PmWikiFisica | Hpc / HpcUniprIt browse

List towards DFT tutorial (Fisica Stati Condensati)

login with ldap passwd from either local or VPN
follow QE tutorials, particularly handson.pdf, see tutorial dir on hpc
PWSCF: download on hpc the tar file of the examples i.e.
- wget http://www.fisica.uniud.it/~giannozz/QE-Tutorial/handson_pwscf.tar.gz
- tar -xzvf handson_pwscf.tar.gz
- cd to Silicon and edit si.scf.in
- xcrystden si.scf.in opens the Si cell
- check commands and parameters on input PW
- tutorial cda slurm batch in elly: sbatch job.sh
- sbatch -p knl job.sh from /hpc/home/roberto.derenzi/tutorial/handson_pwscf/Silicon/1/ (calculation si.scf.in without mpirun!)
- or do it on pc34, e.g. from hpc/tutorial/handson_pwscf/Silicon with job.sh or simply by /home/roberto.derenzi/q-e-qe-6.2.0/bin/pw.x -inp si.scf.in > si.scf.out

Need a linux installation on virtual machines, with xcrystden.

Generated local keys according to Guida Utente from dokuwiki, for password-less use among nodes.

Toshiba pc34 had already private-public keys generates the same way (ssh-keygen -t rsa, CRT CRT). To copy pc34 public key onto login.hpc use

   ssh-copy-id nome.cognome@login.hpc.unipr.it

Here is the Sr2RuO4 pw.x template with comments. Removing the comments the file can be loaded by Xcrystden to check that the lattice is correct. The best is to use the conventional cell (ibril = 0, CELL_PARAMETERS angstrom (in \AA) and ATOM_POSITIONS angstrom, straight out of the cif loaded in VESTA)

Pseudopotentials are into a ~/Pseudo/ folder on login.hcp

To compile on new cluster:

    module load intel intelmpi
    ./configure MPIF90=mpiifort F90=ifort CC=icc

then (workaround for wrong FFT library) modify make.inc like this:

    line 45: -D__FFTW3 -> -D__DFTI
    line 128: remove -lfftw3
    line 52: add -I/hpc/share/tools/intel/mkl/include/

If compiling for KNL, add this

    line 45:  -xMIC-AVX512

To explore n H sites (starting positions in file H_positions) with job submission script test-sc.template

  cat ../test-sc.template > relax.in
  sed '1!d' ../H_positions >> relax.in
  sed -i 's/SCIDX/1/g' relax.in

then

  qsub job.sh