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["matthieu verstraete" <matthieu.jean.verstraete@gmail.com>]

Hello,

what you probably want to do is get the ground state wfk from another dataset. In your case you only have 1 dataset (only gamma qpoint), so the following:

 irdwfk   1            # Read the ground-state wavefunctions

is ok. This means abinis will look for the wf in the file cited in the log (trf1_100Ha_WFK): are you certain you have copied them there correctly from the output of your first run? Note that by specifying ndtset 1 in your GS run, you will generate a file called trf1_100Ha_DS1_WFK Also, it is very important to put different strings in the 3rd and 4th lines of the files file (e.g.trf1_xi and  trf1_xo in the rf tutorial case), otherwise your code reads and writes to the same filename! In this specific case it should work anyway, but it's very dangerous and ugly.

Apart from this I can only echo what Pierre-Matthieu said: we know all the nodes failed, but not why. Do you have the output from the *LOG* files or more from the stderr/stdout of your parallel batch submission? Have you tried with fewer processors? Am I correct in thinking you are running on 128 of them? How much memory per node does it need? 100 Hartree is a huge ecut, and is probably not necessary for the elements you are looking at. If you have done your convergence tests and it is necessary, I'd try changing pseudopotentials before going any further.

Does the code get past the point shown in the log if you try to run it sequentially? Of course at some point it will crash because it doesn't have enough memory, but if it gets further it means you probably have an MPI-specific bug.
If it crashes, try "gdb /your/path/abinis" and run< files.file to see if you can localize the crash point.

On side notes,

* iscf 5 is basically obsolete. The default (7 or 17) are much more robust and usually faster (this is not your problem here of course).

* specifying such a large diemac is not very useful, as the default (10^6) is fine for metals. Useful values are 1-20 or so in systems which really do have dielectric constants which are below 50 or so, or contain vacuum (not your case).


Matthieu

On Wed, Oct 29, 2008 at 11:56 AM, Anglade Pierre-Matthieu <anglade@gmail.com> wrote:

Hi,

When you run in parallel, every process opens its own log file and
sometime that's where you will find the error messages. Have you had a
look at those log files ?

regards

PMA

On Wed, Oct 29, 2008 at 12:10 PM,  <dat36@cam.ac.uk> wrote:
> Dear All,
>             I am trying to calculate the phonon frequencies at Gamma for my
> metallic system using the prescription of the Response Function Tutorial 1 by
> calculating the dynamical matrix at Gamma.
>
> I have calculated the input ground state wavefunctions with the input file:
> # Computation of the ground state WFK for input into rf calcs.
> # First, a SCF density computation.
>
> ndtset 1
>
> #Dataset 1 : usual self-consistent calculation
> kptopt1 1          # Option for the automatic generation of k points,
>                   # taking into account the symmetry
> #Definition of the k-point grid
> kptrlatt -4  4  4      # In cartesian coordinates, this grid is simple cubic,
> and
>          4 -4  4      # actually corresponds to the so-called 8x8x8
> Monkhorst-Pack grid.
>          4  4 -4      # It might as well be obtained through the use of
>                       # ngkpt, nshiftk and shiftk .
>
> prtden1  1         # Print the density, for use by dataset 2
> toldfe1  1.0d-8
>
> #Definition of the unit cell
> acell 3*1.8897        # This is equivalent to   1 Angstrom each
> rprim
>        5.137609105410803      -2.966200000000002       0.000000000000000
>        0.000000000000000       5.932400000000000       0.000000000000000
>        0.000000000000000       0.000000000000000       6.410500000000000
>
>
> #Definition of the atom types
> ntypat 3          # There is only one type of atom
> znucl 8 47 82          # The keyword "znucl" refers to the atomic number of the
>
>                  # possible type(s) of atom. The pseudopotential(s)
>                  # mentioned in the "files" file must correspond
>                  # to the type(s) of atom. Here, the only type is Silicon.
>
>
> #Definition of the atoms
> natom 13           # There are two atoms
> typat 1 1 1 1 1 1 2 2 2 2 2 3 3       # They both are of type 1, that is,
> Silicon.
> xred              # This keyword indicate that the location of the atoms
>                  # will follow, one triplet of number for each atom
>  # Triplet giving the REDUCED coordinate of atom 1.
>  # Triplet giving the REDUCED coordinate of atom 2.
>    0.6222000122070313   0.0000000000000001   0.6888999938964855
>   -0.0000000000000001   0.6222000122070313   0.6888999938964855
>   -0.6222000122070311  -0.6222000122070314   0.6888999938964854
>   -0.0000000000000001  -0.6222000122070314  -0.6888999938964855
>   -0.6222000122070311   0.0000000000000001  -0.6888999938964855
>    0.6222000122070313   0.6222000122070313  -0.6888999938964854
>    0.0000000000000000   0.0000000000000000   0.2413000017404568
>    0.0000000000000000   0.0000000000000000  -0.2413000017404568
>    0.5000000000000000  -0.0000000000000000   0.0000000000000000
>    0.0000000000000000   0.5000000000000001   0.0000000000000000
>   -0.5000000000000000  -0.5000000000000001  -0.0000000000000000
>    0.6666666666666667   0.3333333333333334   0.5000000000000001
>   -0.6666666666666667  -0.3333333333333334  -0.5000000000000001
> #Definition of the planewave basis set
> ecut 100.0         # Maximal kinetic energy cut-off, in Hartree
> nband 70
> #Definition of the SCF procedure
> nstep 100          # Maximal number of SCF cycles
>       # Although this is not mandatory, it is worth to
>                  # precondition the SCF cycle. The model dielectric
>                  # function used as the standard preconditioner
>                  # is described in the "dielng" input variable section.
>                  # Here, we follow the prescription for bulk silicon.
> occopt 7
> tsmear 0.007
> ---------------------------------------------------------------------------------------------
>
> Then the response function calculation with the input:
> # Crystalline Ag5Pb2O6: computation of the dynamical matrix at Gamma
> #
>
> #Response-function calculation, with q=0
>  rfphon   1            # Will consider phonon-type perturbation
>  rfatpol   1 13          # All the atoms will be displaced
>   rfdir   1 1 1        # Along all reduced coordinate axis
>    nqpt   1            # One wavevector is to be considered
>     qpt   0 0 0        # This wavevector is q=0 (Gamma)
>  kptopt   2            # Automatic generation of k points, taking
>                        # into account the time-reversal symmetry only
>  tolvrs   1.0d-8       # SCF stopping criterion
>    iscf   5            # Self-consistent calculation, using algorithm 5
>  irdwfk   1            # Read the ground-state wavefunctions
>
>
> #######################################################################
> #Common input variables
>
> #Definition of the unit cell
> acell 3*1.8897        # This is equivalent to   1 Angstrom each
> rprim
>        5.137609105410803      -2.966200000000002       0.000000000000000
>        0.000000000000000       5.932400000000000       0.000000000000000
>        0.000000000000000       0.000000000000000       6.410500000000000
>
>
> #Definition of the atom types
> ntypat 3          # There is only one type of atom
> znucl 8 47 82          # The keyword "znucl" refers to the atomic number of the
>
>                  # possible type(s) of atom. The pseudopotential(s)
>                  # mentioned in the "files" file must correspond
>                  # to the type(s) of atom. Here, the only type is Silicon.
>
>
> #Definition of the atoms
> natom 13           # There are two atoms
> typat 1 1 1 1 1 1 2 2 2 2 2 3 3       # They both are of type 1, that is,
> Silicon.
> xred              # This keyword indicate that the location of the atoms
>                  # will follow, one triplet of number for each atom
>  # Triplet giving the REDUCED coordinate of atom 1.
>  # Triplet giving the REDUCED coordinate of atom 2.
>    0.6222000122070313   0.0000000000000001   0.6888999938964855
>   -0.0000000000000001   0.6222000122070313   0.6888999938964855
>   -0.6222000122070311  -0.6222000122070314   0.6888999938964854
>   -0.0000000000000001  -0.6222000122070314  -0.6888999938964855
>   -0.6222000122070311   0.0000000000000001  -0.6888999938964855
>    0.6222000122070313   0.6222000122070313  -0.6888999938964854
>    0.0000000000000000   0.0000000000000000   0.2413000017404568
>    0.0000000000000000   0.0000000000000000  -0.2413000017404568
>    0.5000000000000000  -0.0000000000000000   0.0000000000000000
>    0.0000000000000000   0.5000000000000001   0.0000000000000000
>   -0.5000000000000000  -0.5000000000000001  -0.0000000000000000
>    0.6666666666666667   0.3333333333333334   0.5000000000000001
>   -0.6666666666666667  -0.3333333333333334  -0.5000000000000001
> #Definition of the planewave basis set
> ecut 100.0         # Maximal kinetic energy cut-off, in Hartree
> diemac 1000000
>
> #Definition of the SCF procedure
> nstep 100          # Maximal number of SCF cycles
>       # Although this is not mandatory, it is worth to
>                  # precondition the SCF cycle. The model dielectric
>                  # function used as the standard preconditioner
>                  # is described in the "dielng" input variable section.
>                  # Here, we follow the prescription for bulk silicon.
> occopt 7
> tsmear 0.007
>
> #Definition of the k-point grid
> kptrlatt -4  4  4      # In cartesian coordinates, this grid is simple cubic,
> and
>          4 -4  4      # actually corresponds to the so-called 8x8x8
> Monkhorst-Pack grid.
>          4  4 -4      # It might as well be obtained through the use of
>                       # ngkpt, nshiftk and shiftk .
>
> #Gives the number of band, explicitely (do not take the default)
> nband  70               # For an insulator (if described correctly as an
> insulator
>                       # by DFT), there is no need to include conduction bands
>                       # in response-function calculations
>
> #Exchange-correlation functional
> ixc 1             # LDA Teter Pade parametrization
> ---------------------------------------------------------------------------------------------
>
>
> But, when I run this code it fails when it reaches the calculation of the first
> perturbation. The end of the output file looks like:
> -inwffil : will read wavefunctions from disk file trf1_100Ha_WFK
> -P-0000 - newkpt: read input wf with ikpt,npw=   1   62947, make ikpt,npw=   1
>  62947
>
>
>  ==>  initialize data related to q vector <==
>
>  The list of irreducible perturbations for this q vector is:
>    1)    idir= 1    ipert=   1
>    2)    idir= 2    ipert=   1
>    3)    idir= 3    ipert=   1
>    4)    idir= 1    ipert=   7
>    5)    idir= 3    ipert=   7
>    6)    idir= 1    ipert=   9
>    7)    idir= 2    ipert=   9
>    8)    idir= 3    ipert=   9
>    9)    idir= 1    ipert=  12
>   10)    idir= 3    ipert=  12
>
> ================================================================================
>
>  The perturbation idir=   1  ipert=   2 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=   2 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=   2 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=   3 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=   3 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=   3 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=   4 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=   4 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=   4 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=   5 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=   5 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=   5 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=   6 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=   6 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=   6 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=   7 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=   8 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=   8 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=   8 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=  10 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=  10 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=  10 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=  11 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=  11 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=  11 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=  12 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   1  ipert=  13 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   2  ipert=  13 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
>  The perturbation idir=   3  ipert=  13 is
>  symmetric of a previously calculated perturbation.
>  So, its SCF calculation is not needed.
>
>
> --------------------------------------------------------------------------------
>  Perturbation wavevector (in red.coord.)   0.000000  0.000000  0.000000
>  Perturbation : displacement of atom   1   along direction   1
>  Found     2 symmetries that leave the perturbation invariant.
>  symkpt : the number of k-points, thanks to the symmetries,
>  is reduced to   106 .
>
>
>
>
>
>
> The stderr has:
> mpiexec: Warning: tasks 0-127 exited with status 1.
>
> Can anyone tell me what may be wrong?
>
> Thank you,
> David.
>

--
Pierre-Matthieu Anglade

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Matthieu Verstraete

European Theoretical Spectroscopy Facility (ETSF) 
Dpto. Fisica de Materiales, 
U. del Pais Vasco,            
Centro Joxe Mari Korta, Av. de Tolosa, 72,   Phone: +34-943018393
E-20018 Donostia-San Sebastian, Spain        Fax  : +34-943018390

Mail : matthieu.jean.verstraete@gmail.com
http://www-users.york.ac.uk/~mjv500