Schedulers on ICS-ACI
- Exclusive nodes. “qsub -n” guarantees exclusive nodes. The scheduler finds the minimum number of nodes that grants you exclusivity, e.g. gives you 2 exclusive nodes if you request 20 cores (without specifying topology) on and 16-core-per-node system.
Check all running nodes? Environmental variable $PBS_NODEFILE. Other $PBS_xxx variables can also be useful. Check the “pbsnodes” command for all node specifications.
- Email notification. #PBS -m [option] where option can be any combination of the letters a(bort) b(egin) and e(nd). Use with #PBS -M [email adress]
- Memory monitoring using a script, without ‘top’. Find process # in ‘ps’, then look in /proc/#/status. Vsize and Vrss are the requested and active memory.
Specify a node: #PBS -l nodes=[node name], e.g. node name = lionxg93
- Manually turn off symmetry when using EFIELD (VASP detects symmetry based only on geometry).
- Isolated atoms. Don’t forget to use a very small smearing, e.g. 0.1 meV. To avoid slow convergence, use NUPDOWN to constrain the net spin. Always check ground state electron configuration with experiments, keeping in mind that LDA/GGA energies are more likely to be off quantitatively.
- Use KPAR level parallelization when applicable.
- Optical matrix elements can be obtained by uncommenting the line regarding ‘WAVEDERF’; a ‘WAVEDERF’ file will appear after a LOPTICS run. These are <i|r|j>, not <i|p|j>. Same for BerkeleyGW.
- Phonon dispersions and quasi-harmonic treatments from Phonopy.
- Phonon lifetimes and lattice thermal conductivities from Phono3py.
- Ab-initio MD too slow? See if advanced rare event sampling methods work for you.
- Splitting phonon calculation. See ‘additional information’ on http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PH.html
- Use version 7.4 onwards for calculating nonlinear optical properties – two bugs related to symmetry were present in versions before that.
- Optical matrix elements are obtained from wavefunctions and thus have arbitrary phases. Special care is needed when calculating cross terms, e.g. epsilon_xy.
Compilation on ICS-ACI
- For different mpi flavors, use libmkl_blacs_[flavor]_lp64.a, where flavor can be intelmpi, openmpi …
- On aci, use mkl libraries for LAPACK and SCALAPACK. Module load mkl and find all libraries under $MKLROOT.
- Quick and easy visualization, with built-in rendering options. Depth of field can be controlled after rendering script is generated, e.g. for Tachyon under “Camera” specify “projection perspective_dof” and “aperture [number]”
Some ‘goto’ papers
- DFPT, Baroni et al. Rev. Mod. Phys. 73, 515 (2001)
- Point defects in TMDs, Komsa et al. PRB 91, 125304 (2015)
- Charged defects in 2D, Komsa et al. PRX 4, 031044 (2014)
- Defects in solids in general, Freysoldt et al. Rev. Mod. Phys. 86, 253 (2014)
- Raman tensors from symmetry, Loudon Advances in Physics, 50:7, 813-864
- GW-BSE in TMDs, Qiu et. al. PRL 111, 216805 (2013), PRB 93, 235435 (2016)
- Lattice thermal conductivities, Chernatynskiy et al. PRB 82, 134301 (2010), Togo et al. PRB 91, 094306 (2015)
- High-throughput, Curtarolo et al. Nat. Mater. 12, 191 (2013)