Re: [QE-users] Phonon - 6.3- problem

2018-10-10 Thread Suresh A
Dear Christoph Wolf,
 Thanks for your support.
Yes,  I compile it myself using gfortran and
openmpi software.
1)  Do I have to use other version? Could you please suggest me which
version exactly for workstation? I am asking this because you have
mentioned "MaX" version could be a problematic one.

2) I did not add full input and out put file due to space. If you
want them, to find out where the error is, i can send it to you, sir.   And
the memory it requires is ( Taken  from scf output file):

One more thing is we do not have intel compiler in the department
workstation.

3) If you don't mind, I would like to ask this. Our  computer is
workstation. Which one is better one, MPI or OpenMpi?

 Estimated max dynamical RAM per process >  13.46 MB

 Estimated total dynamical RAM > 323.13 MB

 Initial potential from superposition of free atoms

 starting charge   31.99474, renormalised to   32.0

 negative rho (up, down):  1.148E-05 0.000E+00
 Starting wfcs are   96 randomized atomic wfcs

 total cpu time spent up to now is9.7 secs...
  Thank you







 Yours Sincerely,

A.Suresh,
Research Scholar,
School of Physics,
Madurai Kamaraj University,
Madurai.
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Re: [QE-users] Phonon - 6.3- problem

2018-10-10 Thread Christoph Wolf
I see you are using the MAX version. If I remember correctly I also had a
minor problem with that one at some point. Did you compile it yourself?
Which compiler and libraries did you use? In my limited experience intels
compiler and mkl works with the least hassle.

What is the required RAM (scf out file) and the physically available memory?

Input files seem OK, except your ecutrho seems high (for norm-conserving
pseudos 4*ecutwfc).

Best,
Chris
-- 
Postdoctoral Researcher
Center for Quantum Nanoscience, Institute for Basic Science
Ewha Womans University, Seoul, South Korea
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Re: [QE-users] Phonon - 6.3- problem

2018-10-10 Thread Suresh A
Dear Christoph Wolf,
Thanks for your reply. The RAM size in my our department
workstation is 32 GB. I will also try to use small jobs.

The commands I used are
[Dell@centos7 ~]$ /lib64/openmpi/bin/mpirun   -np 24
/home/Dell/qe-6.3/bin/ph.x  
/home/Dell/phonon/relaxed/ph.out^C
[Dell@centos7 ~]$ /lib64/openmpi/bin/mpirun   -np 24
/home/Dell/qe-6.3/bin/ph.x  
/home/Dell/phonon/relaxed/ph.out
^Cmpirun: abort is already in progress...hit ctrl-c again to forcibly
terminate
The following is my input I used for pw.x and ph.in. Below the input file I
have added few lines of output of ph.x also.




  title = 'anat' ,
calculation = 'scf',
   restart_mode = 'from_scratch' ,
 wf_collect = .true.,
 prefix = 'anatase',
 outdir ='/home/Dell/phonon/relaxed/tmp',
 pseudo_dir = '/home/Dell/phonon/pseudo',
tstress = .true. ,
tprnfor = .true. ,/
 
  ibrav = 7,
  A =  3.7547,
  C =  9.1960,
nat = 6 ,
   ntyp = 2 ,
ecutwfc = 90 ,
ecutrho = 900/
 
   conv_thr = 1.D-16   /
ATOMIC_SPECIES
   Ti   47.86700  Ti.pz-mt_fhi.UPF
O   15.99940  O.pz-mt_fhi.UPF
ATOMIC_POSITIONS (angstrom)
Ti  -0.0   0.0   0.0
Ti   0.0   1.877350549   2.299006742
O0.0   0.0  -1.937981509
O   -0.0  -0.0   1.937981509
O   -0.0   1.877350549   0.361025232
O0.0   1.877350549   4.236988251
K_POINTS automatic
8 8 8 0 0 0

phonons of anatase
 
  tr2_ph=1.0d-12,
  prefix='anatase',
  ldisp=.true.,
  amass(1)=47.86700,
  amass(2)=15.99940,
  outdir ='/home/Dell/phonon/relaxed/tmp',
  fildyn='ana.dyn',
  nq1=4, nq2=4, nq3=4
 

output
 Program PHONON v.6.3MaX starts on  8Oct2018 at 12:41:19

 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 on24 processors

 MPI processes distributed on 1 nodes
 R & G space division:  proc/nbgrp/npool/nimage =  24

 Reading data from directory:
 /home/Dell/phonon/relaxed/tmp/anatase.save/

 IMPORTANT: XC functional enforced from input :
 Exchange-correlation  = PW ( 1  4  0  0 0 0)
 Any further DFT definition will be discarded
 Please, verify this is what you really want

   file Ti.pz-mt_fhi.UPF: wavefunction(s)  4f renormalized
   file O.pz-mt_fhi.UPF: wavefunction(s)  4f renormalized

 Parallelization info
 
 sticks:   dense  smooth PW G-vecs:dense   smooth  PW
 Min 198  79 24 8310 2107 363
 Max 199  80 25 8313 2112 366
 Sum47531917587   19947950625
8741.

And the program stucked at

Representation #  9 mode #   9

 Self-consistent Calculation

  iter #   1 total cpu time : 68381.5 secs   av.it.:  10.0
  thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  2.197E-06

  iter #   2 total cpu time : 68609.6 secs   av.it.:  18.5
  thresh= 1.482E-04 alpha_mix =  0.700 |ddv_scf|^2 =  7.406E-06

  iter #   3 total cpu time : 68813.8 secs   av.it.:  16.3
  thresh= 2.721E-04 alpha_mix =  0.700 |ddv_scf|^2 =  6.015E-08

  iter #   4 total cpu time : 69031.9 secs   av.it.:  17.6
  thresh= 2.452E-05 alpha_mix =  0.700 |ddv_scf|^2 =  1.638E-08

  iter #   5 total cpu time : 69241.6 secs   av.it.:  16.9
  thresh= 1.280E-05 alpha_mix =  0.700 |ddv_scf|^2 =  3.902E-10

  iter #   6 total cpu time : 69459.6 secs   av.it.:  17.6
  thresh= 1.975E-06 alpha_mix =  0.700 |ddv_scf|^2 =  8.914E-11

  iter #   7 total cpu time : 69675.9 secs   av.it.:  17.4
  thresh= 9.441E-07 alpha_mix =  0.700 |ddv_scf|^2 =  5.486E-12
After this "System monitor" showed no processor is running. And the program
at terminal was blinking as program is running.

Before I get this error,  I also find for my earlier run that after ph.x
output is created for anatase, q2r.x wasn't run for small number of k point
in scf and small number of kpoint in ph.in.
I will try to run again for anatase as you suggested for small system.
 Yours Sincerely,

A.Suresh,
Research Scholar,
School of Physics,

Re: [QE-users] Phonon - 6.3- problem

2018-10-09 Thread Christoph Wolf
Sometimes a single process can crash and cause others to hang. Are you sure
you have plenty of RAM available (ph.x requires more RAM than pw.x in my
experience).


Try running a smaller job on a single processor first. Also try avoiding
hyperthreading (depending on if you have 30 physical cores or 30 with HT).
Alas, without input files it is hard to say what went wrong.

Best,
Chris

-- 
Postdoctoral Researcher
Center for Quantum Nanoscience, Institute for Basic Science
Ewha Womans University, Seoul, South Korea
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[QE-users] Phonon - 6.3- problem

2018-10-09 Thread Suresh A
Dear All,
   I recently downloaded q-e-6.3 and installed it into my
workstation consisting of 30 processors. While I ran phonon calculation for
anatase unitcell, I observed an error.
 Computing dynamical matrix for
   q = (   0.500   0.250  -0.1020743 ) for this
point, program stopped from running. While I checked processors via system
monitor software in centOS, it showed that all processors not running. And
in terminal cursor was blinking as the program is running. It did not show
any error message for a long time (several hours)  till I cut the program
by CTRL+C.
Any help would be appreciated.
Is this early reported one?


 Yours Sincerely,

A.Suresh,
Research Scholar,
School of Physics,
Madurai Kamaraj University,
Madurai.
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