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6.4.3 -- Internal hdf5 error -- BUG

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6.4.3 -- Internal hdf5 error -- BUG

Posted: Wed Sep 11, 2024 12:51 pm
by nick_papior1

I run a calculation, and get:

Code: Select all

 -----------------------------------------------------------------------------
|                     _     ____    _    _    _____     _                     |
|                    | |   |  _ \  | |  | |  / ____|   | |                    |
|                    | |   | |_) | | |  | | | |  __    | |                    |
|                    |_|   |  _ <  | |  | | | | |_ |   |_|                    |
|                     _    | |_) | | |__| | | |__| |    _                     |
|                    (_)   |____/   \____/   \_____|   (_)                    |
|                                                                             |
|     internal error in: vhdf5.F  at line: 57                                 |
|                                                                             |
|     HDF5 call in vhdf5.F:57 produced error: 32767                           |
|                                                                             |
|     If you are not a developer, you should not encounter this problem.      |
|     Please submit a bug report.                                             |
|                                                                             |
 -----------------------------------------------------------------------------

These correspond to the creation of the file (actually caused by vhd5_base creation).
The lib-error code is not easy to backtrack, 32767. No where in header files etc. of HDF5 is these numbers mentioned, likely because of bitshifts...
So I can't really see what the error is... :(

I here share the `INCAR`:

Code: Select all

# fStarting parameters
SYSTEM = NiPS3
ISTART = 0
ICHARG = 1
LWAVE = .TRUE.
LCHARG = .TRUE.
#LVTOT = .TRUE.
NWRITE = 1

# Parameteres for electronic SCF iterations
ENCUT = 650
ALGO = N
LDIAG = .TRUE.
NELM = 500
NELMIN = 6
NELMDL = -12
EDIFF = 1E-9
LREAL = .FALSE.
LPLANE = .TRUE.

MAGMOM = 2*3 2*-3 4*0 12*0
ISPIN = 2
LMAXPAW = 4
LMAXMIX = 4
ADDGRID = .TRUE.
LASPH = .TRUE.
ISMEAR = 0
SIGMA = 0.05

#Exchange correlation functional
GGA = PE #PBE;  91:PW91; AMO5;  PS:PBESoL;

# vdW correction
IVDW = 12       #VDW correction, DFT-D3, for layered materials
VDW_S8 = 0.722   # intensity of vdW force
VDW_SR = 1.261   # distance dependent factor, vdW force dependence of distance

#Parametersfor Ionic relaxations
IBRION = 1
POTIM = 0.5
NSW = 150
ISIF = 2     #
ISYM = 0
EDIFFG = -1E-9

#Add Hubbard U
LDAU = .TRUE.
LDAUTYPE = 2
LDAUU = 4.0 0.00 0.00
LDAUJ = 0.4 0.00 0.00
LDAUL = 2 -1 -1  #-1: no added, 1: p, 2:d 3:f 

#Other parameters
PREC = A
#NCORE = 4

POSCAR:

Code: Select all

cif2pos.py                              
   1.0000000000000000     
     5.8454491180210209    0.0000000374055909   -0.0046883561986790
    -0.0000000794708995   10.1269269986681554    0.0000001867662977
    -1.9402727102733055    0.0000000834424819    6.4262231334528206
  Ni              P               S             
     4     4    12
Direct
  0.4999999987913456  0.8330462586838545  0.9999999673912540
  0.0000000011943753  0.6669537413102326  0.0000000325292724
  0.9999999988042213  0.3330462586561462  0.9999999674242374
  0.5000000012281043  0.1669537413073643  0.0000000326490811
  0.9429980969598761  0.0000000047174005  0.8313802757135011
  0.0570019030500222  0.9999999952898272  0.1686197242806982
  0.4429980969471875  0.5000000047125240  0.8313802757169608
  0.5570019030352067  0.4999999952945144  0.1686197242903071
  0.7489736380336288  0.8293125765265995  0.7599098964118800
  0.2510263826195741  0.8293125704343302  0.2400900909104304
  0.7391324883878729  0.9999999865856389  0.2400984000466314
  0.2608675116505094  0.0000000134098616  0.7599015999771924
  0.2489736173791878  0.6706874295651619  0.7599099090734190
  0.7510263619510288  0.6706874234992545  0.2400901035563856
  0.2489736380637034  0.3293125764953410  0.7599098964668473
  0.7510263826316071  0.3293125704473884  0.2400900909324285
  0.2391324883431779  0.4999999866042520  0.2400984000178968
  0.7608675116232070  0.5000000134032517  0.7599015999566134
  0.7489736173565009  0.1706874295618923  0.7599099090914654
  0.2510263619496352  0.1706874234951760  0.2400901035635041

  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00
  0.00000000E+00  0.00000000E+00  0.00000000E+00

Here is the makefile.include:

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# Default precompiler options
CPP_OPTIONS = -DHOST=\"LinuxGNU\" \
              -DMPI -DMPI_BLOCK=60000 -Duse_collective \
              -DscaLAPACK \
              -DCACHE_SIZE=6000 \
              -Davoidalloc \
              -Dvasp6 \
              -Duse_bse_te \
              -Dtbdyn \
              -Dfock_dblbuf \
              -D_OPENMP

CPP         = gcc -E -C -w $*$(FUFFIX) >$*$(SUFFIX) $(CPP_OPTIONS)

FC          = mpif90 -fopenmp
FCL         = mpif90 -fopenmp

FREE        = -ffree-form -ffree-line-length-none

FFLAGS = -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fallow-argument-mismatch -fno-second-underscore 

OFLAG = $(FFLAGS)
OFLAG_IN    = $(OFLAG)
DEBUG       = -O0

OBJECTS     = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o
OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o

# For what used to be vasp.5.lib
CPP_LIB     = $(CPP)
FC_LIB      = $(FC)
CC_LIB      = gcc
CFLAGS_LIB  = -O
FFLAGS_LIB  = -O1
FREE_LIB    = $(FREE)

OBJECTS_LIB = linpack_double.o

# For the parser library
CXX_PARS    = g++
LLIBS       = -lstdc++

##
## Customize as of this point! Of course you may change the preceding
## part of this file as well if you like, but it should rarely be
## necessary ...
##

# When compiling on the target machine itself, change this to the
# relevant target when cross-compiling for another architecture
VASP_TARGET_CPU ?= -march=native
FFLAGS = -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fallow-argument-mismatch -fno-second-underscore 

# For gcc-10 and higher (comment out for older versions)
FFLAGS = -m64 -fPIC -O3 -march=native -ftree-vectorize -fexpensive-optimizations -funroll-loops -fprefetch-loop-arrays -fallow-argument-mismatch -fno-second-underscore 

# BLAS and LAPACK (mandatory)
BLASPACK= -L/dtu/sw/dcc/Alma92/2023-aug/generic/build-tools/1.0/lib -L/dtu/sw/dcc/Alma92/2023-aug/generic/build-tools/1.0/lib64 -L/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib -L/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib64 -L/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib -L/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib64 -L/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/lapack/3.12.0/lib -L/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/blis/1.0/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/generic/build-tools/1.0/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/generic/build-tools/1.0/lib64 -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib64 -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/generic/gcc/12.3.0/lib64 -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/lapack/3.12.0/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/blis/1.0/lib -llapack -lblis_omp

# scaLAPACK (mandatory)
SCALAPACK_ROOT=/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/scalapack/2.2.0
SCALAPACK   = -L$(SCALAPACK_ROOT)/lib -lscalapack

LLIBS      += $(SCALAPACK) $(BLASPACK)

# FFTW (mandatory)
FFTW_ROOT = /dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/fftw/3.3.10
LLIBS+= -L/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/fftw/3.3.10/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/fftw/3.3.10/lib
LLIBS      += -L$(FFTW_ROOT)/lib -lfftw3 -lfftw3_omp
INCS       += -I$(FFTW_ROOT)/include

# HDF5-support (optional but strongly recommended)
#CPP_OPTIONS+= -DVASP_HDF5
#HDF5_ROOT  ?= /path/to/your/hdf5/installation
#LLIBS      += -L$(HDF5_ROOT)/lib -lhdf5_fortran
#INCS       += -I$(HDF5_ROOT)/include

# For the VASP-2-Wannier90 interface (optional)
#CPP_OPTIONS    += -DVASP2WANNIER90
#WANNIER90_ROOT ?= /path/to/your/wannier90/installation
#LLIBS          += -L$(WANNIER90_ROOT)/lib -lwannier

# For the fftlib library (recommended)
#CPP_OPTIONS+= -Dsysv
#FCL        += fftlib.o
#CXX_FFTLIB  = g++ -fopenmp -std=c++11 -DFFTLIB_THREADSAFE
#INCS_FFTLIB = -I./include -I$(FFTW_ROOT)/include
#LIBS       += fftlib
#LLIBS      += -ldl
LLIBS += -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/scalapack/2.2.0/lib
ELPA_ROOT = /dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/elpa/2022.11.001
INCS += -I/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/wannier90/3.1.0/include -I/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/hdf5/1.14.0/include 
LLIBS := -lwannier -lfftw3 -lfftw3_omp -lhdf5_fortran -lhdf5 $(LLIBS)
LLIBS := -L/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/wannier90/3.1.0/lib -L/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/hdf5/1.14.0/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/wannier90/3.1.0/lib -Wl,-rpath,/dtu/sw/dcc/Alma92/2023-aug/XeonGold6226R/gnu/12.3.0/hdf5/1.14.0/lib $(LLIBS)
CPP_OPTIONS += -DVASP_HDF5 -DVASP2WANNIER90

Other things seems to work fine (less complex calculations).

PS. I am not the actual user, I compile the software on our cluster for the license holder. Let me know if you need anything else from me.

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