6.4.3 -- Internal hdf5 error -- BUG

Problems running VASP: crashes, internal errors, "wrong" results.


Moderators: Global Moderator, Moderator

Post Reply
Message
Author
nick_papior1
Newbie
Newbie
Posts: 2
Joined: Tue Sep 01, 2020 7:45 am

6.4.3 -- Internal hdf5 error -- BUG

#1 Post by nick_papior1 » Wed Sep 11, 2024 12:51 pm

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:

Code: Select all

# 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.

Top
marie-therese.huebsch
Full Member
Full Member
Posts: 212
Joined: Tue Jan 19, 2021 12:01 am

Re: 6.4.3 -- Internal hdf5 error -- BUG

#2 Post by marie-therese.huebsch » Mon Nov 04, 2024 8:01 am

Hello,

I apologize for the late reply!

Did you solve the issue by now? Could it be that the vaspout.h5 file exists from a previous cancelled run? In that case you need to delete it and start fresh.

If not, could you please create a minimal reproducible and post the input and main output files as a zip according to the forum guidelines?

Marie-Therese

Top
nick_papior1
Newbie
Newbie
Posts: 2
Joined: Tue Sep 01, 2020 7:45 am

Re: 6.4.3 -- Internal hdf5 error -- BUG

#3 Post by nick_papior1 » Mon Nov 25, 2024 1:44 pm

Hi,

This problem was due to the hdf5 library 1.14.0.
I re-installed VASP with 1.14.5, and now it seems to execute without problems. So I think it got fixed, I'll return if there are other issues.

Top
marie-therese.huebsch
Full Member
Full Member
Posts: 212
Joined: Tue Jan 19, 2021 12:01 am

Re: 6.4.3 -- Internal hdf5 error -- BUG

#4 Post by marie-therese.huebsch » Mon Nov 25, 2024 2:06 pm

Hi,

Thank you for the update! And glad to hear everything seems to work now.
In case there are any further issues, we will do our best to quickly resolve it with you.

All the best,
Marie-Therese

Top
Post Reply

Return to “Bug reports”