problem when write NETCDF file

Asked by Mwater on 2018-12-22

I have compiled the siesta41b4 with NETCDF4 suport. The HDF5 and NETCDF-4 are all installed sucessfully, and the siesta compilation is also successful, but as I run the program to write NETCDF files, it break with:

" Error occured in NCDF:
NetCDF: HDF error
Status number: -101
ncdf: Stopped due to error in NetCDF file"

as I set the CDF.Save to false, the program runing without any problem.
is there anything wrong in my compiling or in the setting of the FDF file?

my arch.make file is as follows:

FC=mpif90
FC_SERIAL=gfortran

FFLAGS=-O3 -m64 .....

MPI_INCLUDE=.

MPI_INTERFACE=libmpi_f90.a
FPPFLAGS = -DMPI

MKL_INCLUDE_DIR=/opt/intel/compilers_and_libraries_2016/linux/mkl/include
MKL_LIB_DIR=/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64

NETCDF4_LIB_DIR=/usr/local/netcdf4/lib
NETCDF4_INCLUDE_DIR=/usr/local/netcdf4/include

HDF5_LIB_DIR=/usr/local/hdf5/lib
HDF5_INCLUDE_DIR=/usr/local/hdf5/include

INCFLAGS= -I$(HDF5_INCLUDE_DIR) \
          -I$(NETCDF4_INCLUDE_DIR) \
          -I$(MKL_INCLUDE_DIR)

LIB_PATH=-L$(HDF5_LIB_DIR) \
         -L$(NETCDF4_LIB_DIR)\
         -L$(MKL_LIB_DIR)

LIBS+=$(LIB_PATH) -lmkl_scalapack_lp64 \
                  -Wl,--start-group\
                  -lmkl_gf_lp64 \
                  -lmkl_sequential \
                  -lmkl_core \
                  -lmkl_blacs_intelmpi_lp64 \
                  -Wl,--end-group

LIBS+=$(LIB_PATH) -lnetcdff -lnetcdf -lhdf5_fortran -lhdf5 -lz

COMP_LIBS = libncdf.a libfdict.a

FPPFLAGS += -DCDF -DNCDF -DNCDF_4

Question information

Language:
English Edit question
Status:
Solved
For:
Siesta Edit question
Assignee:
No assignee Edit question
Solved by:
Mwater
Solved:
2019-01-01
Last query:
2019-01-01
Last reply:
2018-12-22
Nick Papior (nickpapior) said : #1

There are currently some untested things in the NetCDF file format.
Could you share your fdf file?

Mwater (mwt123) said : #2

SystemName grn-ele
SystemLabel grn-ele

==================================================
==================================================
# SPECIES AND BASIS
CDF.Save T
CDF.Compress 1
# Number of species
NumberOfSpecies 2
%block ChemicalSpeciesLabel
  1 6 /usr/ion/C10
  2 1 /usr/ion/H10
%endblock ChemicalSpeciesLabel
User.Basis T

Diag.ParallelOverK yes
==================================================
==================================================
# K-points

%block kgrid_Monkhorst_Pack
1 0 0 0.0
0 1 0 0.0
0 0 100 0.0
%endblock kgrid_Monkhorst_Pack

==================================================
==================================================
# UNIT CELL AND ATOMIC POSITIONS

# UNIT CELL

 LatticeConstant 1 Ang
 %block LatticeVectors
  15.000000 0.000000 0.000000
   0.000000 18.000000 0.000000
   0.000000 0.000000 7.41001
 %endblock LatticeVectors

# Atomic coordinates
NumberOfAtoms 18
AtomicCoordinatesFormat Ang
%block AtomicCoordinatesAndAtomicSpecies
   2.92065000 2.92755000 1.42615000 1 3 C
    2.92065000 4.35355000 1.42615000 1 4 C
    2.92065000 5.06655000 2.66114000 1 5 C
    2.92065000 2.21455000 2.66214000 1 6 C
    2.91883000 6.17050000 2.66674000 2 7 H
    2.91895000 1.11050000 2.66747000 2 8 H
    2.92065000 4.35355000 3.89615000 1 9 C
    2.92065000 2.92755000 3.89615000 1 10 C
    2.91932000 6.17181000 5.10955000 2 11 H
    2.91940000 1.10940000 5.11727000 2 12 H
    2.92065000 5.06655000 5.13115000 1 13 C
    2.92065000 2.21455000 5.13115000 1 14 C
    2.92065000 4.35355000 6.36615000 1 15 C
    2.92065000 2.92755000 6.36615000 1 16 C
    2.92065000 5.06655000 7.60114000 1 17 C
    2.92065000 2.21455000 7.60215000 1 18 C
    2.91883000 6.17050000 7.60674000 2 19 H
    2.91895000 1.11050000 7.60748000 2 20 H
%endblock AtomicCoordinatesAndAtomicSpecies

##2.15910000-0.91179600 +2.15910000-0.91179600

==================================================
==================================================
# General variables

ElectronicTemperature 300 K
MeshCutoff 120. Ry
XC.functional GGA
XC.authors PBE
SpinPolarized .false.
==================================================
==================================================
# SCF variables

DM.MixSCF1 T
MaxSCFIterations 100 # Maximum number of SCF iter
DM.MixingWeight 0.2 # New DM amount for next SCF cycle
DM.Tolerance 1.d-5 # Tolerance in maximum difference
DM.UseSaveDM true # to use continuation files
DM.NumberPulay 10

==================================================
==================================================
# MD variables

MD.FinalTimeStep 1
MD.TypeOfRun CG
MD.NumCGsteps 0
MD.UseSaveXV .true.

==================================================
==================================================
# Output variables

WriteMullikenPop 1
WriteBands .false.
SaveRho .false.
SaveDeltaRho .false.
SaveHS .false.
SaveElectrostaticPotential True
SaveTotalPotential no
WriteMDhistory .false.

Mwater (mwt123) said : #3

the problem is solved