The ABINIT Users Mailing List ( CLOSED )

[Fabien Bruneval <fabien.bruneval@polytechnique.fr>]

Dear Maurice,

The first step of the GW calculation is to output the Kohn-Sham energies 
and wavefunctions in a so-called KSS file. If you choose kssform=1 (that 
is the default), the code is going to diagonalize the KS hamiltonian 
using a direct diagonalization with lapack. In this part, there is only 
parallelization over k-points and nothing else. As you are using only 
the gamma point, there is no way to parallelize this part.

You should run the first step in serial.

I have several comment on your input file.

1) try to run a smaller calculation first. GW calculations are extremely 
heavy. Personnaly, I would be scared by a cell containing 288 atoms and 
800 electrons.

2) nbandkss is set to 50, even though your system contains around 400 
occupied bands. You should be aware that the GW calculations requires a 
huge number of empty states.
nbandkss 800 or 1200 would be more reasonable...

Riad Shaltaf and Matteo Giantomasi are currently working on the 
parallelization over bands. I advise you to use the next version of 
abinit as soon as it is available...

Regards,

Fabien





Maurice de Koning wrote:
> Hi,
>
> I'm trying to carry out a GW calculation for hexagonal ice I, running abinip 5.3.4 on a 16-CPU  SGI Altix 
> system. I'm using a large proton-disordered cell containing 96 water molecules, Gamma point only, PBE GGA, Troullier-Martins 
> Pseudopotentials and a large ecut=850 eV. Based on the geometry-optimized structure I am trying 
> to carry out the 3 steps required in the GW calculation. The problem already occurs for the first step, 
> when trying to calculate the Kohn-Sham electronic structure by the diagonalization of the Kohn-Sham Hamiltonian based 
> on the converged density.
>
> The SCF part of the calculation, parallelized over npbands*npftt=8*2=16, 
> seems OK, but the problems seem to
> start when abinip starts writing the _DEN file, after which all hell breaks loose: 
>
> *************************************************************************************************
>  At SCF step   20, etot is converged :
>   for the second time, diff in etot=  1.632E-06 < toldfe=  1.000E-05
>
>  Cartesian components of stress tensor (hartree/bohr^3)
>   sigma(1 1)=  1.48708394E-04  sigma(3 2)=  6.91251884E-08
>   sigma(2 2)=  1.50207276E-04  sigma(3 1)= -1.23849931E-07
>   sigma(3 3)=  1.50516609E-04  sigma(2 1)=  3.56082287E-08
>
>  ioarr: writing density data
>  ioarr: file name is IhGWo_DS1_DEN
> *** glibc detected *** malloc(): memory corruption: 0x6000000004f71ab0 ***
> MPI: On host opala, Program 
> /home/esmeralda/dekoning/dekoning/abinit/abinit-5.3.4/src/main/abinip, Rank 
> 3, Process 21986 received signal SIGSEGV(11)
>
>
> MPI: --------stack traceback-------
> *** glibc detected *** double free or corruption (out): 0x6000000004f67730 ***
> *** glibc detected *** free(): invalid next size (normal): 0x6000000004f20ec0 
> ***
> *** glibc detected *** free(): invalid next size (normal): 0x6000000004f1dc90 
> ***
> *** glibc detected *** free(): invalid next size (normal): 0x6000000004f6a3e0 
> ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004f6f740 
> ***
> *** glibc detected *** free(): invalid next size (normal): 0x6000000004fb6b30 
> ***
> *** glibc detected *** double free or corruption (out): 0x6000000005004830 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004fbdfc0 
> ***
> *** glibc detected *** double free or corruption (!prev): 0x600000000500c840 
> ***
>  ioarr: data written to disk file IhGWo_DS1_DEN
>  bonds_lgth_angles : about to open file IhGWo_DS1_GEO
>
> ======================================================================
>  Calculating and writing out Kohn-Sham electronic Structure file
>  Using diagonalized wavefunctions and energies (kssform=1)
>
>  Additional amount of memory required by "outkss" routine= 1615.00 Mbytes.
>
>
>
>
>  Since the number of g's to be written on file
>  was 0 or too large, it has been set to the max. value.,
>  computed from the union of the sets of G vectors for the different k-points.
>  Number of g-vectors written on file is: 10068
>
>  Since the number of bands to be computed was (-1) or
>  too large, it has been set to the max. value. allowed for each k,
>  thus, the minimum of the number of plane waves for each k point.
>  Number of bands written on file is: 10068
>
>  Since the number of bands to be computed
>  is equal to the nb of G-vectors found for each k-pt,
>  the program will perform complete diagonalizations.
>
>  Amount of disk space required by _STA file= 1547.12 Mbytes.
>
>
>  Sorting g-vecs for an output of states on an unique "big" PW basis.
>  The inversion was not found in the symmetries list.
>  - outkss - COMMENT :
>    GW program uses the original set of symmetries
>  Shells found:
>  number of shell    number of G vectors      cut-off energy
>                1                      1               0.024
>                2                      2               0.024
>                3                      3               0.051
>                4                      4               0.051
>                5                      5               0.056
>                6                      6               0.056
>                7                      7               0.056
>                8                      8               0.056
>                9                      9               0.083
>               10                     10               0.083
>               11                     11               0.083
>               12                     12               0.083
>               13                     13               0.132
>               14                     14               0.132
>               15                     15               0.152
>               16                     16               0.152
>                .......
>             ****                  10048              31.177
>             ****                  10049              31.180
>             ****                  10050              31.180
>             ****                  10051              31.180
>             ****                  10052              31.180
>             ****                  10053              31.182
>             ****                  10054              31.182
>             ****                  10055              31.182
>             ****                  10056              31.182
>             ****                  10057              31.183
>             ****                  10058              31.183
>             ****                  10059              31.183
>             ****                  10060              31.183
>             ****                  10061              31.208
>             ****                  10062              31.208
>             ****                  10063              31.208
>             ****                  10064              31.208
>             ****                  10065              31.210
>             ****                  10066              31.210
>             ****                  10067              31.210
>             ****                  10068              31.210
>
>
>
>  Opening file for KS structure output: IhGWo_DS1_KSS
>  number of Gamma centered plane waves  10068
>  number of Gamma centered shells  10068
>  number of bands  10068
>  maximum angular momentum components      4
>  number of symmetry operations  1 (without inversion)
>    *   g( 1)=  0  1  0
>    *   g( 2)=  0 -1  0
>    *   g( 3)=  0  1  1
>    *   g( 4)=  0 -1  1
>    *   g( 5)=  1  1  0
>    *   g( 6)= -1  1  0
>    *   g( 7)=  1 -1  0
>    *   g( 8)= -1 -1  0
>    *   g(****)=-25 21  5
>    *   g(****)= 25-21  5
>    *   g(****)=-25-21  5
>    *   g(****)= 16 31  1
>    *   g(****)=-16 31  1
>    *   g(****)= 16-31  1
>    *   g(****)=-16-31  1
> -P-0000
> -P-0000  k-point   1
> *** glibc detected *** double free or corruption (!prev): 0x6000000004f5cf90 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004f64fa0 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004f582b0 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004f602c0 ***
> *** glibc detected *** malloc(): memory corruption: 0x6000000004f582b0 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004f67730 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004f6f740 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004f623d0 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004f6a3e0 ***
> -P-0000  Calculating <G|H|G'> elements
> *** glibc detected *** double free or corruption (!prev): 0x6000000004fa28f0 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004faa900 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004fa9080 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004fb1090 ***
> *** glibc detected *** double free or corruption (out): 0x6000000004f682d0 ***
> *** glibc detected *** double free or corruption (out): 0x6000000004f6cfb0 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004fecf30 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004ff4f40 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000004ff5170 
> ***
> *** glibc detected *** free(): invalid pointer: 0x6000000004ffd180 ***
> *** glibc detected *** double free or corruption (out): 0x6000000004fb2910 ***
> *** glibc detected *** double free or corruption (!prev): 0x6000000005037570 
> ***
> *** glibc detected *** free(): invalid pointer: 0x600000000503f580 ***
> ******************************************************************************************************************
>
> Here is the input file:
>
> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------
> #-----------------------------------------------------------------
> # Ice PBE GGA
> #-----------------------------------------------------------------
>
> #Definition of the unit cell
>  acell 13.1493536801862057 15.1976493759670106 14.3247149284289197 angstrom
>
> #Definition of the planewave basis set
>  ecut   850 eV # Maximal kinetic energy cut-off, eV
>
>
> #Definition of k-points
>  nkpt 1
>
> ndtset      1
>
> # Definition of parameters for the calculation of the KSS file
> nbandkss   50         # Number of bands in KSS file (-1 means the maximum 
> possible)
> symmorphi 0           # No symmorphic symmetry operations
> nsym 0
> # Definition of the SCF procedure
> nstep   30        # Maximal number of SCF cycles
> toldfe  1.0d-5    # Will stop when this tolerance is achieved on total energy
> diemac  12.0      
>
> #Parallelization specifications
>  npband 8 npfft 2
>  timopt -1
>  fftalg 401
>  nloalg=4
>  wfoptalg 4
>  fft_opt_lob 2
>  iprcch 0
>  intxc 0
>  istwfk 1 #Do not take advantage of time-reversal symmetry
>
> #Exchange-correlation functional
>  ixc=11            #PBE
>
> #Electron bands
> nband 400
>
> #Output options
>  enunit 2    #Print energies in Hartrees and eV
>  prtden 1
>  prtwf 1
>  prtgeo 1
>  chkexit 1 #Check for soft exit
>
> #Definition of the atoms
>  natom  288
>  ntypat 2
>  typat  96*2 192*1
>  znucl  1 8
>  xred         8.4312914696E-02  8.3660261848E-02  9.3809915685E-02
>               2.5074724775E-01  1.6659125325E-01  1.5681072076E-01
>               8.3324114394E-02  8.3419501461E-02  4.0579067959E-01
>               2.5013948449E-01  1.6724399173E-01  3.4402885286E-01
>               2.5040058344E-01  3.3278509043E-01  9.4311450028E-02
>               8.3103792575E-02  4.1649451464E-01  1.5571120920E-01
>  ......
> ---------------------------------------------------------------------------------------------------------------------------------
>
> Any idea what may be the problem?
>
> Thanks,
>
> Maurice