds for the only case tested for HT and napps=1 (run=50).

Recommendations

For the given workload, the I recommend the following values for optimal performance with respect to the given objective.

Node type	Objective
	time → min	charge → min	time × charge → min
gen1	nodes=4:ppn=3	nodes=1:ppn=4	nodes=3:ppn=4
	run=35 tmax=503.05 charge=4.47	run=01 tmax=1138.83 charge=2.53	run=33 tmax=544.74 charge=3.63
gen2	nodes=4:ppn=4	nodes=1:ppn=8	nodes=2:ppn=8
	run=54 tmax=237.59 charge=2.11	run=22 tmax=472.16 charge=1.05	run=52 tmax=329.10 charge=1.46