Error from NetCDF

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Moderator: Daniele Varsano

Error from NetCDF

Postby cantele » Tue Sep 07, 2010 11:49 am

Dear all,

I previously posted http://www.yambo-code.org/forum/viewtopic.php?f=15&t=140 an error coming from NetCDF during a BSE calculation. Such an error was definitely solved by applying this patch (suggested by A. Marini)
Index: driver/yambo_driver.F
===================================================================
--- driver/yambo_driver.F (revision 530)
+++ driver/yambo_driver.F (working copy)
@@ -152,7 +152,7 @@
!
if (l_em1s) i_err=X_em1(Xen,Xk,q,X(2),Xw(2),.false.)
!
- if (l_em1d.or.(l_gw0.and.l_el_corr)) then
+ if (l_em1d.or.(l_gw0.and.l_el_corr).or.l_bse) then
!
! Plasmon Pole
!

to the 3.2.1-r.448 version.

Now, a similar error occurs in a case in which I'm just trying to initialize Yambo. The error follows:
[ERROR] STOP signal received while in :
[ERROR][NetCDF] NetCDF: Start+count exceeds dimension bound


These are the steps I'm following (starting from a Quantum-ESPRESSO scf+nscf calculation):
i) p2y -N -S
the converter properly works and generates the needed directories and databases. The following l_stderr file is generated:
__ __ ______ ____ _____
/\ \ /\ \\ _ \ /"\_/`\/\ _`\ /\ __`\
\ `\`\\/"/ \ \L\ \/\ \ \ \L\ \ \ \/\ \
`\ `\ /" \ \ __ \ \ \__\ \ \ _ <" \ \ \ \
`\ \ \ \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
\ \_\ \ \_\ \_\ \_\\ \_\ \____/\ \_____\
\/_/ \/_/\/_/\/_/ \/_/\/___/ \/_____/

<---> [01] P(W) 2 Y(ambo) Ver. 4.0
<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies...
<---> Cell data...
<---> Atomic data...
<---> Symmetries...
<---> XC functional...Perdew & Wang (xc)
<---> K-points mesh...
<---> RL vectors...
<02s> IGK arrays...
<03s> Energies...
<03s> :: Electrons : 174.0000
<03s> :: Temperature [ev]: 0.000000
<03s> :: Lattice factors [a.u.]: 45.3534 83.1479 128.5014
<03s> :: K-points : 1
<03s> :: Bands : 350
<03s> :: Spinor components : 1
<03s> :: Spin polarizations : 1
<03s> :: Spin orbit coupling : no
<03s> :: Symmetries [spatial]: 1
<03s> :: [T-rev]: yes
<03s> :: Max WF components : 2470491
<03s> :: RL vectors (WF): 2470491
<03s> :: RL vectors (CHARGE): 19761719
<03s> :: XC potential : Perdew & Wang (xc)
<03s> :: Atomic species : 5
<03s> :: Max atoms/species : 26
<03s> == Writing DB1 ...
<04s> == DB2 (wavefunctions) ...
<04s> :: WF splitter Blocks/bands/block size(Mb): 17 21 395



ii) yambo -N -i -V 1
that is the command I've always used and that worked in all cases. At the end of the execution of such command I don't find the yambo.in file and in addition find, appended to the l_stderr file, the above reported error. I attach the data-file.xml. If useful, these are the first lines of ncdump SAVE/ns.db1
netcdf ns {
dimensions:
D_0000000017 = 17 ;
D_0000000001 = 1 ;
D_0000000003 = 3 ;
D_0000000005 = 5 ;
D_0000000026 = 26 ;
D_0000000002 = 2 ;
D_0019761719 = 19761719 ;
D_0000000350 = 350 ;
D_0002470491 = 2470491 ;
variables:
float DIMENSIONS(D_0000000017) ;
float WF_G_COMPONENTS(D_0000000001) ;
float MAX_ATOMS(D_0000000001) ;
float number_of_atom_species(D_0000000001) ;
float LATTICE_PARAMETER(D_0000000003) ;
float LATTICE_VECTORS(D_0000000003, D_0000000003) ;
float N_ATOMS(D_0000000005) ;
float ATOM_POS(D_0000000005, D_0000000026, D_0000000003) ;
float atomic_numbers(D_0000000005) ;
float SYMMETRY(D_0000000002, D_0000000003, D_0000000003) ;
float G-VECTORS(D_0000000003, D_0019761719) ;
float K-POINTS(D_0000000003, D_0000000001) ;
float EIGENVALUES(D_0000000001, D_0000000001, D_0000000350) ;
float WFC_NG(D_0000000001) ;
float WFC_GRID(D_0000000001, D_0002470491) ;
data:

DIMENSIONS = 7115, 3, 2, 1, 448, 350, 1, 1.976172e+07, 2470491, 1, 2, 1, 1,
0, 174, 3, 10 ;

WF_G_COMPONENTS = 2470491 ;

MAX_ATOMS = 26 ;

number_of_atom_species = 5 ;

LATTICE_PARAMETER = 45.35343, 83.14795, 128.5014 ;

[cantele@manager yambo_init]$ ncdump SAVE/ns.db1 | head -50
netcdf ns {
dimensions:
D_0000000017 = 17 ;
D_0000000001 = 1 ;
D_0000000003 = 3 ;
D_0000000005 = 5 ;
D_0000000026 = 26 ;
D_0000000002 = 2 ;
D_0019761719 = 19761719 ;
D_0000000350 = 350 ;
D_0002470491 = 2470491 ;
variables:
float DIMENSIONS(D_0000000017) ;
float WF_G_COMPONENTS(D_0000000001) ;
float MAX_ATOMS(D_0000000001) ;
float number_of_atom_species(D_0000000001) ;
float LATTICE_PARAMETER(D_0000000003) ;
float LATTICE_VECTORS(D_0000000003, D_0000000003) ;
float N_ATOMS(D_0000000005) ;
float ATOM_POS(D_0000000005, D_0000000026, D_0000000003) ;
float atomic_numbers(D_0000000005) ;
float SYMMETRY(D_0000000002, D_0000000003, D_0000000003) ;
float G-VECTORS(D_0000000003, D_0019761719) ;
float K-POINTS(D_0000000003, D_0000000001) ;
float EIGENVALUES(D_0000000001, D_0000000001, D_0000000350) ;
float WFC_NG(D_0000000001) ;
float WFC_GRID(D_0000000001, D_0002470491) ;
data:

DIMENSIONS = 7115, 3, 2, 1, 448, 350, 1, 1.976172e+07, 2470491, 1, 2, 1, 1,
0, 174, 3, 10 ;

WF_G_COMPONENTS = 2470491 ;

MAX_ATOMS = 26 ;

number_of_atom_species = 5 ;

LATTICE_PARAMETER = 45.35343, 83.14795, 128.5014 ;

LATTICE_VECTORS =
22.67671, 0, 0,
0, 41.57397, 0,
0, 0, 64.25069 ;

N_ATOMS = 26, 10, 2, 6, 2 ;

ATOM_POS =
11.32864, 16.62995, 15.45403,
11.34376, 18.92718, 14.18814,


Thanks in advance for your help.

Giovanni
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Dr. Giovanni Cantele
CNR-SPIN and Univ. di Napoli "Federico II"
Phone: +39 081 676910
E-mail: giovanni.cantele@cnr.it
giovanni.cantele@na.infn.it
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Re: Error from NetCDF

Postby Conor Hogan » Tue Sep 07, 2010 3:26 pm

Hi Giovanni,
I'm afraid I don't see immediately the source of the error. (I don't like very much the "1.976172e+07" appearing in the DIMENSIONS tag, though....)
When you run yambo -N -i -V 1, does yambo report anything at all? What else is in the l_stderr file?
And what does yambo -D produce?
Conor
Dr. Conor Hogan
CNR-ISM, via Fosso del Cavaliere, 00133 Roma, Italy;
Department of Physics and European Theoretical Spectroscopy Facility (ETSF),
University of Rome "Tor Vergata".
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Re: Error from NetCDF

Postby Daniele Varsano » Tue Sep 07, 2010 3:39 pm

Hi,
I do not know what's the error source, anyway nothing strange with the 1.976172e+07, according to the description in
./src/io/ioDB1.F
Code: Select all
  call io_elemental(ID, VAR="DIMENSIONS",VAR_SZ=17)
 61    !
 62    ! Meaning of DIMENSIONS tag in ioDB1 file:
 63    !
 64    !  1 Serial Number
 65    !  2 Major version   3 Minor version   4 Patchlevel
 66    !  5 Bands                   E%nb
 67    !  6 k-points                k%nibz
 68    !  7 G-vectors (total)       ng_vec
 69    !  8 G-vectors (wfc/shell)   wf_ncx
 70    !  9 Time reversal flag      i_time_rev
 71    ! 10 Symmetries              nsym
 72    ! 11 Spinor cmpts            n_spinor
 73    ! 12 Spins                   n_sp_pol
 74    ! 13 Temperature             default_Tel
 75    ! 14 Electrons               default_nel
 76    ! 15 XC kind                 GS_xc_KIND
 77    ! 16 XC functional           GS_xc_FUNCTIONAL
 78    !
 79    ! Added dimensions: (still in SEC=1)
 80    !
 81    !------------ 3.0.3 ------------------
 82    !    G-vectors (wfc/igk)     ng_wf
 83    !------------ 3.0.4 ------------------
 84    !    Max atoms/species       max_atom_species
 85    !    No. of atom species     n_atom_species



this number correspond to G-vectors (total) for the charge that in pwscf is 8 times the wfs g-vector. So it should be right.
Best,

Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Re: Error from NetCDF

Postby Conor Hogan » Tue Sep 07, 2010 3:56 pm

Hi again,
Well I just meant, I hope the output of ncdump is producing the 1.976172e+07, while internally the number is 19761719!
I'd be surprised if that is the problem, but you never know.

The fact that yambo -i does not even create the input points to some problem in the databases. The p2y cuts at writing the wavefunctions, but that is not read at the initialization stage so thats not it. Do you get an error also with yambo -D?
Unless someone else spots something, I might have to ask you to reduce the size of the problem and if it persists, I can try to run it myself.
Conor
Dr. Conor Hogan
CNR-ISM, via Fosso del Cavaliere, 00133 Roma, Italy;
Department of Physics and European Theoretical Spectroscopy Facility (ETSF),
University of Rome "Tor Vergata".
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Re: Error from NetCDF

Postby cantele » Wed Sep 08, 2010 9:56 am

Unfortunately, also yambo -D reports the same error. This is the output:
[RD./SAVE//ns.db1]------------------------------------------
Bands : 350
K-points : 1
G-vectors [RL space]: 19761720
Components [wavefunctions]: 2470491
Symmetries [spatial+T-rev]: 2
Spinor components : 1
Spin polarizations : 1
Temperature [ev]: 0.000000
Electrons : 174.0000
WF G-vectors : 2470491
Max atoms/species : 26
No. of atom species : 5
- S/N 007115 ---------------------------- v.03.02.01 r.448 -
[M 0.247 Gb] Alloc g_vec k_pt dl_sop wf_nc_k wf_igk (0.247)

[ERROR] STOP signal received while in :
[ERROR][NetCDF] NetCDF: Start+count exceeds dimension bound
Dr. Giovanni Cantele
CNR-SPIN and Univ. di Napoli "Federico II"
Phone: +39 081 676910
E-mail: giovanni.cantele@cnr.it
giovanni.cantele@na.infn.it
Web: http://people.na.infn.it/cantele
Skype: giocan74
cantele
 
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Re: Error from NetCDF

Postby Conor Hogan » Wed Sep 08, 2010 12:35 pm

Thanks Giovanni. Once again there this strange 19761720 .ne. 19761719 apparent problem. Now, perhaps this is not the issue at all, but let's try to rule it out for sure: can you report as before the ncdump output for the first 50 lines using
ncdump -p 10
which should print all the integers with 10 significant figures rather than 7?
Dr. Conor Hogan
CNR-ISM, via Fosso del Cavaliere, 00133 Roma, Italy;
Department of Physics and European Theoretical Spectroscopy Facility (ETSF),
University of Rome "Tor Vergata".
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Posts: 143
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Re: Error from NetCDF

Postby cantele » Wed Sep 08, 2010 12:38 pm

ncdump -p 10 SAVE/ns.db1 | head -50
n
etcdf ns {
dimensions:
D_0000000017 = 17 ;
D_0000000001 = 1 ;
D_0000000003 = 3 ;
D_0000000005 = 5 ;
D_0000000026 = 26 ;
D_0000000002 = 2 ;
D_0019761719 = 19761719 ;
D_0000000350 = 350 ;
D_0002470491 = 2470491 ;
variables:
float DIMENSIONS(D_0000000017) ;
float WF_G_COMPONENTS(D_0000000001) ;
float MAX_ATOMS(D_0000000001) ;
float number_of_atom_species(D_0000000001) ;
float LATTICE_PARAMETER(D_0000000003) ;
float LATTICE_VECTORS(D_0000000003, D_0000000003) ;
float N_ATOMS(D_0000000005) ;
float ATOM_POS(D_0000000005, D_0000000026, D_0000000003) ;
float atomic_numbers(D_0000000005) ;
float SYMMETRY(D_0000000002, D_0000000003, D_0000000003) ;
float G-VECTORS(D_0000000003, D_0019761719) ;
float K-POINTS(D_0000000003, D_0000000001) ;
float EIGENVALUES(D_0000000001, D_0000000001, D_0000000350) ;
float WFC_NG(D_0000000001) ;
float WFC_GRID(D_0000000001, D_0002470491) ;
data:

DIMENSIONS = , , , , , , , , , , , , , , , , ;

WF_G_COMPONENTS = ;

MAX_ATOMS = ;

number_of_atom_species = ;

LATTICE_PARAMETER = , , ;

LATTICE_VECTORS =
, , ,
, , ,
, , ;

N_ATOMS = , , , , ;

ATOM_POS =
, , ,
, , ,
, , ,
Dr. Giovanni Cantele
CNR-SPIN and Univ. di Napoli "Federico II"
Phone: +39 081 676910
E-mail: giovanni.cantele@cnr.it
giovanni.cantele@na.infn.it
Web: http://people.na.infn.it/cantele
Skype: giocan74
cantele
 
Posts: 21
Joined: Wed Dec 23, 2009 2:58 pm

Re: Error from NetCDF

Postby Conor Hogan » Wed Sep 08, 2010 1:34 pm

Hmm..ok, not so useful. What I wanted to see is if the large number in
float G-VECTORS(D_0000000003, D_0019761719)
and
DIMENSIONS = , , , , , , , , , , , , , , , , ;
are different - if they are, then this could explain the error (but not why it is there).

What I would perhaps suggest to try circumvent the problem is to run p2y again using a new version of p2y (like revision 4 of the new GPL repository) so that the number of G-vectors will be just enough to expand the wavefunctions, rather than the full set used in the charge....
Dr. Conor Hogan
CNR-ISM, via Fosso del Cavaliere, 00133 Roma, Italy;
Department of Physics and European Theoretical Spectroscopy Facility (ETSF),
University of Rome "Tor Vergata".
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Re: Error from NetCDF

Postby cantele » Thu Sep 09, 2010 2:26 pm

the new version 3.2.2 does work!

Thanks again for support.

Giovanni
Dr. Giovanni Cantele
CNR-SPIN and Univ. di Napoli "Federico II"
Phone: +39 081 676910
E-mail: giovanni.cantele@cnr.it
giovanni.cantele@na.infn.it
Web: http://people.na.infn.it/cantele
Skype: giocan74
cantele
 
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