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[avanderg <avanderg@mines.edu>]

Hello,

The job with mkmem=0 crashed in the same manner as the previous jobs.

Thanks

Abram


avanderg wrote:
> Hello Again,
>
> I am currently running a job with mkmem = 0 as per PMA's suggestion.
> I am running version 5.4.4 (MPI) compiled with the pgi compiler.  The 
> cluster I am running the jobs on is heterogeneous but I constrain the 
> processors to be opteron (what it was compiled on). 
> At Matthieu's suggestion I checked the individual *LOG* files and it 
> appears that one of the processors did exit early during the check for 
> re-using the previous wavefunction.  But the log file doesn't give an 
> error.  When I re-checked the file that has the system errors I got a 
> message saying "One of the processes started by mpirun has exited with 
> a nonzero exit code."  So it appears the error happens on one node but 
> that the node just appears to die.
>
> Thank you again
>
> Abram Van Der Geest
>
>
> P.S. This is the top of the output file:
>
> .Version 5.4.4  of ABINIT
> .(MPI version, prepared for a x86_64_linux_pgi computer)
>
>
>
> Anglade Pierre-Matthieu wrote:
> > Hi,
> >
> > Did you check for memory uses ? 24x24x24  usually makes for quite
> > heavy jobs. May be using
> > "mkmem" could help ?
> >
> > regards
> >
> > PMA
> >
> > On Mon, Mar 24, 2008 at 10:53 PM, avanderg <avanderg@mines.edu> wrote:
> >  
> > > Hello All,
> > >
> > >  I am interested in calculating the frequency dependent dielectric 
> > > tensor
> > >  for GaAs for an accurate number of k-points and value for ecut. So I
> > >  took the tutorial for the frequency dependent tensor for AlAs and
> > >  modified it for GaAs.  I then have turned up the k-points and ecut to
> > >  3*24 and 20.  I ran the job on 8 processors with 4 gigs of ram for 
> > > each
> > >  processor.  Then as far as I can tell the job just dies during either
> > >  the second or the third dataset.  I have the ends of both the 
> > > output and
> > >  log files below.  I have worked my way up to 3*24 k points and the 
> > > jobs
> > >  work up to about 3*20 kpoints.  It is just the jobs with 3*20+ kpoints
> > >  that die during one of the early data sets.  All the related 
> > > messages I
> > >  have seen in previous posts have un-related error messages so I am
> > >  un-able to determine the problem from them.   I was hoping someone 
> > > could
> > >  point me in the correct direction for fixing this problem.
> > >
> > >  Thank you
> > >
> > >  Abram Van Der Geest
> > >
> > >  I have attached the input file and have put the final output for the
> > >  .out file and the .log file below.
> > >
> > >
> > >  End of .out file:
> > >
> > >  "== DATASET  3
> > >  ==================================================================
> > >
> > >   mkfilename : getwfk/=0, take file _WFK from output of DATASET   2.
> > >
> > >   mkfilename : getden/=0, take file _DEN from output of DATASET   2.
> > >
> > >   Real(R)+Recip(G) space primitive vectors, cartesian coordinates
> > >  (Bohr,Bohr^-1):
> > >   R(1)=  0.0000000  5.3000000  5.3000000  G(1)= -0.0943396  0.0943396
> > >  0.0943396
> > >   R(2)=  5.3000000  0.0000000  5.3000000  G(2)=  0.0943396 -0.0943396
> > >  0.0943396
> > >   R(3)=  5.3000000  5.3000000  0.0000000  G(3)=  0.0943396  0.0943396
> > >  -0.0943396
> > >   Unit cell volume ucvol=  2.9775400E+02 bohr^3
> > >   Angles (23,13,12)=  6.00000000E+01  6.00000000E+01  6.00000000E+01 
> > > degrees
> > >
> > >   getcut: wavevector=  0.0000  0.0000  0.0000  ngfft=  32  32  32
> > >          ecut(hartree)=     20.000   => boxcut(ratio)=   2.12070
> > >  -------------------------------------------------------------------------------- 
> > >
> > >
> > >  -inwffil : will read wavefunctions from disk file gaas_fo_DS2_WFK"
> > >
> > >
> > >
> > >
> > >  End of .log file:
> > >
> > >  " xred:                                 |  xred:
> > >  -P-0000      0.0000000   0.0000000   0.0000000  |     0.0000000
> > >  0.0000000   0.0000000
> > >  -P-0000      0.2500000   0.2500000   0.2500000  |     0.2500000
> > >  0.2500000   0.2500000
> > >  -P-0000
> > >  -P-0000  hdr_check: WARNING -
> > >  -P-0000   Restart of self-consistent calculation need translated
> > >  wavefunctions.
> > >  -P-0000   Indeed, critical differences between current calculation and
> > >  -P-0000   restart file have been detected in:
> > >  -P-0000         * the number, position, or weight of k-points
> > >  -P-0000         * the format of wavefunctions (istwfk)
> > >  -P-0000
> > >  ================================================================================ 
> > >
> > >  "
> > >
> > > #Prepare the computation of linear and non-linear optic properties
> > >  #of GaAs crystal : ground-state with few bands,
> > >  #then non-SCF with a larger number of bands, then ddk for different 
> > > directions
> > >  #Note that the k point sampling shoud be finer for significant 
> > > results. The cut-off energy is also too low.
> > >
> > >   ndtset 6
> > >
> > >  #First dataset : SC run with kpoints in the IBZ
> > >    iscf1  3
> > >   nband1  20
> > >   nstep1 1000
> > >   kptopt1 1
> > >   nbdbuf1 0
> > >   prtden1 1   getden1 0   getwfk1 0    ! Usual file handling data
> > >
> > >  #Second dataset : NSC run with large number of bands, and points in 
> > > the IBZ
> > >     iscf2 3
> > >  #    iscf2 -2
> > >    nband2 20  ! This number of bands might be too low for non-linear 
> > > optics and real part of linear optics
> > >    nstep2 1000
> > >   kptopt2  2
> > >  #  getwfk2  0   getden2 0   ! Usual file handling data
> > >   getwfk2  1   getden2 1   ! Usual file handling data
> > >
> > >  #Third dataset : NSC run with large number of bands, and points in 
> > > the the full BZ
> > >     iscf3 -2
> > >    nband3 20  ! This number of bands might be too low for non-linear 
> > > optics and real part of linear optics
> > >    nstep3 1000
> > >   kptopt3  3
> > >   getwfk3  2   getden3 2   ! Usual file handling data
> > >
> > >
> > >  #Fourth datset : ddk response function along axis 1
> > >    iscf4 -3
> > >   nband4 20   ! This number of bands might be too low for non-linear 
> > > optics and real part of linear optics
> > >   nstep4  1  nline4  0
> > >   kptopt4  3
> > >
> > >    nqpt4  1  qpt4  0.0d0 0.0d0 0.0d0
> > >   rfdir4  1 0 0
> > >   rfelfd4  2
> > >   getwfk4  3
> > >
> > >  #Fifth dataset : ddk response function along axis 2
> > >    iscf5 -3
> > >   nband5 20   ! This number of bands might be too low for non-linear 
> > > optics and real part of linear optics
> > >   nstep5  1  nline5  0
> > >   kptopt5  3
> > >
> > >    nqpt5  1  qpt5  0.0d0 0.0d0 0.0d0
> > >   rfdir5  0 1 0
> > >   rfelfd5  2
> > >   getwfk5  3
> > >
> > >   Sixth dataset : ddk response function along axis 3
> > >    iscf6 -3
> > >   nband6 20   ! This number of bands might be too low for non-linear 
> > > optics and real part of linear optics
> > >   nstep6  1  nline6  0
> > >   kptopt6  3
> > >
> > >    nqpt6  1  qpt6  0.0d0 0.0d0 0.0d0
> > >   rfdir6  0 0 1
> > >   rfelfd6  2
> > >   getwfk6  3
> > >
> > >
> > >  #Data common to all datasets
> > >   nshiftk 4
> > >   shiftk  0.5 0.5 0.5
> > >          0.5 0.0 0.0
> > >          0.0 0.5 0.0
> > >          0.0 0.0 0.5
> > >   ngkpt  24  24  24        ! This is much too low : should be at 
> > > least 24x24x24
> > >
> > >   acell   3*10.60
> > >   amu 69.72  74.9216
> > >   diemac 10.0
> > >   ecut 20.00             ! This is also too low
> > >   iscf 3
> > >   ixc 1
> > >   natom  2  nbdbuf 2
> > >   ntypat  2
> > >   rprim   0 .5 .5  .5 0 .5  .5 .5 0
> > >   xred 3*0.00d0 3*0.25d0
> > >   tnons 72*0.0
> > >   typat  1 2  tolwfr  1.e-20
> > >   znucl  31 33
> > >
> > >
> > >     
> >
> >
> >
> >